Starting phenix.real_space_refine on Sun Feb 18 15:22:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r86_4752/02_2024/6r86_4752.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r86_4752/02_2024/6r86_4752.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/6r86_4752/02_2024/6r86_4752.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r86_4752/02_2024/6r86_4752.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r86_4752/02_2024/6r86_4752.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r86_4752/02_2024/6r86_4752.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= 0.001 sd= 0.022 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 3539 5.49 5 S 126 5.16 5 C 69720 2.51 5 N 24387 2.21 5 O 34672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 ARG 204": "NH1" <-> "NH2" Residue "7 ARG 23": "NH1" <-> "NH2" Residue "7 ARG 91": "NH1" <-> "NH2" Residue "7 TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 171": "NH1" <-> "NH2" Residue "O ARG 19": "NH1" <-> "NH2" Residue "O ARG 108": "NH1" <-> "NH2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 3": "NH1" <-> "NH2" 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 "U TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 54": "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 4": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "c TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 36": "NH1" <-> "NH2" Residue "E ARG 9": "NH1" <-> "NH2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "E TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 67": "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 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 22": "NH1" <-> "NH2" Residue "H ARG 140": "NH1" <-> "NH2" Residue "h TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 60": "NH1" <-> "NH2" Residue "h PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 132446 Number of models: 1 Model: "" Number of chains: 49 Chain: "R" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2784 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 11, 'TRANS': 344} 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: 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: 69730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3260, 69730 Classifications: {'RNA': 3260} Modifications used: {'rna2p_pur': 209, 'rna2p_pyr': 127, 'rna3p_pur': 1597, 'rna3p_pyr': 1327} Link IDs: {'rna2p': 336, 'rna3p': 2923} Chain breaks: 3 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 215 SG CYS R 77 34.670 95.237 113.543 1.00137.02 S Time building chain proxies: 49.58, per 1000 atoms: 0.37 Number of scatterers: 132446 At special positions: 0 Unit cell: (235.228, 209.212, 262.328, 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 3539 15.00 O 34672 8.00 N 24387 7.00 C 69720 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: 49.82 Conformation dependent library (CDL) restraints added in 9.0 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=" NE2 HIS R 90 " 14172 Ramachandran restraints generated. 7086 Oldfield, 0 Emsley, 7086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13502 Finding SS restraints... Secondary structure from input PDB file: 230 helices and 74 sheets defined 33.9% alpha, 13.9% beta 1095 base pairs and 1950 stacking pairs defined. Time for finding SS restraints: 43.37 Creating SS restraints... Processing helix chain 'R' and resid 15 through 23 removed outlier: 3.899A pdb=" N TYR R 19 " --> pdb=" O ASN R 16 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE R 20 " --> pdb=" O ASP R 17 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE R 21 " --> pdb=" O LEU R 18 " (cutoff:3.500A) removed outlier: 3.988A 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: 3.617A pdb=" N ARG R 105 " --> pdb=" O LYS R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 114 through 123 Processing helix chain 'R' and resid 157 through 173 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 218 through 227 removed outlier: 4.079A pdb=" N ALA R 222 " --> pdb=" O ASN R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 268 through 274 removed outlier: 3.711A pdb=" N GLN R 272 " --> pdb=" O THR R 268 " (cutoff:3.500A) Processing helix chain 'R' and resid 311 through 330 Processing helix chain 'R' and resid 331 through 337 removed outlier: 3.545A pdb=" N LEU R 335 " --> pdb=" O TRP R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 347 through 354 removed outlier: 3.900A 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 441 Processing helix chain 'R' and resid 445 through 454 Processing helix chain 'R' and resid 459 through 463 Processing helix chain 'R' and resid 473 through 482 removed outlier: 3.778A pdb=" N TYR R 477 " --> pdb=" O THR R 473 " (cutoff:3.500A) Processing helix chain 'R' and resid 483 through 493 removed outlier: 3.706A pdb=" N ALA R 487 " --> pdb=" O MET R 483 " (cutoff:3.500A) Processing helix chain 'R' and resid 507 through 515 Processing helix chain 'R' and resid 517 through 527 removed outlier: 3.963A 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: 3.550A pdb=" N TYR X 35 " --> pdb=" O SER X 31 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE X 38 " --> pdb=" O PHE X 34 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU X 41 " --> pdb=" O ALA X 37 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 63 Processing helix chain 'X' and resid 77 through 88 Processing helix chain 'X' and resid 103 through 108 removed outlier: 3.856A pdb=" N VAL X 107 " --> pdb=" O ALA X 103 " (cutoff:3.500A) Processing helix chain 'X' and resid 122 through 133 removed outlier: 3.658A 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 223 Processing helix chain 'i' and resid 60 through 64 removed outlier: 3.657A pdb=" N ALA i 63 " --> pdb=" O ARG i 60 " (cutoff:3.500A) Processing helix chain 'i' and resid 66 through 70 removed outlier: 3.586A pdb=" N HIS i 69 " --> pdb=" O SER i 66 " (cutoff:3.500A) Processing helix chain 'i' and resid 81 through 106 removed outlier: 4.152A pdb=" N ALA i 92 " --> pdb=" O ARG i 88 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLU i 96 " --> pdb=" O ALA i 92 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ILE i 100 " --> pdb=" O GLU i 96 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS i 106 " --> pdb=" O LYS i 102 " (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 121 through 130 Processing helix chain 'J' and resid 140 through 151 removed outlier: 3.573A pdb=" N ILE J 144 " --> pdb=" O SER J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 174 removed outlier: 4.395A 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 removed outlier: 3.800A pdb=" N LEU J 202 " --> pdb=" O ALA J 198 " (cutoff:3.500A) Processing helix chain 'J' and resid 235 through 244 Processing helix chain 'j' and resid 5 through 10 Processing helix chain 'j' and resid 13 through 33 Processing helix chain 'j' and resid 41 through 43 No H-bonds generated for 'chain 'j' and resid 41 through 43' Processing helix chain 'j' and resid 44 through 70 removed outlier: 4.862A pdb=" N SER j 50 " --> pdb=" O THR j 46 " (cutoff:3.500A) removed outlier: 3.840A 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: 3.827A pdb=" N VAL j 66 " --> pdb=" O GLN j 62 " (cutoff:3.500A) Processing helix chain 'j' and resid 85 through 90 removed outlier: 3.521A 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: 3.663A 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 173 Processing helix chain 'K' and resid 184 through 189 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 254 removed outlier: 3.913A pdb=" N ASP K 254 " --> pdb=" O ALA K 250 " (cutoff:3.500A) Processing helix chain 'k' and resid 34 through 49 removed outlier: 3.706A pdb=" N PHE k 39 " --> pdb=" O ASN k 35 " (cutoff:3.500A) Processing helix chain 'k' and resid 51 through 63 removed outlier: 3.918A pdb=" N ARG k 62 " --> pdb=" O ILE k 58 " (cutoff:3.500A) Processing helix chain 'k' and resid 65 through 77 Processing helix chain 'k' and resid 79 through 99 removed outlier: 3.510A pdb=" N ALA k 83 " --> pdb=" O SER k 79 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA k 85 " --> pdb=" O THR k 81 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL k 87 " --> pdb=" O ALA k 83 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER k 97 " --> pdb=" O ILE k 93 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG k 99 " --> pdb=" O ALA k 95 " (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: 3.625A pdb=" N VAL 7 154 " --> pdb=" O SER 7 150 " (cutoff:3.500A) Processing helix chain 'l' and resid 4 through 8 Processing helix chain 'l' and resid 50 through 58 removed outlier: 3.564A pdb=" N ARG l 55 " --> pdb=" O ALA l 51 " (cutoff:3.500A) Processing helix chain 'l' and resid 66 through 68 No H-bonds generated for 'chain 'l' and resid 66 through 68' Processing helix chain 'l' and resid 69 through 76 removed outlier: 3.523A 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: 3.899A pdb=" N ALA M 76 " --> pdb=" O ARG M 72 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLU M 77 " --> pdb=" O GLY M 73 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU M 78 " --> pdb=" O PRO M 74 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS M 87 " --> pdb=" O GLY M 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 108 through 113 removed outlier: 3.644A pdb=" N LEU M 112 " --> pdb=" O HIS M 109 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY M 113 " --> pdb=" O ILE M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 164 Processing helix chain 'm' and resid 7 through 16 removed outlier: 3.891A pdb=" N PHE m 11 " --> pdb=" O ASP m 7 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG m 16 " --> pdb=" O LEU m 12 " (cutoff:3.500A) Processing helix chain 'm' and resid 58 through 68 removed outlier: 3.702A pdb=" N ALA m 62 " --> pdb=" O ASP m 58 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS m 64 " --> pdb=" O GLY m 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 27 through 46 removed outlier: 3.908A pdb=" N ALA N 43 " --> pdb=" O ARG N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 84 Processing helix chain 'N' and resid 86 through 94 Processing helix chain 'N' and resid 105 through 122 removed outlier: 3.635A pdb=" N PHE N 109 " --> pdb=" O ASN N 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 166 through 179 removed outlier: 4.243A pdb=" N GLU N 176 " --> pdb=" O LEU N 172 " (cutoff:3.500A) Processing helix chain 'N' and resid 179 through 192 removed outlier: 3.789A pdb=" N ALA N 187 " --> pdb=" O ARG N 183 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA N 191 " --> pdb=" O ALA N 187 " (cutoff:3.500A) Processing helix chain 'n' and resid 6 through 19 removed outlier: 3.835A pdb=" N LYS n 10 " --> pdb=" O SER n 6 " (cutoff:3.500A) Processing helix chain 'n' and resid 26 through 30 Processing helix chain 'O' and resid 77 through 88 Processing helix chain 'O' and resid 89 through 97 removed outlier: 3.703A pdb=" N SER O 97 " --> pdb=" O LYS O 93 " (cutoff:3.500A) Processing helix chain 'O' and resid 97 through 111 removed outlier: 3.583A pdb=" N LYS O 101 " --> pdb=" O SER O 97 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA O 111 " --> pdb=" O GLU O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 138 removed outlier: 3.953A pdb=" N ALA O 136 " --> pdb=" O LYS O 132 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LYS O 137 " --> pdb=" O LYS O 133 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA O 138 " --> pdb=" O ALA O 134 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 90 removed outlier: 4.303A pdb=" N LEU o 85 " --> pdb=" O SER o 81 " (cutoff:3.500A) Processing helix chain 'p' and resid 3 through 12 removed outlier: 3.798A 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 52 removed outlier: 3.612A pdb=" N LEU p 51 " --> pdb=" O LYS p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 75 through 79 removed outlier: 3.600A pdb=" N ALA p 79 " --> pdb=" O PRO p 76 " (cutoff:3.500A) Processing helix chain 'p' and resid 97 through 110 Processing helix chain 'p' and resid 148 through 157 removed outlier: 3.763A pdb=" N ILE p 151 " --> pdb=" O TYR p 148 " (cutoff:3.500A) Proline residue: p 154 - end of helix removed outlier: 3.881A pdb=" N LYS p 157 " --> pdb=" O PRO p 154 " (cutoff:3.500A) Processing helix chain 'p' and resid 158 through 162 Processing helix chain 'p' and resid 167 through 172 Processing helix chain 'p' and resid 188 through 193 Processing helix chain 'Q' and resid 15 through 28 removed outlier: 4.076A pdb=" N VAL Q 22 " --> pdb=" O ARG Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 55 removed outlier: 3.653A pdb=" N ASN Q 50 " --> pdb=" O GLU Q 46 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 86 Processing helix chain 'Q' and resid 95 through 100 Processing helix chain 'Q' and resid 138 through 144 Processing helix chain 'Q' and resid 149 through 185 removed outlier: 4.816A pdb=" N VAL Q 162 " --> pdb=" O ALA Q 158 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR Q 167 " --> pdb=" O SER Q 163 " (cutoff:3.500A) removed outlier: 4.546A 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 25 through 36 removed outlier: 4.001A pdb=" N GLU 5 31 " --> pdb=" O LYS 5 27 " (cutoff:3.500A) Processing helix chain '5' and resid 40 through 52 removed outlier: 3.615A pdb=" N GLU 5 49 " --> pdb=" O GLN 5 45 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN 5 50 " --> pdb=" O LYS 5 46 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU 5 52 " --> pdb=" O LEU 5 48 " (cutoff:3.500A) Processing helix chain '5' and resid 71 through 76 Processing helix chain '5' and resid 84 through 104 removed outlier: 3.819A pdb=" N LEU 5 94 " --> pdb=" O PHE 5 90 " (cutoff:3.500A) Processing helix chain '5' and resid 131 through 135 removed outlier: 3.609A pdb=" N ARG 5 135 " --> pdb=" O ALA 5 132 " (cutoff:3.500A) Processing helix chain '5' and resid 169 through 177 removed outlier: 4.100A pdb=" N ARG 5 175 " --> pdb=" O ARG 5 171 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 40 removed outlier: 3.673A pdb=" N PHE S 35 " --> pdb=" O LYS S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 53 removed outlier: 3.711A pdb=" N LYS S 50 " --> pdb=" O LYS S 46 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE S 53 " --> pdb=" O LEU S 49 " (cutoff:3.500A) Processing helix chain 'S' and resid 64 through 72 Processing helix chain 'S' and resid 107 through 117 Processing helix chain 'S' and resid 124 through 131 Processing helix chain 's' and resid 41 through 45 removed outlier: 3.611A pdb=" N PHE s 45 " --> pdb=" O VAL s 42 " (cutoff:3.500A) Processing helix chain 's' and resid 61 through 79 removed outlier: 3.587A pdb=" N ARG s 68 " --> pdb=" O LEU s 64 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N MET s 75 " --> pdb=" O ALA s 71 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL s 78 " --> pdb=" O TYR s 74 " (cutoff:3.500A) Processing helix chain 's' and resid 143 through 148 removed outlier: 3.674A pdb=" N VAL s 147 " --> pdb=" O ASN s 143 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL s 148 " --> pdb=" O LYS s 144 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 143 through 148' Processing helix chain 's' and resid 154 through 158 removed outlier: 3.830A pdb=" N PHE s 158 " --> pdb=" O ARG s 155 " (cutoff:3.500A) Processing helix chain 's' and resid 176 through 187 removed outlier: 3.778A pdb=" N GLU s 185 " --> pdb=" O LEU s 181 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA s 186 " --> pdb=" O LYS s 182 " (cutoff:3.500A) Processing helix chain 's' and resid 204 through 212 removed outlier: 3.516A 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: 3.519A pdb=" N LYS T 43 " --> pdb=" O ASN T 39 " (cutoff:3.500A) Processing helix chain 'T' and resid 61 through 72 Processing helix chain 'T' and resid 84 through 89 removed outlier: 3.791A pdb=" N LEU T 89 " --> pdb=" O ARG T 85 " (cutoff:3.500A) Processing helix chain 'T' and resid 90 through 112 removed outlier: 3.608A pdb=" N VAL T 101 " --> pdb=" O ARG T 97 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU T 102 " --> pdb=" O ARG T 98 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG T 104 " --> pdb=" O ARG T 100 " (cutoff:3.500A) Processing helix chain 'T' and resid 116 through 129 removed outlier: 3.830A pdb=" N LYS T 125 " --> pdb=" O HIS T 121 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY T 129 " --> pdb=" O LYS T 125 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 152 Processing helix chain 'U' and resid 33 through 47 removed outlier: 3.864A pdb=" N LYS U 47 " --> pdb=" O TYR U 43 " (cutoff:3.500A) Processing helix chain 'U' and resid 98 through 114 Processing helix chain 'U' and resid 137 through 142 Processing helix chain 'V' and resid 54 through 58 Processing helix chain 'V' and resid 99 through 123 removed outlier: 3.532A pdb=" N GLN V 103 " --> pdb=" O SER V 99 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA V 121 " --> pdb=" O ALA V 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 19 through 24 removed outlier: 3.504A pdb=" N THR W 23 " --> pdb=" O VAL W 19 " (cutoff:3.500A) Processing helix chain 'W' and resid 29 through 41 removed outlier: 3.690A pdb=" N ASP W 39 " --> pdb=" O LYS W 35 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE W 41 " --> pdb=" O LEU W 37 " (cutoff:3.500A) Processing helix chain 'W' and resid 72 through 87 Processing helix chain 'P' and resid 40 through 47 removed outlier: 3.593A pdb=" N GLU P 44 " --> pdb=" O LYS P 40 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP P 45 " --> pdb=" O LYS P 41 " (cutoff:3.500A) removed outlier: 3.611A 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: 3.663A pdb=" N ILE P 112 " --> pdb=" O GLU P 108 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA P 113 " --> pdb=" O ILE P 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 108 through 113' Processing helix chain 'P' and resid 125 through 133 removed outlier: 3.654A 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 45 removed outlier: 3.867A pdb=" N GLU r 40 " --> pdb=" O GLN r 36 " (cutoff:3.500A) Processing helix chain 'r' and resid 57 through 65 removed outlier: 4.517A pdb=" N ARG r 61 " --> pdb=" O THR r 57 " (cutoff:3.500A) Processing helix chain 'r' and resid 70 through 80 removed outlier: 3.556A pdb=" N PHE r 73 " --> pdb=" O LEU r 70 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS r 75 " --> pdb=" O ASP r 72 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU r 76 " --> pdb=" O PHE r 73 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU r 77 " --> pdb=" O GLU r 74 " (cutoff:3.500A) Proline residue: r 78 - end of helix Processing helix chain 'r' and resid 93 through 103 removed outlier: 3.774A 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) removed outlier: 3.592A pdb=" N ASN r 103 " --> pdb=" O VAL r 99 " (cutoff:3.500A) Processing helix chain 'x' and resid 120 through 125 removed outlier: 3.607A pdb=" N LEU x 125 " --> pdb=" O GLU x 121 " (cutoff:3.500A) Processing helix chain 'x' and resid 126 through 133 Processing helix chain 'Y' and resid 33 through 41 Processing helix chain 'Y' and resid 45 through 49 removed outlier: 3.649A pdb=" N ILE Y 49 " --> pdb=" O PRO Y 46 " (cutoff:3.500A) Processing helix chain 'Y' and resid 52 through 59 removed outlier: 4.073A pdb=" N ARG Y 56 " --> pdb=" O THR Y 52 " (cutoff:3.500A) Processing helix chain 'Z' and resid 58 through 62 Processing helix chain 'Z' and resid 69 through 80 removed outlier: 4.006A pdb=" N ASN Z 80 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) Processing helix chain 'Z' and resid 91 through 104 removed outlier: 4.266A pdb=" N LYS Z 100 " --> pdb=" O LYS Z 96 " (cutoff:3.500A) Processing helix chain 'Z' and resid 132 through 140 removed outlier: 4.214A pdb=" N ARG Z 138 " --> pdb=" O ASP Z 134 " (cutoff:3.500A) Processing helix chain 'a' and resid 12 through 21 Processing helix chain 'a' and resid 23 through 31 removed outlier: 4.616A pdb=" N VAL a 29 " --> pdb=" O SER a 25 " (cutoff:3.500A) Processing helix chain 'a' and resid 36 through 43 Processing helix chain 'a' and resid 113 through 121 Processing helix chain 'b' and resid 58 through 64 removed outlier: 3.628A pdb=" N LYS b 64 " --> pdb=" O LYS b 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 97 through 101 Processing helix chain 'b' and resid 104 through 123 removed outlier: 3.833A pdb=" N GLU b 108 " --> pdb=" O PRO b 104 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU b 109 " --> pdb=" O SER b 105 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL b 113 " --> pdb=" O GLU b 109 " (cutoff:3.500A) Processing helix chain 'b' and resid 128 through 132 Processing helix chain 'C' and resid 37 through 48 Processing helix chain 'c' and resid 6 through 11 removed outlier: 3.778A pdb=" N LYS c 10 " --> pdb=" O THR c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 41 through 45 Processing helix chain 'c' and resid 64 through 69 removed outlier: 3.691A pdb=" N TRP c 69 " --> pdb=" O ALA c 66 " (cutoff:3.500A) Processing helix chain 'c' and resid 83 through 92 removed outlier: 4.280A pdb=" N ASP c 88 " --> pdb=" O GLU c 84 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLN c 89 " --> pdb=" O ASP c 85 " (cutoff:3.500A) Processing helix chain 'c' and resid 105 through 108 Processing helix chain 'c' and resid 131 through 142 removed outlier: 4.040A pdb=" N LYS c 137 " --> pdb=" O LEU c 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 14 removed outlier: 3.848A pdb=" N THR D 11 " --> pdb=" O VAL D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 34 removed outlier: 3.558A pdb=" N LEU D 29 " --> pdb=" O GLN D 25 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN D 32 " --> pdb=" O LYS D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 92 removed outlier: 4.019A pdb=" N THR D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL D 79 " --> pdb=" O ALA D 75 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU D 88 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N MET D 89 " --> pdb=" O ARG D 85 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLU D 91 " --> pdb=" O ARG D 87 " (cutoff:3.500A) Processing helix chain 'd' and resid 12 through 17 removed outlier: 3.589A pdb=" N ALA d 16 " --> pdb=" O GLN d 12 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N HIS d 17 " --> pdb=" O THR d 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 12 through 17' Processing helix chain 'd' and resid 36 through 57 removed outlier: 3.724A 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 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: 3.563A pdb=" N ASP E 176 " --> pdb=" O GLY E 173 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS E 177 " --> pdb=" O ARG E 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 173 through 177' Processing helix chain 'E' and resid 181 through 190 removed outlier: 3.603A 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 27 through 36 removed outlier: 3.548A pdb=" N GLN e 36 " --> pdb=" O LYS e 32 " (cutoff:3.500A) Processing helix chain 'e' and resid 49 through 64 removed outlier: 3.554A pdb=" N MET e 61 " --> pdb=" O GLU e 57 " (cutoff:3.500A) Processing helix chain 'e' and resid 73 through 81 Processing helix chain 'F' and resid 130 through 135 Processing helix chain 'F' and resid 136 through 138 No H-bonds generated for 'chain 'F' and resid 136 through 138' Processing helix chain 'F' and resid 141 through 154 removed outlier: 3.543A pdb=" N TYR F 154 " --> pdb=" O ARG F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 169 removed outlier: 3.727A pdb=" N LYS F 168 " --> pdb=" O GLN F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 198 Processing helix chain 'F' and resid 228 through 233 Processing helix chain 'F' and resid 372 through 380 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 Processing helix chain 'f' and resid 52 through 60 Processing helix chain 'G' and resid 31 through 44 Processing helix chain 'G' and resid 114 through 129 Processing helix chain 'G' and resid 132 through 138 removed outlier: 3.800A pdb=" N ARG G 138 " --> pdb=" O LEU G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 159 removed outlier: 3.710A pdb=" N ILE G 159 " --> pdb=" O LEU G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 173 Processing helix chain 'G' and resid 174 through 179 Processing helix chain 'G' and resid 190 through 195 removed outlier: 3.970A pdb=" N LYS G 193 " --> pdb=" O GLY G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 220 Processing helix chain 'G' and resid 234 through 239 Processing helix chain 'G' and resid 240 through 243 removed outlier: 3.632A pdb=" N HIS G 243 " --> pdb=" O PRO G 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 240 through 243' Processing helix chain 'G' and resid 252 through 263 Processing helix chain 'G' and resid 286 through 292 Processing helix chain 'G' and resid 295 through 299 removed outlier: 3.710A pdb=" N ILE G 299 " --> pdb=" O GLN G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 326 Processing helix chain 'G' and resid 329 through 335 removed outlier: 4.182A pdb=" N VAL G 333 " --> pdb=" O PRO G 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 352 through 360 removed outlier: 3.638A pdb=" N THR G 356 " --> pdb=" O ALA G 352 " (cutoff:3.500A) Processing helix chain 'g' and resid 54 through 58 Processing helix chain 'g' and resid 78 through 83 Processing helix chain 'g' and resid 101 through 115 removed outlier: 3.980A pdb=" N VAL g 106 " --> pdb=" O ALA g 102 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL g 107 " --> pdb=" O LYS g 103 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA g 114 " --> pdb=" O ALA g 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 15 Processing helix chain 'H' and resid 20 through 26 Processing helix chain 'H' and resid 29 through 38 removed outlier: 4.226A pdb=" N ARG H 35 " --> pdb=" O TYR H 31 " (cutoff:3.500A) removed outlier: 3.937A 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 112 Processing helix chain 'H' and resid 158 through 169 Processing helix chain 'H' and resid 191 through 200 removed outlier: 3.648A pdb=" N PHE H 200 " --> pdb=" O ARG H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 215 Processing helix chain 'H' and resid 215 through 222 removed outlier: 3.547A 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: 3.674A pdb=" N HIS H 244 " --> pdb=" O TYR H 240 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU H 245 " --> pdb=" O THR H 241 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP H 250 " --> pdb=" O ALA H 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 261 through 270 removed outlier: 3.707A 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 37 through 42 Processing helix chain 'I' and resid 97 through 101 removed outlier: 3.902A pdb=" N LYS I 100 " --> pdb=" O ASN I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 150 removed outlier: 3.671A pdb=" N VAL I 135 " --> pdb=" O LYS I 131 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA I 144 " --> pdb=" O VAL I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 154 through 160 removed outlier: 3.611A pdb=" N SER I 160 " --> pdb=" O LYS I 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 147 removed outlier: 3.581A pdb=" N GLY L 146 " --> pdb=" O ASP L 143 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS L 147 " --> pdb=" O LEU L 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 143 through 147' Processing helix chain 'L' and resid 179 through 184 removed outlier: 3.862A 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 removed outlier: 3.754A pdb=" N LYS R 393 " --> pdb=" O ALA R 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 275 through 282 removed outlier: 4.473A pdb=" N ASN R 275 " --> pdb=" O SER R 252 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE R 250 " --> pdb=" O LEU R 277 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N HIS R 279 " --> pdb=" O GLY R 248 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY R 248 " --> pdb=" O HIS R 279 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR R 281 " --> pdb=" O PHE R 246 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE R 246 " --> pdb=" O THR R 281 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ILE R 341 " --> pdb=" O LYS R 368 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'X' and resid 2 through 4 removed outlier: 6.077A pdb=" N THR X 3 " --> pdb=" O THR X 206 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'X' and resid 17 through 19 Processing sheet with id=AA5, first strand: chain 'X' and resid 64 through 65 removed outlier: 3.507A pdb=" N VAL X 72 " --> pdb=" O GLN X 95 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'X' and resid 114 through 117 removed outlier: 6.519A pdb=" N ALA X 115 " --> pdb=" O PHE X 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'X' and resid 152 through 154 removed outlier: 6.692A pdb=" N GLY X 159 " --> pdb=" O VAL X 182 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'i' and resid 19 through 24 removed outlier: 4.495A pdb=" N LYS i 19 " --> pdb=" O VAL i 35 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 74 through 76 Processing sheet with id=AB1, first strand: chain 'J' and resid 205 through 206 removed outlier: 4.322A pdb=" N SER J 113 " --> pdb=" O ARG J 88 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL J 134 " --> pdb=" O GLY J 230 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 153 through 155 Processing sheet with id=AB3, first strand: chain 'j' and resid 116 through 117 Processing sheet with id=AB4, first strand: chain 'K' and resid 177 through 180 removed outlier: 6.398A pdb=" N VAL K 151 " --> pdb=" O ALA K 178 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL K 180 " --> pdb=" O VAL K 151 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ILE K 153 " --> pdb=" O VAL K 180 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '7' and resid 3 through 11 removed outlier: 6.911A pdb=" N ILE 7 4 " --> pdb=" O ASN 7 59 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU 7 52 " --> pdb=" O VAL 7 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '7' and resid 17 through 20 Processing sheet with id=AB7, first strand: chain '7' and resid 132 through 136 removed outlier: 6.131A pdb=" N ARG 7 91 " --> pdb=" O VAL 7 181 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N VAL 7 181 " --> pdb=" O ARG 7 91 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL 7 93 " --> pdb=" O ILE 7 179 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ILE 7 179 " --> pdb=" O VAL 7 93 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '7' and resid 100 through 104 Processing sheet with id=AB9, first strand: chain 'l' and resid 16 through 17 Processing sheet with id=AC1, first strand: chain 'M' and resid 46 through 48 removed outlier: 4.826A pdb=" N ILE M 14 " --> pdb=" O ASN M 132 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ASN M 132 " --> pdb=" O ILE M 14 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS M 16 " --> pdb=" O VAL M 130 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL M 130 " --> pdb=" O LYS M 16 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'm' and resid 3 through 5 removed outlier: 3.621A pdb=" N ARG m 3 " --> pdb=" O LEU m 51 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL m 55 " --> pdb=" O ILE m 5 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N THR m 22 " --> pdb=" O ARG m 46 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ALA m 23 " --> pdb=" O ASN m 76 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 22 through 24 Processing sheet with id=AC4, first strand: chain 'N' and resid 57 through 59 Processing sheet with id=AC5, first strand: chain 'N' and resid 156 through 157 removed outlier: 7.152A pdb=" N LYS c 126 " --> pdb=" O PRO c 100 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE c 102 " --> pdb=" O LYS c 126 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL c 125 " --> pdb=" O GLU c 146 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 56 through 59 removed outlier: 7.960A pdb=" N LYS O 43 " --> pdb=" O ILE O 38 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ILE O 38 " --> pdb=" O LYS O 43 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU O 45 " --> pdb=" O VAL O 36 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG O 19 " --> pdb=" O ILE O 35 " (cutoff:3.500A) removed outlier: 5.407A 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: 4.279A pdb=" N ILE p 61 " --> pdb=" O ALA p 39 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLU p 131 " --> pdb=" O TRP p 120 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N TRP p 120 " --> pdb=" O GLU p 131 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Q' and resid 6 through 10 removed outlier: 6.585A pdb=" N ILE Q 33 " --> pdb=" O LYS Q 103 " (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: 6.644A pdb=" N THR 5 151 " --> pdb=" O VAL 5 114 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N VAL 5 114 " --> pdb=" O THR 5 151 " (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 128 Processing sheet with id=AD5, first strand: chain 'S' and resid 62 through 63 removed outlier: 6.284A 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 123 removed outlier: 6.751A pdb=" N VAL S 101 " --> pdb=" O ILE S 122 " (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 133 through 134 removed outlier: 3.557A pdb=" N ILE s 165 " --> pdb=" O HIS s 50 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 's' and resid 57 through 60 removed outlier: 6.460A pdb=" N LEU s 96 " --> pdb=" O HIS s 122 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU s 124 " --> pdb=" O HIS s 94 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N HIS s 94 " --> pdb=" O LEU s 124 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 's' and resid 189 through 192 removed outlier: 3.521A pdb=" N ASP s 192 " --> pdb=" O PHE s 195 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE s 195 " --> pdb=" O ASP s 192 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'T' and resid 23 through 24 removed outlier: 3.554A pdb=" N VAL T 51 " --> pdb=" O TRP T 23 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'U' and resid 58 through 64 removed outlier: 6.358A pdb=" N ILE U 10 " --> pdb=" O VAL U 59 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE U 61 " --> pdb=" O GLN U 8 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLN U 8 " --> pdb=" O ILE U 61 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N GLN U 63 " --> pdb=" O GLU U 6 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU U 6 " --> pdb=" O GLN U 63 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'U' and resid 88 through 96 removed outlier: 6.581A pdb=" N ARG U 80 " --> pdb=" O ILE U 123 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ILE U 123 " --> pdb=" O ARG U 80 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'V' and resid 83 through 92 removed outlier: 3.649A pdb=" N ARG V 83 " --> pdb=" O VAL V 80 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN V 66 " --> pdb=" O GLY V 73 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE V 75 " --> pdb=" O VAL V 64 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N VAL V 64 " --> pdb=" O ILE V 75 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ASN V 77 " --> pdb=" O GLY V 62 " (cutoff:3.500A) removed outlier: 8.126A 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 56 removed outlier: 3.757A pdb=" N VAL W 66 " --> pdb=" O THR W 55 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'W' and resid 42 through 43 removed outlier: 3.513A pdb=" N VAL W 43 " --> pdb=" O ALA W 46 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA W 46 " --> pdb=" O VAL W 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'P' and resid 12 through 16 Processing sheet with id=AE9, first strand: chain 'r' and resid 50 through 52 removed outlier: 3.942A pdb=" N VAL r 190 " --> pdb=" O PHE r 197 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN r 195 " --> pdb=" O ASP r 192 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'x' and resid 24 through 25 removed outlier: 6.125A pdb=" N ASN x 24 " --> pdb=" O GLY x 100 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE x 102 " --> pdb=" O ASN x 24 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ALA x 99 " --> pdb=" O VAL x 79 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N MET x 57 " --> pdb=" O VAL x 39 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N VAL x 39 " --> pdb=" O MET x 57 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N MET x 59 " --> pdb=" O ILE x 37 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS x 63 " --> pdb=" O ASN x 33 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASN x 33 " --> pdb=" O LYS x 63 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'x' and resid 85 through 86 Processing sheet with id=AF3, first strand: chain 'Y' and resid 4 through 5 Processing sheet with id=AF4, first strand: chain 'Y' and resid 19 through 22 Processing sheet with id=AF5, first strand: chain 'Z' and resid 63 through 66 removed outlier: 3.554A pdb=" N GLN Z 65 " --> pdb=" O GLN Z 85 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LYS Z 121 " --> pdb=" O THR Z 112 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR Z 112 " --> pdb=" O LYS Z 121 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TYR Z 123 " --> pdb=" O VAL Z 110 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL Z 110 " --> pdb=" O TYR Z 123 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ARG Z 125 " --> pdb=" O LEU Z 108 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'a' and resid 33 through 34 Processing sheet with id=AF7, first strand: chain 'a' and resid 94 through 99 removed outlier: 3.628A pdb=" N ILE a 97 " --> pdb=" O VAL a 85 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL a 85 " --> pdb=" O ILE a 97 " (cutoff:3.500A) removed outlier: 11.491A pdb=" N LEU a 99 " --> pdb=" O ASP a 83 " (cutoff:3.500A) removed outlier: 10.865A pdb=" N ASP a 83 " --> pdb=" O LEU a 99 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ALA a 79 " --> pdb=" O VAL a 73 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N VAL a 73 " --> pdb=" O ALA a 79 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLN a 81 " --> pdb=" O SER a 71 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LYS a 69 " --> pdb=" O ASP a 83 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL a 85 " --> pdb=" O GLU a 67 " (cutoff:3.500A) removed outlier: 9.538A pdb=" N GLU a 67 " --> pdb=" O VAL a 85 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLU a 55 " --> pdb=" O THR a 107 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'b' and resid 69 through 76 removed outlier: 6.638A pdb=" N LYS b 69 " --> pdb=" O GLU b 47 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA b 44 " --> pdb=" O ILE b 25 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ILE b 25 " --> pdb=" O ALA b 44 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ILE b 46 " --> pdb=" O VAL b 23 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL b 23 " --> pdb=" O ILE b 46 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LYS b 9 " --> pdb=" O ILE b 25 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL b 10 " --> pdb=" O THR b 83 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 7 through 11 removed outlier: 3.891A 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: 5.857A pdb=" N LEU c 73 " --> pdb=" O LEU c 113 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 47 through 50 removed outlier: 3.665A pdb=" N ILE D 54 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA D 65 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL E 82 " --> pdb=" O ALA D 65 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 71 through 77 removed outlier: 7.024A pdb=" N LYS E 60 " --> pdb=" O LYS E 46 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ARG E 64 " --> pdb=" O ARG E 42 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ARG E 42 " --> pdb=" O ARG E 64 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 101 through 103 removed outlier: 5.945A pdb=" N ILE E 136 " --> pdb=" O ARG E 149 " (cutoff:3.500A) removed outlier: 6.566A 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: 6.507A pdb=" N LYS e 22 " --> pdb=" O LEU e 93 " (cutoff:3.500A) removed outlier: 6.266A 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: 7.704A pdb=" N LEU F 356 " --> pdb=" O ASP F 59 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ASP F 59 " --> pdb=" O LEU F 356 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE F 335 " --> pdb=" O VAL F 220 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N VAL F 220 " --> pdb=" O ILE F 335 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA F 217 " --> pdb=" O ILE F 278 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ILE F 278 " --> pdb=" O ALA F 217 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ALA F 219 " --> pdb=" O THR F 276 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N THR F 276 " --> pdb=" O ALA F 219 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LYS F 281 " --> pdb=" O LYS F 325 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET F 323 " --> pdb=" O TYR F 283 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL F 285 " --> pdb=" O PHE F 321 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N PHE F 321 " --> pdb=" O VAL F 285 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ARG F 70 " --> pdb=" O ASP F 59 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASP F 59 " --> pdb=" O ARG F 70 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL F 72 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL F 57 " --> pdb=" O VAL F 72 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLU F 74 " --> pdb=" O THR F 55 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR F 55 " --> pdb=" O GLU F 74 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL F 76 " --> pdb=" O MET F 53 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N MET F 53 " --> pdb=" O VAL F 76 " (cutoff:3.500A) removed outlier: 7.039A 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: 5.284A pdb=" N LEU F 99 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N THR F 95 " --> pdb=" O LEU F 99 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N SER F 101 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL F 93 " --> pdb=" O SER F 101 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR F 103 " --> pdb=" O GLY F 91 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N VAL F 86 " --> pdb=" O HIS F 163 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N HIS F 163 " --> pdb=" O VAL F 86 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 98 through 106 removed outlier: 5.284A pdb=" N LEU F 99 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N THR F 95 " --> pdb=" O LEU F 99 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N SER F 101 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL F 93 " --> pdb=" O SER F 101 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR F 103 " --> pdb=" O GLY F 91 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 226 through 227 Processing sheet with id=AH2, first strand: chain 'f' and resid 49 through 50 removed outlier: 3.552A pdb=" N VAL f 107 " --> pdb=" O GLU f 11 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 19 through 20 removed outlier: 4.610A pdb=" N VAL G 151 " --> pdb=" O THR G 7 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU G 150 " --> pdb=" O VAL G 248 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU G 206 " --> pdb=" O ILE G 249 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N THR G 251 " --> pdb=" O LEU G 206 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL G 208 " --> pdb=" O THR G 251 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL G 207 " --> pdb=" O ALA G 228 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 62 through 64 Processing sheet with id=AH5, first strand: chain 'G' and resid 186 through 187 Processing sheet with id=AH6, first strand: chain 'g' and resid 72 through 76 Processing sheet with id=AH7, first strand: chain 'H' and resid 73 through 79 removed outlier: 5.104A pdb=" N VAL H 74 " --> pdb=" O SER H 66 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N SER H 66 " --> pdb=" O VAL H 74 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'h' and resid 8 through 18 removed outlier: 9.994A pdb=" N VAL h 9 " --> pdb=" O ILE h 32 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE h 32 " --> pdb=" O VAL h 9 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N GLY h 11 " --> pdb=" O ILE h 30 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N ILE h 30 " --> pdb=" O GLY h 11 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N HIS h 13 " --> pdb=" O SER h 28 " (cutoff:3.500A) removed outlier: 10.305A pdb=" N SER h 28 " --> pdb=" O HIS h 13 " (cutoff:3.500A) removed outlier: 11.945A pdb=" N SER h 15 " --> pdb=" O ASN h 26 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N ASN h 26 " --> pdb=" O SER h 15 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN h 17 " --> pdb=" O ASN h 24 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ASN h 26 " --> pdb=" O PHE h 85 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N PHE h 85 " --> pdb=" O ASN h 26 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N THR h 84 " --> pdb=" O VAL h 71 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N VAL h 71 " --> pdb=" O THR h 84 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS h 63 " --> pdb=" O ALA h 55 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG h 48 " --> pdb=" O PHE h 101 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N VAL h 52 " --> pdb=" O SER h 97 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N SER h 97 " --> pdb=" O VAL h 52 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'I' and resid 77 through 80 removed outlier: 7.191A pdb=" N THR I 62 " --> pdb=" O HIS I 57 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N HIS I 57 " --> pdb=" O THR I 62 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LEU I 64 " --> pdb=" O LEU I 55 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N THR I 38 " --> pdb=" O TYR I 54 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N VAL I 39 " --> pdb=" O THR I 87 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'L' and resid 35 through 40 removed outlier: 4.277A pdb=" N ALA L 168 " --> pdb=" O VAL L 36 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU L 38 " --> pdb=" O ALA L 166 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ALA L 166 " --> pdb=" O LEU L 38 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ASN L 40 " --> pdb=" O CYS L 164 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N CYS L 164 " --> pdb=" O ASN L 40 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'L' and resid 70 through 71 removed outlier: 5.785A pdb=" N ASP L 70 " --> pdb=" O ASP L 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI2 1886 hydrogen bonds defined for protein. 5325 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2689 hydrogen bonds 4300 hydrogen bond angles 0 basepair planarities 1095 basepair parallelities 1950 stacking parallelities Total time for adding SS restraints: 244.49 Time building geometry restraints manager: 54.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.33: 22615 1.33 - 1.48: 72390 1.48 - 1.64: 47246 1.64 - 1.79: 124 1.79 - 1.95: 76 Bond restraints: 142451 Sorted by residual: bond pdb=" C LYS F 237 " pdb=" N LEU F 238 " ideal model delta sigma weight residual 1.329 1.174 0.154 1.86e-02 2.89e+03 6.89e+01 bond pdb=" C GLU J 131 " pdb=" N PRO J 132 " ideal model delta sigma weight residual 1.337 1.377 -0.040 9.80e-03 1.04e+04 1.67e+01 bond pdb=" C LEU f 51 " pdb=" N ALA f 52 " ideal model delta sigma weight residual 1.329 1.289 0.040 1.21e-02 6.83e+03 1.08e+01 bond pdb=" C ILE G 299 " pdb=" N ARG G 300 " ideal model delta sigma weight residual 1.330 1.378 -0.048 1.47e-02 4.63e+03 1.06e+01 bond pdb=" N GLY H 149 " pdb=" CA GLY H 149 " ideal model delta sigma weight residual 1.464 1.434 0.031 1.12e-02 7.97e+03 7.52e+00 ... (remaining 142446 not shown) Histogram of bond angle deviations from ideal: 94.39 - 102.97: 6725 102.97 - 111.55: 79597 111.55 - 120.13: 68762 120.13 - 128.72: 50535 128.72 - 137.30: 4011 Bond angle restraints: 209630 Sorted by residual: angle pdb=" C PRO N 61 " pdb=" N THR N 62 " pdb=" CA THR N 62 " ideal model delta sigma weight residual 121.54 136.36 -14.82 1.91e+00 2.74e-01 6.02e+01 angle pdb=" C GLN K 38 " pdb=" N ALA K 39 " pdb=" CA ALA K 39 " ideal model delta sigma weight residual 121.31 131.44 -10.13 1.49e+00 4.50e-01 4.62e+01 angle pdb=" C ALA V 133 " pdb=" N GLN V 134 " pdb=" CA GLN V 134 " ideal model delta sigma weight residual 120.60 130.98 -10.38 1.53e+00 4.27e-01 4.60e+01 angle pdb=" O3' G 1 857 " pdb=" C3' G 1 857 " pdb=" C2' G 1 857 " ideal model delta sigma weight residual 109.50 119.46 -9.96 1.50e+00 4.44e-01 4.41e+01 angle pdb=" N VAL r 80 " pdb=" CA VAL r 80 " pdb=" C VAL r 80 " ideal model delta sigma weight residual 112.83 106.36 6.47 9.90e-01 1.02e+00 4.27e+01 ... (remaining 209625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 80760 35.99 - 71.98: 8553 71.98 - 107.97: 843 107.97 - 143.96: 45 143.96 - 179.95: 95 Dihedral angle restraints: 90296 sinusoidal: 69378 harmonic: 20918 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 -107.32 -72.68 0 5.00e+00 4.00e-02 2.11e+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 -114.18 -65.82 0 5.00e+00 4.00e-02 1.73e+02 dihedral pdb=" CA ALA N 47 " pdb=" C ALA N 47 " pdb=" N PRO N 48 " pdb=" CA PRO N 48 " ideal model delta harmonic sigma weight residual -180.00 -118.17 -61.83 0 5.00e+00 4.00e-02 1.53e+02 ... (remaining 90293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 25092 0.123 - 0.247: 1054 0.247 - 0.370: 133 0.370 - 0.493: 31 0.493 - 0.616: 6 Chirality restraints: 26316 Sorted by residual: chirality pdb=" C3' G 1 857 " pdb=" C4' G 1 857 " pdb=" O3' G 1 857 " pdb=" C2' G 1 857 " both_signs ideal model delta sigma weight residual False -2.74 -2.13 -0.62 2.00e-01 2.50e+01 9.50e+00 chirality pdb=" C3' G 1 269 " pdb=" C4' G 1 269 " pdb=" O3' G 1 269 " pdb=" C2' G 1 269 " both_signs ideal model delta sigma weight residual False -2.74 -2.17 -0.58 2.00e-01 2.50e+01 8.40e+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 -2.18 -0.56 2.00e-01 2.50e+01 7.87e+00 ... (remaining 26313 not shown) Planarity restraints: 13421 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP c 46 " -0.025 2.00e-02 2.50e+03 5.03e-02 2.53e+01 pdb=" C ASP c 46 " 0.087 2.00e-02 2.50e+03 pdb=" O ASP c 46 " -0.032 2.00e-02 2.50e+03 pdb=" N LYS c 47 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO Q 110 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO Q 111 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO Q 111 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO Q 111 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN m 32 " 0.020 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C ASN m 32 " -0.069 2.00e-02 2.50e+03 pdb=" O ASN m 32 " 0.026 2.00e-02 2.50e+03 pdb=" N LYS m 33 " 0.023 2.00e-02 2.50e+03 ... (remaining 13418 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 3268 2.63 - 3.20: 101235 3.20 - 3.76: 250356 3.76 - 4.33: 339060 4.33 - 4.90: 477738 Nonbonded interactions: 1171657 Sorted by model distance: nonbonded pdb=" CB HIS R 96 " pdb="ZN ZN R 601 " model vdw 2.061 2.104 nonbonded pdb=" O2 U 11958 " pdb=" O6 G 12083 " model vdw 2.163 2.432 nonbonded pdb=" O4 U 13047 " pdb=" N1 A 13094 " model vdw 2.179 3.120 nonbonded pdb=" O2' A 1 645 " pdb=" OP2 A 1 647 " model vdw 2.196 2.440 nonbonded pdb=" O2' G 12375 " pdb=" OP2 G 12377 " model vdw 2.218 2.440 ... (remaining 1171652 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: 2.910 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: 16.810 Check model and map are aligned: 1.400 Set scattering table: 0.910 Process input model: 502.500 Find NCS groups from input model: 3.020 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:2.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 530.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 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 : 0.007 0.154 142451 Z= 0.429 Angle : 1.075 15.560 209630 Z= 0.582 Chirality : 0.060 0.616 26316 Planarity : 0.007 0.104 13421 Dihedral : 22.891 179.947 76794 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.45 % Favored : 92.18 % Rotamer: Outliers : 0.39 % Allowed : 2.31 % Favored : 97.30 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.57 % Cis-general : 0.00 % Twisted Proline : 0.74 % 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: -4.05 (0.08), residues: 7086 helix: -3.06 (0.08), residues: 2269 sheet: -2.13 (0.15), residues: 956 loop : -2.62 (0.08), residues: 3861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.004 TRP F 255 HIS 0.013 0.003 HIS V 54 PHE 0.042 0.004 PHE i 7 TYR 0.044 0.003 TYR J 133 ARG 0.017 0.001 ARG N 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14172 Ramachandran restraints generated. 7086 Oldfield, 0 Emsley, 7086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14172 Ramachandran restraints generated. 7086 Oldfield, 0 Emsley, 7086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1783 residues out of total 6052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1760 time to evaluate : 6.351 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: R 240 MET cc_start: 0.7228 (mmm) cc_final: 0.7002 (mmt) REVERT: R 352 LYS cc_start: 0.5729 (tttt) cc_final: 0.5328 (mttm) REVERT: X 3 THR cc_start: 0.8663 (m) cc_final: 0.8276 (p) REVERT: X 20 THR cc_start: 0.8757 (p) cc_final: 0.8532 (t) REVERT: X 75 GLN cc_start: 0.8005 (mp10) cc_final: 0.7657 (mp10) REVERT: X 99 GLU cc_start: 0.6777 (pp20) cc_final: 0.5974 (pm20) REVERT: i 21 LYS cc_start: 0.8162 (ttpt) cc_final: 0.7387 (ttmt) REVERT: i 54 ILE cc_start: 0.9448 (mm) cc_final: 0.9228 (mm) REVERT: J 93 ASN cc_start: 0.8230 (p0) cc_final: 0.7920 (p0) REVERT: J 140 SER cc_start: 0.9201 (p) cc_final: 0.8981 (p) REVERT: K 33 ASN cc_start: 0.8823 (t0) cc_final: 0.8354 (t0) REVERT: K 48 ARG cc_start: 0.7450 (ttt-90) cc_final: 0.7133 (ttt90) REVERT: K 85 ASN cc_start: 0.7722 (t0) cc_final: 0.7279 (m-40) REVERT: k 71 LYS cc_start: 0.8800 (ttpp) cc_final: 0.8489 (ttpt) REVERT: 7 46 THR cc_start: 0.8629 (m) cc_final: 0.8133 (p) REVERT: 7 181 VAL cc_start: 0.8521 (t) cc_final: 0.8308 (p) REVERT: l 20 ASN cc_start: 0.8385 (m-40) cc_final: 0.8074 (m110) REVERT: m 61 LYS cc_start: 0.8240 (mtpp) cc_final: 0.7985 (tptp) REVERT: N 7 LEU cc_start: 0.8852 (mt) cc_final: 0.8614 (mt) REVERT: N 23 LYS cc_start: 0.8404 (ttmt) cc_final: 0.7860 (tptp) REVERT: N 85 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7658 (pp) REVERT: n 8 ARG cc_start: 0.8317 (ttm-80) cc_final: 0.8075 (ttm170) REVERT: n 17 LYS cc_start: 0.8246 (tttt) cc_final: 0.8007 (tttt) REVERT: p 13 LYS cc_start: 0.8453 (mptt) cc_final: 0.7943 (mptt) REVERT: p 81 TYR cc_start: 0.7544 (m-10) cc_final: 0.7317 (m-80) REVERT: p 192 LYS cc_start: 0.8096 (tttt) cc_final: 0.7834 (ttmt) REVERT: Q 135 TYR cc_start: 0.8225 (p90) cc_final: 0.7894 (p90) REVERT: 5 42 THR cc_start: 0.8430 (t) cc_final: 0.8225 (p) REVERT: 5 50 GLN cc_start: 0.8837 (mt0) cc_final: 0.8450 (mt0) REVERT: 5 65 SER cc_start: 0.8677 (p) cc_final: 0.8452 (m) REVERT: s 73 LYS cc_start: 0.8193 (mmtp) cc_final: 0.7986 (ttpt) REVERT: s 130 ILE cc_start: 0.8878 (mt) cc_final: 0.8666 (mt) REVERT: U 28 ARG cc_start: 0.8374 (mtp85) cc_final: 0.8145 (mtp180) REVERT: U 72 VAL cc_start: 0.9344 (t) cc_final: 0.8684 (m) REVERT: V 13 TYR cc_start: 0.8693 (m-80) cc_final: 0.8310 (m-80) REVERT: V 48 ILE cc_start: 0.9040 (mm) cc_final: 0.8770 (mm) REVERT: V 90 ASN cc_start: 0.8974 (m-40) cc_final: 0.8694 (m-40) REVERT: W 81 LYS cc_start: 0.8659 (mtmt) cc_final: 0.8349 (mtpt) REVERT: Y 26 SER cc_start: 0.8634 (m) cc_final: 0.8013 (t) REVERT: Z 63 ILE cc_start: 0.9154 (pp) cc_final: 0.8934 (pt) REVERT: Z 74 LYS cc_start: 0.8359 (ttmm) cc_final: 0.8102 (ttmt) REVERT: b 46 ILE cc_start: 0.8206 (pp) cc_final: 0.7993 (pt) REVERT: C 19 LYS cc_start: 0.8839 (pttt) cc_final: 0.8521 (pttp) REVERT: c 58 MET cc_start: 0.8459 (mtm) cc_final: 0.8223 (mtm) REVERT: c 87 ARG cc_start: 0.8826 (ttm170) cc_final: 0.8248 (ttm170) REVERT: d 8 THR cc_start: 0.9108 (t) cc_final: 0.8779 (m) REVERT: d 42 ASN cc_start: 0.8313 (t0) cc_final: 0.8028 (t0) REVERT: E 38 HIS cc_start: 0.8898 (m-70) cc_final: 0.8524 (m90) REVERT: E 188 LYS cc_start: 0.8798 (tttt) cc_final: 0.8315 (ttpt) REVERT: F 7 GLU cc_start: 0.7331 (mt-10) cc_final: 0.6307 (mt-10) REVERT: F 34 LYS cc_start: 0.8521 (tttt) cc_final: 0.8257 (tttt) REVERT: F 299 ASP cc_start: 0.8387 (t0) cc_final: 0.8154 (t0) REVERT: G 157 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7943 (mt-10) REVERT: H 57 ASN cc_start: 0.8128 (m-40) cc_final: 0.7613 (m110) REVERT: H 69 ILE cc_start: 0.8652 (pp) cc_final: 0.7911 (mt) REVERT: H 88 ILE cc_start: 0.9145 (mt) cc_final: 0.8901 (mt) REVERT: H 196 ARG cc_start: 0.8310 (tpt90) cc_final: 0.8046 (tpt-90) REVERT: H 250 ASP cc_start: 0.7818 (t70) cc_final: 0.7486 (t0) REVERT: I 8 LYS cc_start: 0.7384 (mtmt) cc_final: 0.7150 (mmtt) outliers start: 23 outliers final: 6 residues processed: 1774 average time/residue: 1.4197 time to fit residues: 4145.8901 Evaluate side-chains 1146 residues out of total 6052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1139 time to evaluate : 6.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain 5 residue 114 VAL Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain F residue 104 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 892 optimal weight: 7.9990 chunk 801 optimal weight: 9.9990 chunk 444 optimal weight: 10.0000 chunk 273 optimal weight: 2.9990 chunk 540 optimal weight: 4.9990 chunk 428 optimal weight: 7.9990 chunk 828 optimal weight: 50.0000 chunk 320 optimal weight: 9.9990 chunk 503 optimal weight: 1.9990 chunk 616 optimal weight: 0.8980 chunk 959 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 ASN ** J 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 166 ASN J 237 ASN j 59 ASN j 61 GLN j 99 GLN K 38 GLN K 41 GLN K 138 HIS K 145 ASN K 191 ASN K 192 GLN k 92 ASN N 103 ASN N 120 GLN N 137 GLN n 4 GLN n 19 GLN o 109 ASN p 37 HIS p 117 ASN p 181 ASN p 195 ASN 5 34 GLN 5 121 GLN S 45 ASN S 73 GLN U 88 HIS U 122 HIS ** U 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 157 GLN V 103 GLN W 87 ASN r 39 HIS r 56 ASN ** x 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 53 HIS Z 94 GLN b 29 HIS b 57 HIS b 127 ASN C 22 GLN C 59 HIS ** c 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 74 ASN d 12 GLN ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 ASN E 209 HIS F 121 ASN F 293 ASN F 371 GLN f 15 ASN f 57 GLN G 48 GLN G 114 ASN G 296 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 52 GLN ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 GLN H 151 GLN h 26 ASN h 42 GLN I 57 HIS L 35 GLN L 44 GLN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 142451 Z= 0.331 Angle : 0.754 13.851 209630 Z= 0.395 Chirality : 0.046 0.389 26316 Planarity : 0.006 0.095 13421 Dihedral : 24.055 179.819 62767 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.00 % Favored : 92.70 % Rotamer: Outliers : 3.19 % Allowed : 9.73 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.57 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.26 % 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: -2.88 (0.09), residues: 7086 helix: -1.47 (0.10), residues: 2278 sheet: -1.84 (0.15), residues: 961 loop : -2.22 (0.09), residues: 3847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP O 85 HIS 0.007 0.002 HIS H 40 PHE 0.024 0.002 PHE J 229 TYR 0.030 0.002 TYR H 207 ARG 0.012 0.001 ARG s 210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14172 Ramachandran restraints generated. 7086 Oldfield, 0 Emsley, 7086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14172 Ramachandran restraints generated. 7086 Oldfield, 0 Emsley, 7086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1398 residues out of total 6052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1210 time to evaluate : 6.372 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: R 95 TYR cc_start: 0.7400 (t80) cc_final: 0.7133 (t80) REVERT: R 240 MET cc_start: 0.7139 (mmm) cc_final: 0.6616 (mmt) REVERT: R 352 LYS cc_start: 0.5769 (tttt) cc_final: 0.5284 (mttm) REVERT: R 483 MET cc_start: 0.1417 (tpp) cc_final: 0.0752 (mmm) REVERT: R 486 MET cc_start: -0.1286 (mpp) cc_final: -0.2321 (mmm) REVERT: X 50 HIS cc_start: 0.8092 (m-70) cc_final: 0.7737 (m170) REVERT: X 200 ASN cc_start: 0.8485 (p0) cc_final: 0.8179 (p0) REVERT: i 21 LYS cc_start: 0.8152 (ttpt) cc_final: 0.7294 (ttmt) REVERT: i 51 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8831 (pp) REVERT: i 103 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7485 (mtpp) REVERT: J 51 TYR cc_start: 0.8783 (m-10) cc_final: 0.7940 (m-80) REVERT: j 49 LYS cc_start: 0.8295 (mmtp) cc_final: 0.7953 (mmtt) REVERT: j 108 GLN cc_start: 0.7605 (mt0) cc_final: 0.7366 (mt0) REVERT: K 66 SER cc_start: 0.9193 (m) cc_final: 0.8901 (t) REVERT: K 155 ASN cc_start: 0.8608 (p0) cc_final: 0.8216 (p0) REVERT: 7 46 THR cc_start: 0.8756 (m) cc_final: 0.8531 (p) REVERT: 7 94 TYR cc_start: 0.7849 (p90) cc_final: 0.7397 (p90) REVERT: 7 142 ASP cc_start: 0.6299 (m-30) cc_final: 0.5979 (m-30) REVERT: 7 177 ASP cc_start: 0.8708 (m-30) cc_final: 0.8480 (m-30) REVERT: l 20 ASN cc_start: 0.8353 (m-40) cc_final: 0.8046 (m110) REVERT: M 92 ARG cc_start: 0.8002 (mtm-85) cc_final: 0.7787 (ptp-170) REVERT: M 97 SER cc_start: 0.8707 (OUTLIER) cc_final: 0.8133 (m) REVERT: M 99 THR cc_start: 0.9160 (m) cc_final: 0.8803 (m) REVERT: m 61 LYS cc_start: 0.8380 (mtpp) cc_final: 0.8113 (ttmm) REVERT: n 8 ARG cc_start: 0.8182 (ttm-80) cc_final: 0.7942 (ttm170) REVERT: O 121 MET cc_start: 0.7824 (ttm) cc_final: 0.7227 (ttt) REVERT: p 30 TYR cc_start: 0.8891 (m-10) cc_final: 0.8632 (m-80) REVERT: p 192 LYS cc_start: 0.8239 (tttt) cc_final: 0.7747 (ttmt) REVERT: Q 56 ASP cc_start: 0.7316 (m-30) cc_final: 0.6908 (m-30) REVERT: Q 135 TYR cc_start: 0.8302 (p90) cc_final: 0.7802 (p90) REVERT: 5 50 GLN cc_start: 0.8921 (mt0) cc_final: 0.8709 (mt0) REVERT: 5 173 ARG cc_start: 0.8845 (mtm110) cc_final: 0.8630 (mtm110) REVERT: S 145 ASN cc_start: 0.7778 (t0) cc_final: 0.7564 (t0) REVERT: s 32 ILE cc_start: 0.8775 (mm) cc_final: 0.8549 (mt) REVERT: s 130 ILE cc_start: 0.8924 (mt) cc_final: 0.8699 (mt) REVERT: T 5 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7574 (mtt90) REVERT: U 141 LYS cc_start: 0.8800 (ttmt) cc_final: 0.8490 (ttpp) REVERT: V 48 ILE cc_start: 0.9067 (mm) cc_final: 0.8826 (mm) REVERT: W 75 TYR cc_start: 0.8852 (t80) cc_final: 0.7216 (t80) REVERT: W 83 TYR cc_start: 0.8396 (t80) cc_final: 0.8111 (t80) REVERT: x 74 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7626 (ptp) REVERT: Y 26 SER cc_start: 0.8751 (m) cc_final: 0.8122 (t) REVERT: Y 60 LYS cc_start: 0.9008 (mppt) cc_final: 0.8683 (mtmt) REVERT: b 6 LYS cc_start: 0.8161 (mmmt) cc_final: 0.7914 (mmtp) REVERT: C 19 LYS cc_start: 0.8934 (pttt) cc_final: 0.8673 (pttp) REVERT: C 78 LYS cc_start: 0.8273 (ttmm) cc_final: 0.7858 (tppp) REVERT: c 87 ARG cc_start: 0.8846 (ttm170) cc_final: 0.8615 (ttm170) REVERT: d 42 ASN cc_start: 0.8277 (t0) cc_final: 0.8037 (t0) REVERT: E 118 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7390 (mt-10) REVERT: e 61 MET cc_start: 0.8460 (tmm) cc_final: 0.8248 (tmm) REVERT: F 7 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6548 (mt-10) REVERT: F 34 LYS cc_start: 0.8465 (tttt) cc_final: 0.8215 (tttt) REVERT: F 112 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8142 (t0) REVERT: F 167 ARG cc_start: 0.7940 (ptt-90) cc_final: 0.7702 (ptt-90) REVERT: F 349 LYS cc_start: 0.8731 (tmtt) cc_final: 0.8523 (tptm) REVERT: f 70 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7625 (mtt90) REVERT: G 201 GLN cc_start: 0.8277 (pt0) cc_final: 0.8077 (pt0) REVERT: G 324 LEU cc_start: 0.8776 (tp) cc_final: 0.8533 (tt) REVERT: g 73 THR cc_start: 0.9117 (t) cc_final: 0.8896 (m) REVERT: g 87 MET cc_start: 0.7464 (mpp) cc_final: 0.7258 (mpp) REVERT: H 69 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8019 (mt) REVERT: H 95 TRP cc_start: 0.9046 (OUTLIER) cc_final: 0.8669 (t60) REVERT: H 177 GLU cc_start: 0.7791 (pp20) cc_final: 0.7542 (pp20) REVERT: H 198 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.7308 (t80) REVERT: H 250 ASP cc_start: 0.7851 (t70) cc_final: 0.7562 (t0) REVERT: I 8 LYS cc_start: 0.7487 (mtmt) cc_final: 0.7165 (mmtt) outliers start: 188 outliers final: 120 residues processed: 1304 average time/residue: 1.3434 time to fit residues: 2969.5355 Evaluate side-chains 1181 residues out of total 6052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1051 time to evaluate : 6.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 341 ILE Chi-restraints excluded: chain R residue 361 ASN Chi-restraints excluded: chain R residue 373 THR Chi-restraints excluded: chain R residue 380 LEU Chi-restraints excluded: chain R residue 447 LEU Chi-restraints excluded: chain i residue 22 VAL Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 64 THR Chi-restraints excluded: chain i residue 73 SER Chi-restraints excluded: chain i residue 103 LYS Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 93 ASN Chi-restraints excluded: chain J residue 157 ASN Chi-restraints excluded: chain J residue 172 ASN Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain j residue 69 LEU Chi-restraints excluded: chain j residue 99 GLN Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 146 LYS Chi-restraints excluded: chain K residue 161 GLU Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain k residue 3 VAL Chi-restraints excluded: chain k residue 11 LEU Chi-restraints excluded: chain k residue 18 THR Chi-restraints excluded: chain k residue 34 SER Chi-restraints excluded: chain k residue 42 SER Chi-restraints excluded: chain 7 residue 68 LEU Chi-restraints excluded: chain 7 residue 102 ASN Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain M residue 159 THR Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain n residue 47 THR Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain p residue 18 VAL Chi-restraints excluded: chain p residue 126 THR Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 44 SER Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain Q residue 175 THR Chi-restraints excluded: chain 5 residue 16 SER Chi-restraints excluded: chain 5 residue 87 SER Chi-restraints excluded: chain 5 residue 96 GLN Chi-restraints excluded: chain 5 residue 114 VAL Chi-restraints excluded: chain 5 residue 129 THR Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain s residue 174 ASN Chi-restraints excluded: chain s residue 181 LEU Chi-restraints excluded: chain s residue 196 VAL Chi-restraints excluded: chain T residue 5 ARG Chi-restraints excluded: chain T residue 59 SER Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain U residue 8 GLN Chi-restraints excluded: chain U residue 32 SER Chi-restraints excluded: chain U residue 39 SER Chi-restraints excluded: chain U residue 145 THR Chi-restraints excluded: chain W residue 16 THR Chi-restraints excluded: chain W residue 47 VAL Chi-restraints excluded: chain W residue 54 VAL Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain W residue 100 THR Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain r residue 76 LEU Chi-restraints excluded: chain x residue 74 MET Chi-restraints excluded: chain x residue 93 LEU Chi-restraints excluded: chain Y residue 9 SER Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Z residue 48 SER Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 83 THR Chi-restraints excluded: chain c residue 8 THR Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain e residue 33 SER Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 76 GLU Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 70 ARG Chi-restraints excluded: chain f residue 97 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain g residue 51 SER Chi-restraints excluded: chain g residue 59 SER Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 101 SER Chi-restraints excluded: chain g residue 119 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 95 TRP Chi-restraints excluded: chain H residue 198 TYR Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain h residue 4 SER Chi-restraints excluded: chain h residue 62 SER Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain L residue 82 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 533 optimal weight: 5.9990 chunk 297 optimal weight: 0.8980 chunk 798 optimal weight: 10.0000 chunk 653 optimal weight: 0.4980 chunk 264 optimal weight: 10.0000 chunk 961 optimal weight: 20.0000 chunk 1038 optimal weight: 10.0000 chunk 856 optimal weight: 5.9990 chunk 953 optimal weight: 5.9990 chunk 327 optimal weight: 3.9990 chunk 771 optimal weight: 6.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 454 ASN ** X 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN k 92 ASN M 68 HIS N 17 HIS N 120 GLN ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 32 ASN ** n 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 70 ASN S 45 ASN s 54 ASN s 143 ASN T 34 GLN ** U 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 103 GLN W 40 HIS ** W 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 53 HIS ** c 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 74 ASN E 38 HIS F 3 HIS F 121 ASN f 15 ASN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 HIS H 63 GLN ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8246 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 142451 Z= 0.347 Angle : 0.717 12.306 209630 Z= 0.374 Chirality : 0.044 0.399 26316 Planarity : 0.005 0.097 13421 Dihedral : 23.817 179.910 62765 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.87 % Favored : 91.84 % Rotamer: Outliers : 4.14 % Allowed : 12.10 % Favored : 83.76 % Cbeta Deviations : 0.00 % 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: -2.36 (0.09), residues: 7086 helix: -0.82 (0.10), residues: 2277 sheet: -1.68 (0.15), residues: 984 loop : -2.02 (0.09), residues: 3825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP O 85 HIS 0.016 0.002 HIS H 90 PHE 0.026 0.002 PHE J 229 TYR 0.032 0.002 TYR G 194 ARG 0.026 0.001 ARG s 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14172 Ramachandran restraints generated. 7086 Oldfield, 0 Emsley, 7086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14172 Ramachandran restraints generated. 7086 Oldfield, 0 Emsley, 7086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1344 residues out of total 6052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 1100 time to evaluate : 6.443 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: R 233 MET cc_start: 0.5653 (ppp) cc_final: 0.4055 (mmm) REVERT: R 240 MET cc_start: 0.7441 (mmm) cc_final: 0.6907 (mtt) REVERT: R 351 LYS cc_start: 0.2582 (tptm) cc_final: 0.2181 (ptmt) REVERT: R 352 LYS cc_start: 0.5741 (tttt) cc_final: 0.5144 (mttm) REVERT: R 483 MET cc_start: 0.1392 (tpp) cc_final: 0.0724 (mmm) REVERT: R 486 MET cc_start: -0.0930 (mpp) cc_final: -0.1154 (mmm) REVERT: X 35 TYR cc_start: 0.7427 (m-80) cc_final: 0.7099 (m-80) REVERT: X 50 HIS cc_start: 0.8086 (m-70) cc_final: 0.7867 (m170) REVERT: X 200 ASN cc_start: 0.8451 (p0) cc_final: 0.8047 (p0) REVERT: i 21 LYS cc_start: 0.8212 (ttpt) cc_final: 0.7454 (ttmm) REVERT: i 51 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8567 (pp) REVERT: i 54 ILE cc_start: 0.9498 (OUTLIER) cc_final: 0.9273 (mt) REVERT: K 155 ASN cc_start: 0.8582 (p0) cc_final: 0.8328 (p0) REVERT: k 13 LYS cc_start: 0.8492 (ttpt) cc_final: 0.8044 (tttp) REVERT: l 17 THR cc_start: 0.8075 (OUTLIER) cc_final: 0.7665 (p) REVERT: l 20 ASN cc_start: 0.8340 (m-40) cc_final: 0.7977 (m110) REVERT: M 13 LYS cc_start: 0.8944 (ptpp) cc_final: 0.8663 (ptpp) REVERT: M 92 ARG cc_start: 0.8105 (mtm-85) cc_final: 0.7784 (ptp-170) REVERT: M 97 SER cc_start: 0.8664 (OUTLIER) cc_final: 0.8144 (m) REVERT: M 99 THR cc_start: 0.9134 (m) cc_final: 0.8844 (m) REVERT: m 61 LYS cc_start: 0.8282 (mtpp) cc_final: 0.8060 (ttmm) REVERT: N 23 LYS cc_start: 0.8097 (ttmt) cc_final: 0.7486 (tptp) REVERT: N 85 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8053 (pp) REVERT: N 153 ASP cc_start: 0.7270 (t0) cc_final: 0.7069 (t0) REVERT: n 8 ARG cc_start: 0.8196 (ttm-80) cc_final: 0.7911 (ttm170) REVERT: p 30 TYR cc_start: 0.8950 (m-10) cc_final: 0.8708 (m-80) REVERT: p 131 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7683 (mt-10) REVERT: p 142 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.7860 (mt) REVERT: p 187 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8139 (ttt90) REVERT: p 192 LYS cc_start: 0.8278 (tttt) cc_final: 0.7756 (ttmt) REVERT: Q 56 ASP cc_start: 0.7272 (m-30) cc_final: 0.6884 (m-30) REVERT: Q 135 TYR cc_start: 0.8455 (p90) cc_final: 0.7976 (p90) REVERT: Q 168 TYR cc_start: 0.9393 (t80) cc_final: 0.8565 (t80) REVERT: s 75 MET cc_start: 0.8170 (mmp) cc_final: 0.7695 (mmt) REVERT: s 149 GLU cc_start: 0.8476 (tp30) cc_final: 0.8269 (tp30) REVERT: T 5 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7535 (mtt90) REVERT: U 141 LYS cc_start: 0.8811 (ttmt) cc_final: 0.8535 (ttpp) REVERT: V 48 ILE cc_start: 0.9200 (mm) cc_final: 0.8991 (mm) REVERT: V 139 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7877 (mtp85) REVERT: W 35 LYS cc_start: 0.9143 (tmtt) cc_final: 0.8915 (tptm) REVERT: W 75 TYR cc_start: 0.8885 (t80) cc_final: 0.7317 (t80) REVERT: W 102 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8003 (mt-10) REVERT: x 11 PHE cc_start: 0.7935 (m-80) cc_final: 0.7605 (m-80) REVERT: Y 26 SER cc_start: 0.8722 (m) cc_final: 0.8194 (t) REVERT: Y 47 ARG cc_start: 0.8074 (mtp-110) cc_final: 0.7771 (mtp-110) REVERT: Y 60 LYS cc_start: 0.8913 (mppt) cc_final: 0.8683 (mtmt) REVERT: b 48 ARG cc_start: 0.7834 (mtm-85) cc_final: 0.7605 (mtm180) REVERT: C 19 LYS cc_start: 0.8919 (pttt) cc_final: 0.8631 (pttp) REVERT: C 78 LYS cc_start: 0.8281 (ttmm) cc_final: 0.7971 (tppp) REVERT: c 87 ARG cc_start: 0.8866 (ttm170) cc_final: 0.8126 (ttm110) REVERT: d 42 ASN cc_start: 0.8388 (t0) cc_final: 0.8163 (t0) REVERT: E 68 LYS cc_start: 0.8263 (ttmm) cc_final: 0.7909 (ttmm) REVERT: E 118 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7433 (mt-10) REVERT: e 61 MET cc_start: 0.8583 (tmm) cc_final: 0.8226 (tmm) REVERT: F 7 GLU cc_start: 0.7234 (mt-10) cc_final: 0.5883 (mt-10) REVERT: F 112 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.8229 (t0) REVERT: F 349 LYS cc_start: 0.8619 (tmtt) cc_final: 0.8401 (tptm) REVERT: f 70 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7644 (mtt90) REVERT: G 324 LEU cc_start: 0.8789 (tp) cc_final: 0.8578 (tt) REVERT: g 73 THR cc_start: 0.8995 (t) cc_final: 0.8776 (m) REVERT: H 69 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.7985 (mt) REVERT: H 177 GLU cc_start: 0.7842 (pp20) cc_final: 0.6897 (pp20) REVERT: H 183 TRP cc_start: 0.8664 (t-100) cc_final: 0.8012 (t-100) REVERT: H 250 ASP cc_start: 0.7905 (t70) cc_final: 0.7649 (t0) REVERT: I 8 LYS cc_start: 0.7530 (mtmt) cc_final: 0.7107 (mptt) REVERT: I 169 ASP cc_start: 0.7705 (m-30) cc_final: 0.7483 (t0) outliers start: 244 outliers final: 170 residues processed: 1227 average time/residue: 1.2613 time to fit residues: 2629.9065 Evaluate side-chains 1238 residues out of total 6052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1056 time to evaluate : 6.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 341 ILE Chi-restraints excluded: chain R residue 361 ASN Chi-restraints excluded: chain R residue 373 THR Chi-restraints excluded: chain R residue 447 LEU Chi-restraints excluded: chain R residue 474 MET Chi-restraints excluded: chain i residue 22 VAL Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 64 THR Chi-restraints excluded: chain i residue 73 SER Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 93 ASN Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain j residue 22 VAL Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain j residue 69 LEU Chi-restraints excluded: chain j residue 109 ILE Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 201 THR Chi-restraints excluded: chain K residue 232 HIS Chi-restraints excluded: chain k residue 18 THR Chi-restraints excluded: chain k residue 27 SER Chi-restraints excluded: chain k residue 34 SER Chi-restraints excluded: chain k residue 42 SER Chi-restraints excluded: chain 7 residue 17 THR Chi-restraints excluded: chain 7 residue 68 LEU Chi-restraints excluded: chain 7 residue 90 MET Chi-restraints excluded: chain 7 residue 132 VAL Chi-restraints excluded: chain 7 residue 151 VAL Chi-restraints excluded: chain l residue 17 THR Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain m residue 15 THR Chi-restraints excluded: chain m residue 53 THR Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain O residue 38 ILE Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain p residue 18 VAL Chi-restraints excluded: chain p residue 101 THR Chi-restraints excluded: chain p residue 142 ILE Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain p residue 187 ARG Chi-restraints excluded: chain p residue 196 THR Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 44 SER Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain Q residue 175 THR Chi-restraints excluded: chain 5 residue 7 THR Chi-restraints excluded: chain 5 residue 16 SER Chi-restraints excluded: chain 5 residue 36 ILE Chi-restraints excluded: chain 5 residue 78 VAL Chi-restraints excluded: chain 5 residue 87 SER Chi-restraints excluded: chain 5 residue 96 GLN Chi-restraints excluded: chain 5 residue 114 VAL Chi-restraints excluded: chain 5 residue 120 ASN Chi-restraints excluded: chain 5 residue 129 THR Chi-restraints excluded: chain 5 residue 144 SER Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 175 ARG Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 167 SER Chi-restraints excluded: chain s residue 110 LEU Chi-restraints excluded: chain s residue 143 ASN Chi-restraints excluded: chain s residue 148 VAL Chi-restraints excluded: chain s residue 174 ASN Chi-restraints excluded: chain s residue 181 LEU Chi-restraints excluded: chain s residue 189 VAL Chi-restraints excluded: chain s residue 196 VAL Chi-restraints excluded: chain T residue 5 ARG Chi-restraints excluded: chain T residue 59 SER Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 8 GLN Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 32 SER Chi-restraints excluded: chain U residue 39 SER Chi-restraints excluded: chain U residue 145 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 96 ILE Chi-restraints excluded: chain V residue 139 ARG Chi-restraints excluded: chain W residue 16 THR Chi-restraints excluded: chain W residue 47 VAL Chi-restraints excluded: chain W residue 55 THR Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain r residue 76 LEU Chi-restraints excluded: chain r residue 188 VAL Chi-restraints excluded: chain x residue 14 SER Chi-restraints excluded: chain x residue 56 ASP Chi-restraints excluded: chain x residue 74 MET Chi-restraints excluded: chain x residue 93 LEU Chi-restraints excluded: chain x residue 135 VAL Chi-restraints excluded: chain Y residue 9 SER Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Z residue 48 SER Chi-restraints excluded: chain Z residue 59 SER Chi-restraints excluded: chain Z residue 102 LEU Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain a residue 97 ILE Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 83 THR Chi-restraints excluded: chain b residue 100 THR Chi-restraints excluded: chain c residue 8 THR Chi-restraints excluded: chain c residue 16 SER Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 75 LEU Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain d residue 8 THR Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain e residue 33 SER Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 76 GLU Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 70 ARG Chi-restraints excluded: chain f residue 91 SER Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain f residue 97 LEU Chi-restraints excluded: chain f residue 106 THR Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain g residue 51 SER Chi-restraints excluded: chain g residue 59 SER Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 101 SER Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain g residue 119 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain h residue 4 SER Chi-restraints excluded: chain h residue 80 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 162 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 950 optimal weight: 5.9990 chunk 722 optimal weight: 7.9990 chunk 499 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 458 optimal weight: 3.9990 chunk 645 optimal weight: 6.9990 chunk 965 optimal weight: 50.0000 chunk 1021 optimal weight: 6.9990 chunk 504 optimal weight: 4.9990 chunk 914 optimal weight: 5.9990 chunk 275 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 90 HIS ** X 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 108 GLN K 41 GLN K 252 ASN N 120 GLN ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 32 ASN ** n 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 42 ASN s 54 ASN U 65 ASN ** U 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 103 GLN W 87 ASN ** x 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 53 HIS ** c 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN F 243 HIS f 15 ASN g 104 ASN H 17 GLN ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 142451 Z= 0.337 Angle : 0.691 13.785 209630 Z= 0.362 Chirality : 0.043 0.401 26316 Planarity : 0.005 0.088 13421 Dihedral : 23.703 179.891 62765 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.73 % Favored : 92.00 % Rotamer: Outliers : 4.96 % Allowed : 13.31 % Favored : 81.74 % 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: -2.04 (0.09), residues: 7086 helix: -0.45 (0.11), residues: 2277 sheet: -1.57 (0.15), residues: 998 loop : -1.88 (0.09), residues: 3811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J 203 HIS 0.013 0.002 HIS H 90 PHE 0.023 0.002 PHE J 229 TYR 0.031 0.002 TYR G 194 ARG 0.009 0.001 ARG X 4 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14172 Ramachandran restraints generated. 7086 Oldfield, 0 Emsley, 7086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14172 Ramachandran restraints generated. 7086 Oldfield, 0 Emsley, 7086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1392 residues out of total 6052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 1100 time to evaluate : 6.466 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: R 240 MET cc_start: 0.7375 (mmm) cc_final: 0.7047 (mtp) REVERT: R 351 LYS cc_start: 0.2503 (tptm) cc_final: 0.2299 (ptpt) REVERT: R 352 LYS cc_start: 0.5629 (tttt) cc_final: 0.5067 (mttm) REVERT: R 483 MET cc_start: 0.1373 (tpp) cc_final: 0.0709 (mmm) REVERT: R 486 MET cc_start: -0.1198 (mpp) cc_final: -0.1493 (mmm) REVERT: X 50 HIS cc_start: 0.8089 (m-70) cc_final: 0.7696 (m170) REVERT: X 200 ASN cc_start: 0.8444 (p0) cc_final: 0.8187 (p0) REVERT: i 21 LYS cc_start: 0.8141 (ttpt) cc_final: 0.7398 (ttmm) REVERT: i 51 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8534 (pp) REVERT: i 54 ILE cc_start: 0.9489 (OUTLIER) cc_final: 0.9176 (mt) REVERT: j 76 GLN cc_start: 0.9125 (mt0) cc_final: 0.8908 (mt0) REVERT: j 104 GLN cc_start: 0.8374 (mt0) cc_final: 0.8166 (mt0) REVERT: K 155 ASN cc_start: 0.8623 (p0) cc_final: 0.8379 (p0) REVERT: 7 94 TYR cc_start: 0.8104 (p90) cc_final: 0.7822 (p90) REVERT: 7 102 ASN cc_start: 0.8189 (t0) cc_final: 0.7938 (t0) REVERT: 7 142 ASP cc_start: 0.6112 (m-30) cc_final: 0.5904 (t0) REVERT: l 17 THR cc_start: 0.8056 (OUTLIER) cc_final: 0.7626 (p) REVERT: M 64 LYS cc_start: 0.8428 (ttmt) cc_final: 0.8223 (tttt) REVERT: M 92 ARG cc_start: 0.8136 (mtm-85) cc_final: 0.7753 (ptp-170) REVERT: M 97 SER cc_start: 0.8592 (OUTLIER) cc_final: 0.8126 (m) REVERT: M 99 THR cc_start: 0.9111 (m) cc_final: 0.8868 (m) REVERT: m 36 LYS cc_start: 0.8107 (ptmm) cc_final: 0.7649 (ptmm) REVERT: N 23 LYS cc_start: 0.8112 (ttmt) cc_final: 0.7513 (tptp) REVERT: N 85 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.7915 (pp) REVERT: O 108 ARG cc_start: 0.8676 (tpt90) cc_final: 0.8290 (tpt170) REVERT: O 124 ARG cc_start: 0.8617 (mtp85) cc_final: 0.8146 (mtm180) REVERT: p 127 TYR cc_start: 0.8388 (m-80) cc_final: 0.8099 (m-80) REVERT: p 142 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7960 (mt) REVERT: p 187 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8136 (ttt90) REVERT: p 192 LYS cc_start: 0.8317 (tttt) cc_final: 0.7802 (ttmt) REVERT: Q 56 ASP cc_start: 0.7196 (m-30) cc_final: 0.6821 (m-30) REVERT: 5 173 ARG cc_start: 0.8733 (mtm110) cc_final: 0.8364 (mtm110) REVERT: s 75 MET cc_start: 0.8144 (mmp) cc_final: 0.7844 (mmt) REVERT: s 143 ASN cc_start: 0.8961 (t0) cc_final: 0.8543 (m-40) REVERT: T 5 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7523 (mtt90) REVERT: U 141 LYS cc_start: 0.8830 (ttmt) cc_final: 0.8562 (ttpp) REVERT: V 18 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.8039 (t0) REVERT: V 48 ILE cc_start: 0.9238 (mm) cc_final: 0.8952 (mm) REVERT: V 139 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8150 (mtp85) REVERT: W 35 LYS cc_start: 0.9138 (tmtt) cc_final: 0.8898 (tptm) REVERT: W 75 TYR cc_start: 0.8929 (t80) cc_final: 0.7398 (t80) REVERT: x 23 MET cc_start: 0.8362 (ptp) cc_final: 0.8141 (ptt) REVERT: Y 26 SER cc_start: 0.8750 (m) cc_final: 0.8223 (t) REVERT: Y 38 SER cc_start: 0.8849 (OUTLIER) cc_final: 0.8470 (p) REVERT: Y 60 LYS cc_start: 0.8962 (mppt) cc_final: 0.8683 (mtmt) REVERT: Z 33 ARG cc_start: 0.7653 (mtp-110) cc_final: 0.7447 (mtp-110) REVERT: Z 103 TYR cc_start: 0.8884 (m-80) cc_final: 0.8650 (m-10) REVERT: C 19 LYS cc_start: 0.8901 (pttt) cc_final: 0.8638 (pttp) REVERT: C 78 LYS cc_start: 0.8336 (ttmm) cc_final: 0.8124 (tppp) REVERT: c 87 ARG cc_start: 0.8858 (ttm170) cc_final: 0.8581 (ttm170) REVERT: E 68 LYS cc_start: 0.8323 (ttmm) cc_final: 0.8036 (ttmm) REVERT: E 118 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7443 (mt-10) REVERT: e 61 MET cc_start: 0.8617 (tmm) cc_final: 0.8343 (tmm) REVERT: F 7 GLU cc_start: 0.7006 (mt-10) cc_final: 0.6659 (mt-10) REVERT: F 59 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.7231 (t0) REVERT: F 112 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8291 (t0) REVERT: F 349 LYS cc_start: 0.8631 (tmtt) cc_final: 0.8397 (tptm) REVERT: f 70 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7639 (mtt90) REVERT: g 73 THR cc_start: 0.9007 (t) cc_final: 0.8773 (m) REVERT: H 69 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.7972 (mt) REVERT: H 177 GLU cc_start: 0.7790 (pp20) cc_final: 0.6901 (pp20) REVERT: H 183 TRP cc_start: 0.8734 (t-100) cc_final: 0.7780 (t-100) REVERT: H 250 ASP cc_start: 0.7880 (t70) cc_final: 0.7641 (t0) REVERT: h 103 TYR cc_start: 0.8798 (p90) cc_final: 0.8588 (p90) REVERT: I 8 LYS cc_start: 0.7572 (mtmt) cc_final: 0.7165 (mptt) REVERT: I 169 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7600 (t0) outliers start: 292 outliers final: 206 residues processed: 1264 average time/residue: 1.2397 time to fit residues: 2670.4752 Evaluate side-chains 1229 residues out of total 6052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1007 time to evaluate : 6.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 341 ILE Chi-restraints excluded: chain R residue 348 VAL Chi-restraints excluded: chain R residue 361 ASN Chi-restraints excluded: chain R residue 373 THR Chi-restraints excluded: chain R residue 380 LEU Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 447 LEU Chi-restraints excluded: chain R residue 474 MET Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 146 ILE Chi-restraints excluded: chain i residue 22 VAL Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 64 THR Chi-restraints excluded: chain i residue 71 THR Chi-restraints excluded: chain i residue 73 SER Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 93 ASN Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain j residue 22 VAL Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain j residue 69 LEU Chi-restraints excluded: chain j residue 109 ILE Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 201 THR Chi-restraints excluded: chain K residue 232 HIS Chi-restraints excluded: chain k residue 3 VAL Chi-restraints excluded: chain k residue 18 THR Chi-restraints excluded: chain k residue 19 SER Chi-restraints excluded: chain k residue 27 SER Chi-restraints excluded: chain k residue 34 SER Chi-restraints excluded: chain k residue 42 SER Chi-restraints excluded: chain 7 residue 6 THR Chi-restraints excluded: chain 7 residue 68 LEU Chi-restraints excluded: chain 7 residue 71 VAL Chi-restraints excluded: chain 7 residue 90 MET Chi-restraints excluded: chain 7 residue 104 VAL Chi-restraints excluded: chain 7 residue 132 VAL Chi-restraints excluded: chain 7 residue 151 VAL Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 17 THR Chi-restraints excluded: chain l residue 68 LYS Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 156 LYS Chi-restraints excluded: chain m residue 15 THR Chi-restraints excluded: chain m residue 53 THR Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain n residue 17 LYS Chi-restraints excluded: chain n residue 51 ILE Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 38 ILE Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain p residue 18 VAL Chi-restraints excluded: chain p residue 19 LEU Chi-restraints excluded: chain p residue 89 VAL Chi-restraints excluded: chain p residue 101 THR Chi-restraints excluded: chain p residue 126 THR Chi-restraints excluded: chain p residue 138 GLN Chi-restraints excluded: chain p residue 142 ILE Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain p residue 187 ARG Chi-restraints excluded: chain p residue 196 THR Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 44 SER Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain Q residue 175 THR Chi-restraints excluded: chain 5 residue 16 SER Chi-restraints excluded: chain 5 residue 36 ILE Chi-restraints excluded: chain 5 residue 87 SER Chi-restraints excluded: chain 5 residue 96 GLN Chi-restraints excluded: chain 5 residue 114 VAL Chi-restraints excluded: chain 5 residue 120 ASN Chi-restraints excluded: chain 5 residue 144 SER Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 157 VAL Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain s residue 21 TYR Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 69 ILE Chi-restraints excluded: chain s residue 110 LEU Chi-restraints excluded: chain s residue 174 ASN Chi-restraints excluded: chain s residue 181 LEU Chi-restraints excluded: chain s residue 189 VAL Chi-restraints excluded: chain s residue 196 VAL Chi-restraints excluded: chain T residue 5 ARG Chi-restraints excluded: chain T residue 59 SER Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 8 GLN Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 32 SER Chi-restraints excluded: chain U residue 39 SER Chi-restraints excluded: chain U residue 145 THR Chi-restraints excluded: chain V residue 18 ASP Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 96 ILE Chi-restraints excluded: chain V residue 139 ARG Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain W residue 16 THR Chi-restraints excluded: chain W residue 47 VAL Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain W residue 100 THR Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain r residue 76 LEU Chi-restraints excluded: chain r residue 188 VAL Chi-restraints excluded: chain x residue 14 SER Chi-restraints excluded: chain x residue 56 ASP Chi-restraints excluded: chain x residue 93 LEU Chi-restraints excluded: chain x residue 135 VAL Chi-restraints excluded: chain Y residue 9 SER Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 47 ARG Chi-restraints excluded: chain Z residue 48 SER Chi-restraints excluded: chain Z residue 59 SER Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain Z residue 102 LEU Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain a residue 97 ILE Chi-restraints excluded: chain a residue 111 LEU Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 83 THR Chi-restraints excluded: chain b residue 98 THR Chi-restraints excluded: chain b residue 100 THR Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain c residue 8 THR Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 75 LEU Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain d residue 8 THR Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain e residue 33 SER Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 76 GLU Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 70 ARG Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain f residue 97 LEU Chi-restraints excluded: chain f residue 106 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain g residue 51 SER Chi-restraints excluded: chain g residue 59 SER Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 101 SER Chi-restraints excluded: chain g residue 107 VAL Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain g residue 119 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain h residue 4 SER Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain I residue 169 ASP Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 162 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 850 optimal weight: 70.0000 chunk 579 optimal weight: 5.9990 chunk 14 optimal weight: 30.0000 chunk 760 optimal weight: 5.9990 chunk 421 optimal weight: 10.0000 chunk 871 optimal weight: 7.9990 chunk 706 optimal weight: 10.0000 chunk 1 optimal weight: 30.0000 chunk 521 optimal weight: 5.9990 chunk 917 optimal weight: 7.9990 chunk 257 optimal weight: 2.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 HIS ** j 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 108 GLN K 41 GLN M 109 HIS N 120 GLN ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 32 ASN p 175 ASN p 181 ASN ** S 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 54 ASN T 121 HIS ** U 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 98 HIS V 103 GLN V 131 GLN ** W 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 14 HIS ** c 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 ASN F 121 ASN F 184 ASN f 15 ASN g 52 GLN ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 21 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.096 142451 Z= 0.544 Angle : 0.834 11.849 209630 Z= 0.428 Chirality : 0.050 0.427 26316 Planarity : 0.006 0.110 13421 Dihedral : 23.764 179.731 62765 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.98 % Favored : 90.74 % Rotamer: Outliers : 5.92 % Allowed : 13.66 % Favored : 80.41 % Cbeta Deviations : 0.00 % 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: -2.11 (0.09), residues: 7086 helix: -0.49 (0.11), residues: 2290 sheet: -1.52 (0.16), residues: 1003 loop : -1.97 (0.09), residues: 3793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP J 203 HIS 0.016 0.002 HIS g 21 PHE 0.037 0.002 PHE U 150 TYR 0.035 0.002 TYR G 194 ARG 0.013 0.001 ARG s 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14172 Ramachandran restraints generated. 7086 Oldfield, 0 Emsley, 7086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14172 Ramachandran restraints generated. 7086 Oldfield, 0 Emsley, 7086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1417 residues out of total 6052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 349 poor density : 1068 time to evaluate : 6.514 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: R 98 MET cc_start: 0.8143 (mmp) cc_final: 0.7920 (mmt) REVERT: R 240 MET cc_start: 0.7497 (mmm) cc_final: 0.6835 (mtp) REVERT: R 352 LYS cc_start: 0.5868 (tttt) cc_final: 0.5284 (mttm) REVERT: R 381 GLU cc_start: 0.8040 (tp30) cc_final: 0.7458 (tp30) REVERT: R 454 ASN cc_start: 0.4987 (m110) cc_final: 0.4641 (t0) REVERT: R 483 MET cc_start: 0.1496 (tpp) cc_final: 0.0785 (mmm) REVERT: X 12 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7462 (mp0) REVERT: X 35 TYR cc_start: 0.7469 (m-80) cc_final: 0.7159 (m-80) REVERT: X 50 HIS cc_start: 0.8098 (m-70) cc_final: 0.7750 (m170) REVERT: X 200 ASN cc_start: 0.8644 (p0) cc_final: 0.8244 (p0) REVERT: i 51 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8611 (pp) REVERT: i 54 ILE cc_start: 0.9510 (OUTLIER) cc_final: 0.9222 (mt) REVERT: J 104 GLN cc_start: 0.8357 (mt0) cc_final: 0.8153 (mt0) REVERT: j 5 LYS cc_start: 0.7674 (mttp) cc_final: 0.6945 (mttm) REVERT: K 54 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7268 (mm-30) REVERT: 7 51 GLN cc_start: 0.8898 (mp10) cc_final: 0.8635 (mp10) REVERT: 7 102 ASN cc_start: 0.8190 (t0) cc_final: 0.7951 (t0) REVERT: M 92 ARG cc_start: 0.8156 (mtm-85) cc_final: 0.7873 (ptp-170) REVERT: M 97 SER cc_start: 0.8688 (OUTLIER) cc_final: 0.8203 (m) REVERT: M 99 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8931 (m) REVERT: M 132 ASN cc_start: 0.7649 (p0) cc_final: 0.7247 (p0) REVERT: m 36 LYS cc_start: 0.8359 (ptmm) cc_final: 0.7943 (ptmm) REVERT: N 23 LYS cc_start: 0.8169 (ttmt) cc_final: 0.7549 (tptm) REVERT: N 80 VAL cc_start: 0.8999 (OUTLIER) cc_final: 0.8765 (m) REVERT: N 85 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8035 (pp) REVERT: O 121 MET cc_start: 0.8329 (tmm) cc_final: 0.7973 (ttm) REVERT: p 127 TYR cc_start: 0.8493 (m-80) cc_final: 0.8255 (m-80) REVERT: p 142 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.7962 (mt) REVERT: p 175 ASN cc_start: 0.7830 (OUTLIER) cc_final: 0.7341 (m110) REVERT: p 187 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8035 (ttt90) REVERT: p 192 LYS cc_start: 0.8339 (tttt) cc_final: 0.7842 (ttmt) REVERT: Q 56 ASP cc_start: 0.7222 (m-30) cc_final: 0.6907 (m-30) REVERT: Q 167 TYR cc_start: 0.8792 (t80) cc_final: 0.8361 (t80) REVERT: 5 69 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7601 (ptp-170) REVERT: 5 72 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8633 (mt0) REVERT: 5 173 ARG cc_start: 0.8795 (mtm110) cc_final: 0.8560 (mtm110) REVERT: 5 175 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.7067 (ptt180) REVERT: S 133 LYS cc_start: 0.9106 (mttp) cc_final: 0.8835 (mttp) REVERT: s 75 MET cc_start: 0.8284 (mmp) cc_final: 0.8024 (mmt) REVERT: s 143 ASN cc_start: 0.9088 (m-40) cc_final: 0.8393 (t0) REVERT: s 202 LYS cc_start: 0.7327 (mttt) cc_final: 0.7063 (pttt) REVERT: T 5 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7528 (mtt90) REVERT: U 141 LYS cc_start: 0.8893 (ttmt) cc_final: 0.8573 (ttpp) REVERT: V 48 ILE cc_start: 0.9267 (mm) cc_final: 0.8997 (mm) REVERT: V 139 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7911 (mtp85) REVERT: W 35 LYS cc_start: 0.9166 (tmtt) cc_final: 0.8957 (tptm) REVERT: x 72 LYS cc_start: 0.9123 (pttt) cc_final: 0.8749 (ptpp) REVERT: Y 26 SER cc_start: 0.8892 (m) cc_final: 0.8250 (t) REVERT: Y 57 LYS cc_start: 0.8127 (tptp) cc_final: 0.7901 (tttp) REVERT: Y 60 LYS cc_start: 0.8931 (mppt) cc_final: 0.8670 (mtmt) REVERT: C 19 LYS cc_start: 0.8971 (pttt) cc_final: 0.8667 (pttp) REVERT: C 78 LYS cc_start: 0.8430 (ttmm) cc_final: 0.8217 (tppp) REVERT: d 21 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8198 (mm) REVERT: E 68 LYS cc_start: 0.8524 (ttmm) cc_final: 0.8073 (ttmm) REVERT: E 69 TYR cc_start: 0.8968 (t80) cc_final: 0.8610 (t80) REVERT: E 118 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7517 (mt-10) REVERT: E 143 GLU cc_start: 0.8779 (pm20) cc_final: 0.8493 (pm20) REVERT: E 245 LEU cc_start: 0.8984 (tp) cc_final: 0.8765 (tp) REVERT: e 61 MET cc_start: 0.8588 (tmm) cc_final: 0.8302 (tmm) REVERT: F 7 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6755 (mt-10) REVERT: F 59 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7371 (t0) REVERT: F 109 HIS cc_start: 0.7365 (t-90) cc_final: 0.7050 (t70) REVERT: F 166 ILE cc_start: 0.9427 (tp) cc_final: 0.9206 (tp) REVERT: F 349 LYS cc_start: 0.8643 (tmtt) cc_final: 0.8378 (tptm) REVERT: f 70 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7719 (mtt90) REVERT: G 357 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7659 (tp30) REVERT: H 17 GLN cc_start: 0.8550 (tt0) cc_final: 0.8192 (tt0) REVERT: H 69 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.7956 (mt) REVERT: H 79 TYR cc_start: 0.8869 (m-80) cc_final: 0.8577 (m-80) REVERT: H 190 ILE cc_start: 0.6703 (OUTLIER) cc_final: 0.6356 (tp) REVERT: H 250 ASP cc_start: 0.7935 (t70) cc_final: 0.7697 (t0) REVERT: I 108 LYS cc_start: 0.7283 (tmtt) cc_final: 0.6930 (tttm) outliers start: 349 outliers final: 250 residues processed: 1270 average time/residue: 1.2248 time to fit residues: 2653.9698 Evaluate side-chains 1284 residues out of total 6052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 1013 time to evaluate : 6.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 341 ILE Chi-restraints excluded: chain R residue 348 VAL Chi-restraints excluded: chain R residue 361 ASN Chi-restraints excluded: chain R residue 373 THR Chi-restraints excluded: chain R residue 380 LEU Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 447 LEU Chi-restraints excluded: chain R residue 474 MET Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 12 GLU Chi-restraints excluded: chain X residue 46 ILE Chi-restraints excluded: chain X residue 94 ILE Chi-restraints excluded: chain X residue 146 ILE Chi-restraints excluded: chain i residue 22 VAL Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 64 THR Chi-restraints excluded: chain i residue 68 THR Chi-restraints excluded: chain i residue 71 THR Chi-restraints excluded: chain i residue 73 SER Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 93 ASN Chi-restraints excluded: chain J residue 140 SER Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain j residue 22 VAL Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain j residue 69 LEU Chi-restraints excluded: chain j residue 109 ILE Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 201 THR Chi-restraints excluded: chain k residue 3 VAL Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 18 THR Chi-restraints excluded: chain k residue 19 SER Chi-restraints excluded: chain k residue 27 SER Chi-restraints excluded: chain k residue 34 SER Chi-restraints excluded: chain k residue 42 SER Chi-restraints excluded: chain 7 residue 6 THR Chi-restraints excluded: chain 7 residue 52 LEU Chi-restraints excluded: chain 7 residue 68 LEU Chi-restraints excluded: chain 7 residue 70 THR Chi-restraints excluded: chain 7 residue 71 VAL Chi-restraints excluded: chain 7 residue 90 MET Chi-restraints excluded: chain 7 residue 104 VAL Chi-restraints excluded: chain 7 residue 132 VAL Chi-restraints excluded: chain 7 residue 151 VAL Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 17 THR Chi-restraints excluded: chain l residue 68 LYS Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 154 THR Chi-restraints excluded: chain M residue 156 LYS Chi-restraints excluded: chain M residue 159 THR Chi-restraints excluded: chain m residue 51 LEU Chi-restraints excluded: chain m residue 53 THR Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 140 SER Chi-restraints excluded: chain n residue 17 LYS Chi-restraints excluded: chain n residue 51 ILE Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 38 ILE Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain p residue 18 VAL Chi-restraints excluded: chain p residue 19 LEU Chi-restraints excluded: chain p residue 89 VAL Chi-restraints excluded: chain p residue 90 ASN Chi-restraints excluded: chain p residue 101 THR Chi-restraints excluded: chain p residue 126 THR Chi-restraints excluded: chain p residue 138 GLN Chi-restraints excluded: chain p residue 142 ILE Chi-restraints excluded: chain p residue 175 ASN Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain p residue 187 ARG Chi-restraints excluded: chain p residue 196 THR Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 44 SER Chi-restraints excluded: chain Q residue 62 THR Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain Q residue 175 THR Chi-restraints excluded: chain 5 residue 7 THR Chi-restraints excluded: chain 5 residue 16 SER Chi-restraints excluded: chain 5 residue 36 ILE Chi-restraints excluded: chain 5 residue 42 THR Chi-restraints excluded: chain 5 residue 69 ARG Chi-restraints excluded: chain 5 residue 72 GLN Chi-restraints excluded: chain 5 residue 78 VAL Chi-restraints excluded: chain 5 residue 87 SER Chi-restraints excluded: chain 5 residue 114 VAL Chi-restraints excluded: chain 5 residue 117 ILE Chi-restraints excluded: chain 5 residue 119 VAL Chi-restraints excluded: chain 5 residue 120 ASN Chi-restraints excluded: chain 5 residue 129 THR Chi-restraints excluded: chain 5 residue 137 ASN Chi-restraints excluded: chain 5 residue 144 SER Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 157 VAL Chi-restraints excluded: chain 5 residue 175 ARG Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain s residue 21 TYR Chi-restraints excluded: chain s residue 41 THR Chi-restraints excluded: chain s residue 69 ILE Chi-restraints excluded: chain s residue 110 LEU Chi-restraints excluded: chain s residue 134 ILE Chi-restraints excluded: chain s residue 181 LEU Chi-restraints excluded: chain s residue 196 VAL Chi-restraints excluded: chain s residue 200 SER Chi-restraints excluded: chain T residue 5 ARG Chi-restraints excluded: chain T residue 36 ASN Chi-restraints excluded: chain T residue 59 SER Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 8 GLN Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 32 SER Chi-restraints excluded: chain U residue 39 SER Chi-restraints excluded: chain U residue 145 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 93 VAL Chi-restraints excluded: chain V residue 96 ILE Chi-restraints excluded: chain V residue 139 ARG Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain W residue 47 VAL Chi-restraints excluded: chain W residue 55 THR Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain W residue 100 THR Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain r residue 76 LEU Chi-restraints excluded: chain r residue 188 VAL Chi-restraints excluded: chain x residue 14 SER Chi-restraints excluded: chain x residue 56 ASP Chi-restraints excluded: chain x residue 74 MET Chi-restraints excluded: chain x residue 93 LEU Chi-restraints excluded: chain x residue 124 ASP Chi-restraints excluded: chain x residue 131 SER Chi-restraints excluded: chain x residue 135 VAL Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Y residue 9 SER Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Z residue 48 SER Chi-restraints excluded: chain Z residue 59 SER Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain Z residue 102 LEU Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain a residue 97 ILE Chi-restraints excluded: chain a residue 111 LEU Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 26 VAL Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 83 THR Chi-restraints excluded: chain b residue 98 THR Chi-restraints excluded: chain b residue 100 THR Chi-restraints excluded: chain b residue 127 ASN Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain c residue 8 THR Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 75 LEU Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain d residue 8 THR Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 21 ILE Chi-restraints excluded: chain d residue 42 ASN Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain e residue 33 SER Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 76 GLU Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain F residue 7 GLU Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 318 LYS Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 70 ARG Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain f residue 97 LEU Chi-restraints excluded: chain f residue 106 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain g residue 51 SER Chi-restraints excluded: chain g residue 59 SER Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 101 SER Chi-restraints excluded: chain g residue 107 VAL Chi-restraints excluded: chain g residue 119 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 229 ASP Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain h residue 4 SER Chi-restraints excluded: chain h residue 80 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 162 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 343 optimal weight: 4.9990 chunk 920 optimal weight: 10.0000 chunk 201 optimal weight: 5.9990 chunk 599 optimal weight: 0.9990 chunk 252 optimal weight: 0.9990 chunk 1022 optimal weight: 2.9990 chunk 848 optimal weight: 50.0000 chunk 473 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 338 optimal weight: 3.9990 chunk 536 optimal weight: 0.0670 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 454 ASN ** X 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 170 GLN ** J 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 34 GLN ** j 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN N 28 GLN n 32 ASN ** n 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 182 ASN p 195 ASN ** 5 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 73 GLN s 54 ASN ** U 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 87 ASN Z 53 HIS ** c 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 42 ASN E 8 GLN E 132 ASN F 173 GLN F 184 ASN f 15 ASN g 52 GLN H 90 HIS L 21 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 142451 Z= 0.169 Angle : 0.615 13.910 209630 Z= 0.325 Chirality : 0.039 0.389 26316 Planarity : 0.004 0.063 13421 Dihedral : 23.643 179.836 62765 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.70 % Favored : 93.01 % Rotamer: Outliers : 3.97 % Allowed : 16.14 % Favored : 79.89 % 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: -1.63 (0.10), residues: 7086 helix: 0.04 (0.11), residues: 2265 sheet: -1.32 (0.16), residues: 982 loop : -1.73 (0.10), residues: 3839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP O 85 HIS 0.008 0.001 HIS H 90 PHE 0.028 0.001 PHE U 150 TYR 0.026 0.001 TYR H 207 ARG 0.009 0.000 ARG s 184 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14172 Ramachandran restraints generated. 7086 Oldfield, 0 Emsley, 7086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14172 Ramachandran restraints generated. 7086 Oldfield, 0 Emsley, 7086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1337 residues out of total 6052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1103 time to evaluate : 6.390 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: R 34 MET cc_start: 0.3793 (tpt) cc_final: 0.3043 (tpt) REVERT: R 240 MET cc_start: 0.7334 (mmm) cc_final: 0.6954 (mtt) REVERT: R 352 LYS cc_start: 0.5552 (tttt) cc_final: 0.5118 (mttm) REVERT: R 376 ARG cc_start: 0.6473 (mtp-110) cc_final: 0.5776 (mtp180) REVERT: R 381 GLU cc_start: 0.8027 (tp30) cc_final: 0.7575 (tp30) REVERT: R 454 ASN cc_start: 0.4590 (m-40) cc_final: 0.4381 (t0) REVERT: R 483 MET cc_start: 0.1386 (tpp) cc_final: 0.0771 (mmm) REVERT: X 35 TYR cc_start: 0.7287 (m-80) cc_final: 0.6986 (m-80) REVERT: X 50 HIS cc_start: 0.8019 (m-70) cc_final: 0.7639 (m170) REVERT: X 200 ASN cc_start: 0.8445 (p0) cc_final: 0.8041 (p0) REVERT: i 51 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8790 (pp) REVERT: 7 86 TYR cc_start: 0.8213 (m-80) cc_final: 0.7767 (m-80) REVERT: 7 102 ASN cc_start: 0.8244 (t0) cc_final: 0.7973 (t0) REVERT: l 17 THR cc_start: 0.7861 (OUTLIER) cc_final: 0.7544 (p) REVERT: M 92 ARG cc_start: 0.8119 (mtm-85) cc_final: 0.7870 (ptp-170) REVERT: M 97 SER cc_start: 0.8409 (OUTLIER) cc_final: 0.7943 (m) REVERT: M 99 THR cc_start: 0.9190 (OUTLIER) cc_final: 0.8954 (m) REVERT: M 132 ASN cc_start: 0.7587 (p0) cc_final: 0.7177 (p0) REVERT: N 23 LYS cc_start: 0.8116 (ttmt) cc_final: 0.7494 (tptp) REVERT: N 85 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7774 (pp) REVERT: n 36 ARG cc_start: 0.7003 (mtp-110) cc_final: 0.6482 (mtp85) REVERT: O 121 MET cc_start: 0.8170 (tmm) cc_final: 0.7715 (ttt) REVERT: p 127 TYR cc_start: 0.8319 (m-80) cc_final: 0.8048 (m-80) REVERT: p 142 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7845 (mt) REVERT: p 187 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.7892 (ttt90) REVERT: p 192 LYS cc_start: 0.8238 (tttt) cc_final: 0.7761 (ttmt) REVERT: Q 56 ASP cc_start: 0.7166 (m-30) cc_final: 0.6772 (m-30) REVERT: 5 173 ARG cc_start: 0.8797 (mtm110) cc_final: 0.8559 (mtm110) REVERT: S 133 LYS cc_start: 0.9062 (mttp) cc_final: 0.8817 (mttp) REVERT: s 143 ASN cc_start: 0.9010 (m-40) cc_final: 0.8601 (m-40) REVERT: s 184 ARG cc_start: 0.8463 (mmm160) cc_final: 0.8089 (tpt-90) REVERT: T 5 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7817 (mtm110) REVERT: U 3 HIS cc_start: 0.7093 (t70) cc_final: 0.6771 (t-170) REVERT: U 141 LYS cc_start: 0.8793 (ttmt) cc_final: 0.8518 (ttpp) REVERT: V 48 ILE cc_start: 0.9179 (mm) cc_final: 0.8979 (mm) REVERT: V 139 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8185 (mtp85) REVERT: W 35 LYS cc_start: 0.9151 (tmtt) cc_final: 0.8889 (tptm) REVERT: W 75 TYR cc_start: 0.8768 (t80) cc_final: 0.7402 (t80) REVERT: x 128 ARG cc_start: 0.8565 (tpp80) cc_final: 0.8333 (tpp80) REVERT: Y 26 SER cc_start: 0.8728 (m) cc_final: 0.8215 (t) REVERT: Y 38 SER cc_start: 0.8793 (OUTLIER) cc_final: 0.8460 (p) REVERT: Y 47 ARG cc_start: 0.8111 (mtp-110) cc_final: 0.7810 (mtp-110) REVERT: Y 60 LYS cc_start: 0.8872 (mppt) cc_final: 0.8603 (mtmt) REVERT: Z 33 ARG cc_start: 0.7647 (mtp-110) cc_final: 0.7305 (mtp-110) REVERT: b 48 ARG cc_start: 0.8894 (ttm110) cc_final: 0.8568 (mtm110) REVERT: C 19 LYS cc_start: 0.8916 (pttt) cc_final: 0.8647 (pttp) REVERT: c 34 MET cc_start: 0.8064 (mmm) cc_final: 0.7834 (ttm) REVERT: c 87 ARG cc_start: 0.8873 (ttm170) cc_final: 0.8275 (ttm110) REVERT: d 28 LYS cc_start: 0.7825 (tttp) cc_final: 0.7435 (mtpt) REVERT: E 68 LYS cc_start: 0.8385 (ttmm) cc_final: 0.8087 (ttmm) REVERT: E 69 TYR cc_start: 0.8811 (t80) cc_final: 0.8564 (t80) REVERT: E 118 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7361 (mt-10) REVERT: E 143 GLU cc_start: 0.8525 (pm20) cc_final: 0.8250 (pm20) REVERT: e 61 MET cc_start: 0.8593 (tmm) cc_final: 0.8328 (tmm) REVERT: F 7 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6395 (mt-10) REVERT: F 14 LEU cc_start: 0.8564 (mt) cc_final: 0.8274 (tp) REVERT: F 112 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.8241 (t0) REVERT: F 349 LYS cc_start: 0.8587 (tmtt) cc_final: 0.8338 (tptm) REVERT: f 64 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8022 (p) REVERT: G 34 ILE cc_start: 0.9087 (mt) cc_final: 0.8865 (tp) REVERT: G 60 THR cc_start: 0.8322 (m) cc_final: 0.8116 (p) REVERT: G 357 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7508 (tp30) REVERT: H 17 GLN cc_start: 0.8370 (tt0) cc_final: 0.7911 (tp40) REVERT: H 69 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.7953 (mt) REVERT: H 177 GLU cc_start: 0.7906 (pp20) cc_final: 0.6950 (pp20) REVERT: H 183 TRP cc_start: 0.8722 (t-100) cc_final: 0.8147 (t-100) REVERT: H 250 ASP cc_start: 0.7804 (t70) cc_final: 0.7587 (t0) REVERT: I 8 LYS cc_start: 0.7524 (mtmt) cc_final: 0.7107 (mptt) REVERT: I 108 LYS cc_start: 0.7190 (tmtt) cc_final: 0.6856 (tttm) outliers start: 234 outliers final: 157 residues processed: 1237 average time/residue: 1.3385 time to fit residues: 2842.2172 Evaluate side-chains 1201 residues out of total 6052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1031 time to evaluate : 6.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 341 ILE Chi-restraints excluded: chain R residue 361 ASN Chi-restraints excluded: chain R residue 380 LEU Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 447 LEU Chi-restraints excluded: chain R residue 474 MET Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain i residue 22 VAL Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 93 ASN Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain j residue 69 LEU Chi-restraints excluded: chain j residue 109 ILE Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 232 HIS Chi-restraints excluded: chain k residue 18 THR Chi-restraints excluded: chain k residue 34 SER Chi-restraints excluded: chain k residue 42 SER Chi-restraints excluded: chain k residue 79 SER Chi-restraints excluded: chain 7 residue 17 THR Chi-restraints excluded: chain 7 residue 64 HIS Chi-restraints excluded: chain 7 residue 68 LEU Chi-restraints excluded: chain 7 residue 70 THR Chi-restraints excluded: chain 7 residue 71 VAL Chi-restraints excluded: chain 7 residue 132 VAL Chi-restraints excluded: chain 7 residue 151 VAL Chi-restraints excluded: chain 7 residue 164 ILE Chi-restraints excluded: chain l residue 17 THR Chi-restraints excluded: chain l residue 68 LYS Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain m residue 53 THR Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 38 ILE Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain p residue 18 VAL Chi-restraints excluded: chain p residue 19 LEU Chi-restraints excluded: chain p residue 90 ASN Chi-restraints excluded: chain p residue 126 THR Chi-restraints excluded: chain p residue 138 GLN Chi-restraints excluded: chain p residue 142 ILE Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain p residue 187 ARG Chi-restraints excluded: chain p residue 196 THR Chi-restraints excluded: chain Q residue 44 SER Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain Q residue 176 LYS Chi-restraints excluded: chain 5 residue 16 SER Chi-restraints excluded: chain 5 residue 36 ILE Chi-restraints excluded: chain 5 residue 87 SER Chi-restraints excluded: chain 5 residue 114 VAL Chi-restraints excluded: chain 5 residue 120 ASN Chi-restraints excluded: chain 5 residue 144 SER Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 150 VAL Chi-restraints excluded: chain s residue 21 TYR Chi-restraints excluded: chain s residue 110 LEU Chi-restraints excluded: chain s residue 137 VAL Chi-restraints excluded: chain s residue 174 ASN Chi-restraints excluded: chain s residue 188 GLU Chi-restraints excluded: chain s residue 189 VAL Chi-restraints excluded: chain s residue 196 VAL Chi-restraints excluded: chain s residue 200 SER Chi-restraints excluded: chain T residue 5 ARG Chi-restraints excluded: chain T residue 36 ASN Chi-restraints excluded: chain T residue 59 SER Chi-restraints excluded: chain U residue 8 GLN Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 32 SER Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain V residue 96 ILE Chi-restraints excluded: chain V residue 139 ARG Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain r residue 76 LEU Chi-restraints excluded: chain r residue 188 VAL Chi-restraints excluded: chain x residue 14 SER Chi-restraints excluded: chain x residue 56 ASP Chi-restraints excluded: chain x residue 93 LEU Chi-restraints excluded: chain x residue 124 ASP Chi-restraints excluded: chain x residue 135 VAL Chi-restraints excluded: chain Y residue 9 SER Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Z residue 48 SER Chi-restraints excluded: chain Z residue 59 SER Chi-restraints excluded: chain Z residue 102 LEU Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain a residue 111 LEU Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 68 ILE Chi-restraints excluded: chain b residue 83 THR Chi-restraints excluded: chain b residue 100 THR Chi-restraints excluded: chain b residue 128 GLN Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain c residue 8 THR Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 133 LEU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain d residue 8 THR Chi-restraints excluded: chain d residue 42 ASN Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain e residue 33 SER Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 74 ASN Chi-restraints excluded: chain e residue 76 GLU Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain f residue 106 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain g residue 51 SER Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 229 ASP Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 80 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain L residue 174 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 986 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 582 optimal weight: 0.8980 chunk 746 optimal weight: 10.0000 chunk 578 optimal weight: 8.9990 chunk 860 optimal weight: 10.0000 chunk 571 optimal weight: 3.9990 chunk 1018 optimal weight: 7.9990 chunk 637 optimal weight: 0.9980 chunk 621 optimal weight: 0.8980 chunk 470 optimal weight: 7.9990 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 11 ASN X 170 GLN ** J 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 108 GLN K 41 GLN ** K 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 58 HIS N 28 GLN n 19 GLN n 32 ASN ** n 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 175 ASN ** 5 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 54 ASN T 34 GLN ** U 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 142 GLN V 103 GLN W 87 ASN Z 53 HIS ** c 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 GLN f 15 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 142451 Z= 0.283 Angle : 0.650 12.509 209630 Z= 0.340 Chirality : 0.041 0.373 26316 Planarity : 0.005 0.064 13421 Dihedral : 23.577 179.982 62765 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.86 % Favored : 91.89 % Rotamer: Outliers : 4.57 % Allowed : 16.28 % Favored : 79.16 % 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: -1.55 (0.10), residues: 7086 helix: 0.11 (0.11), residues: 2276 sheet: -1.28 (0.16), residues: 990 loop : -1.70 (0.10), residues: 3820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP O 85 HIS 0.009 0.001 HIS F 163 PHE 0.021 0.001 PHE J 229 TYR 0.028 0.002 TYR p 30 ARG 0.011 0.001 ARG 5 126 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14172 Ramachandran restraints generated. 7086 Oldfield, 0 Emsley, 7086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14172 Ramachandran restraints generated. 7086 Oldfield, 0 Emsley, 7086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1311 residues out of total 6052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 1042 time to evaluate : 6.352 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: R 34 MET cc_start: 0.3777 (tpt) cc_final: 0.3057 (tpt) REVERT: R 240 MET cc_start: 0.7318 (mmm) cc_final: 0.6920 (mtt) REVERT: R 352 LYS cc_start: 0.5565 (tttt) cc_final: 0.5159 (mttm) REVERT: R 381 GLU cc_start: 0.7968 (tp30) cc_final: 0.7494 (tp30) REVERT: R 454 ASN cc_start: 0.4609 (m-40) cc_final: 0.4407 (t0) REVERT: R 483 MET cc_start: 0.1749 (tpp) cc_final: -0.0124 (tpt) REVERT: R 486 MET cc_start: -0.1123 (mmm) cc_final: -0.3344 (mtm) REVERT: X 35 TYR cc_start: 0.7300 (m-80) cc_final: 0.6994 (m-80) REVERT: X 50 HIS cc_start: 0.8009 (m-70) cc_final: 0.7605 (m170) REVERT: X 200 ASN cc_start: 0.8452 (p0) cc_final: 0.8046 (p0) REVERT: i 51 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8823 (pp) REVERT: J 100 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7527 (ttt180) REVERT: 7 86 TYR cc_start: 0.8228 (m-80) cc_final: 0.7586 (m-80) REVERT: 7 102 ASN cc_start: 0.8248 (t0) cc_final: 0.8026 (t0) REVERT: l 17 THR cc_start: 0.7965 (OUTLIER) cc_final: 0.7613 (p) REVERT: M 92 ARG cc_start: 0.8157 (mtm-85) cc_final: 0.7893 (ptp-170) REVERT: M 97 SER cc_start: 0.8405 (OUTLIER) cc_final: 0.7971 (m) REVERT: M 99 THR cc_start: 0.9219 (OUTLIER) cc_final: 0.8987 (m) REVERT: M 132 ASN cc_start: 0.7659 (p0) cc_final: 0.7256 (p0) REVERT: N 23 LYS cc_start: 0.8135 (ttmt) cc_final: 0.7500 (tptp) REVERT: N 85 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7839 (pp) REVERT: n 36 ARG cc_start: 0.7072 (mtp-110) cc_final: 0.6484 (mtp85) REVERT: O 74 ARG cc_start: 0.8144 (ttp80) cc_final: 0.7937 (ttp80) REVERT: O 121 MET cc_start: 0.8238 (tmm) cc_final: 0.7749 (ttt) REVERT: p 127 TYR cc_start: 0.8398 (m-80) cc_final: 0.8177 (m-80) REVERT: p 142 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.7935 (mt) REVERT: p 187 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8122 (ttt90) REVERT: p 192 LYS cc_start: 0.8259 (tttt) cc_final: 0.7784 (ttmt) REVERT: Q 56 ASP cc_start: 0.7195 (m-30) cc_final: 0.6845 (m-30) REVERT: Q 58 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9187 (mp) REVERT: 5 69 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7045 (ptp-170) REVERT: 5 173 ARG cc_start: 0.8791 (mtm110) cc_final: 0.8090 (mtm-85) REVERT: 5 175 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7243 (ptm160) REVERT: S 133 LYS cc_start: 0.9066 (mttp) cc_final: 0.8825 (mttp) REVERT: s 74 TYR cc_start: 0.8583 (t80) cc_final: 0.7653 (t80) REVERT: s 143 ASN cc_start: 0.9004 (m-40) cc_final: 0.8586 (m-40) REVERT: s 184 ARG cc_start: 0.8509 (mmm160) cc_final: 0.8150 (tpt-90) REVERT: T 5 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7450 (mtt90) REVERT: U 141 LYS cc_start: 0.8813 (ttmt) cc_final: 0.8520 (ttpp) REVERT: V 48 ILE cc_start: 0.9205 (mm) cc_final: 0.8983 (mm) REVERT: V 139 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8228 (mtp85) REVERT: W 35 LYS cc_start: 0.9149 (tmtt) cc_final: 0.8890 (tptm) REVERT: Y 26 SER cc_start: 0.8811 (m) cc_final: 0.8254 (t) REVERT: Y 32 GLN cc_start: 0.9220 (tp40) cc_final: 0.8911 (tp40) REVERT: Y 38 SER cc_start: 0.8819 (OUTLIER) cc_final: 0.8467 (p) REVERT: Y 47 ARG cc_start: 0.8086 (mtp-110) cc_final: 0.7696 (mtp-110) REVERT: Y 60 LYS cc_start: 0.8894 (mppt) cc_final: 0.8615 (mtmt) REVERT: b 48 ARG cc_start: 0.8958 (ttm110) cc_final: 0.8360 (mtm180) REVERT: C 19 LYS cc_start: 0.8950 (pttt) cc_final: 0.8684 (pttp) REVERT: d 28 LYS cc_start: 0.7899 (tttp) cc_final: 0.7475 (mtpt) REVERT: E 68 LYS cc_start: 0.8409 (ttmm) cc_final: 0.8082 (ttmm) REVERT: E 69 TYR cc_start: 0.8795 (t80) cc_final: 0.8543 (t80) REVERT: E 118 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7359 (mt-10) REVERT: E 143 GLU cc_start: 0.8523 (pm20) cc_final: 0.8313 (pm20) REVERT: e 61 MET cc_start: 0.8601 (tmm) cc_final: 0.8322 (tmm) REVERT: F 7 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6498 (mt-10) REVERT: F 59 ASP cc_start: 0.7705 (OUTLIER) cc_final: 0.7346 (t0) REVERT: F 112 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.8218 (t0) REVERT: F 348 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.6967 (mtt180) REVERT: F 349 LYS cc_start: 0.8585 (tmtt) cc_final: 0.8332 (tptm) REVERT: f 23 VAL cc_start: 0.8874 (OUTLIER) cc_final: 0.8497 (m) REVERT: f 64 VAL cc_start: 0.8596 (OUTLIER) cc_final: 0.8025 (p) REVERT: f 70 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7624 (mtt90) REVERT: G 34 ILE cc_start: 0.9096 (mt) cc_final: 0.8884 (tp) REVERT: G 357 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7523 (tp30) REVERT: H 17 GLN cc_start: 0.8445 (tt0) cc_final: 0.7988 (tp40) REVERT: H 34 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.7963 (tptp) REVERT: H 69 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.7983 (mt) REVERT: H 79 TYR cc_start: 0.8819 (m-80) cc_final: 0.8552 (m-80) REVERT: H 177 GLU cc_start: 0.7923 (pp20) cc_final: 0.7612 (pp20) REVERT: I 8 LYS cc_start: 0.7547 (mtmt) cc_final: 0.7155 (mptt) REVERT: I 108 LYS cc_start: 0.7228 (tmtt) cc_final: 0.6899 (tttm) REVERT: L 63 MET cc_start: -0.1395 (tmm) cc_final: -0.2743 (mmp) outliers start: 269 outliers final: 196 residues processed: 1209 average time/residue: 1.2512 time to fit residues: 2601.2545 Evaluate side-chains 1235 residues out of total 6052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 1017 time to evaluate : 6.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 341 ILE Chi-restraints excluded: chain R residue 348 VAL Chi-restraints excluded: chain R residue 361 ASN Chi-restraints excluded: chain R residue 373 THR Chi-restraints excluded: chain R residue 380 LEU Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 447 LEU Chi-restraints excluded: chain R residue 474 MET Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 94 ILE Chi-restraints excluded: chain X residue 146 ILE Chi-restraints excluded: chain i residue 22 VAL Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 64 THR Chi-restraints excluded: chain i residue 73 SER Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 93 ASN Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain J residue 172 ASN Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain j residue 69 LEU Chi-restraints excluded: chain j residue 109 ILE Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 232 HIS Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 18 THR Chi-restraints excluded: chain k residue 34 SER Chi-restraints excluded: chain k residue 42 SER Chi-restraints excluded: chain k residue 79 SER Chi-restraints excluded: chain 7 residue 6 THR Chi-restraints excluded: chain 7 residue 17 THR Chi-restraints excluded: chain 7 residue 52 LEU Chi-restraints excluded: chain 7 residue 68 LEU Chi-restraints excluded: chain 7 residue 70 THR Chi-restraints excluded: chain 7 residue 71 VAL Chi-restraints excluded: chain 7 residue 132 VAL Chi-restraints excluded: chain 7 residue 151 VAL Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 17 THR Chi-restraints excluded: chain l residue 68 LYS Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain m residue 51 LEU Chi-restraints excluded: chain m residue 53 THR Chi-restraints excluded: chain m residue 61 LYS Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 38 ILE Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain p residue 18 VAL Chi-restraints excluded: chain p residue 19 LEU Chi-restraints excluded: chain p residue 90 ASN Chi-restraints excluded: chain p residue 126 THR Chi-restraints excluded: chain p residue 138 GLN Chi-restraints excluded: chain p residue 142 ILE Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain p residue 187 ARG Chi-restraints excluded: chain p residue 196 THR Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 44 SER Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 62 THR Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain Q residue 175 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain 5 residue 16 SER Chi-restraints excluded: chain 5 residue 36 ILE Chi-restraints excluded: chain 5 residue 69 ARG Chi-restraints excluded: chain 5 residue 87 SER Chi-restraints excluded: chain 5 residue 114 VAL Chi-restraints excluded: chain 5 residue 120 ASN Chi-restraints excluded: chain 5 residue 144 SER Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 175 ARG Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 150 VAL Chi-restraints excluded: chain s residue 21 TYR Chi-restraints excluded: chain s residue 110 LEU Chi-restraints excluded: chain s residue 137 VAL Chi-restraints excluded: chain s residue 152 ARG Chi-restraints excluded: chain s residue 174 ASN Chi-restraints excluded: chain s residue 189 VAL Chi-restraints excluded: chain s residue 196 VAL Chi-restraints excluded: chain s residue 200 SER Chi-restraints excluded: chain T residue 5 ARG Chi-restraints excluded: chain T residue 59 SER Chi-restraints excluded: chain T residue 143 ILE Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 8 GLN Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 32 SER Chi-restraints excluded: chain U residue 39 SER Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain V residue 96 ILE Chi-restraints excluded: chain V residue 139 ARG Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 47 VAL Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain r residue 76 LEU Chi-restraints excluded: chain r residue 188 VAL Chi-restraints excluded: chain x residue 14 SER Chi-restraints excluded: chain x residue 56 ASP Chi-restraints excluded: chain x residue 93 LEU Chi-restraints excluded: chain x residue 124 ASP Chi-restraints excluded: chain x residue 135 VAL Chi-restraints excluded: chain Y residue 9 SER Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Z residue 48 SER Chi-restraints excluded: chain Z residue 59 SER Chi-restraints excluded: chain Z residue 102 LEU Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain a residue 111 LEU Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 68 ILE Chi-restraints excluded: chain b residue 83 THR Chi-restraints excluded: chain b residue 98 THR Chi-restraints excluded: chain b residue 100 THR Chi-restraints excluded: chain b residue 128 GLN Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain c residue 8 THR Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 75 LEU Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain c residue 133 LEU Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain d residue 8 THR Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain e residue 33 SER Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 76 GLU Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 318 LYS Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 348 ARG Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 70 ARG Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain f residue 97 LEU Chi-restraints excluded: chain f residue 106 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 319 LYS Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain g residue 14 THR Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 51 SER Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain g residue 126 LEU Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 34 LYS Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 229 ASP Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 80 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain L residue 174 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 630 optimal weight: 0.8980 chunk 406 optimal weight: 10.0000 chunk 608 optimal weight: 0.9990 chunk 306 optimal weight: 4.9990 chunk 200 optimal weight: 8.9990 chunk 197 optimal weight: 0.0870 chunk 647 optimal weight: 6.9990 chunk 694 optimal weight: 0.0670 chunk 503 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 800 optimal weight: 8.9990 overall best weight: 0.5696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 106 ASN X 170 GLN ** J 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN K 45 ASN N 12 ASN N 28 GLN N 120 GLN n 32 ASN ** n 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 137 ASN 5 145 HIS s 54 ASN ** U 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 103 GLN W 87 ASN Z 53 HIS f 15 ASN H 90 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 142451 Z= 0.138 Angle : 0.572 13.478 209630 Z= 0.299 Chirality : 0.036 0.330 26316 Planarity : 0.004 0.060 13421 Dihedral : 23.484 179.922 62765 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.65 % Favored : 93.17 % Rotamer: Outliers : 3.28 % Allowed : 17.82 % Favored : 78.90 % 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: -1.25 (0.10), residues: 7086 helix: 0.45 (0.11), residues: 2279 sheet: -1.18 (0.16), residues: 951 loop : -1.55 (0.10), residues: 3856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 203 HIS 0.006 0.001 HIS H 90 PHE 0.016 0.001 PHE J 229 TYR 0.023 0.001 TYR p 30 ARG 0.010 0.000 ARG M 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14172 Ramachandran restraints generated. 7086 Oldfield, 0 Emsley, 7086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14172 Ramachandran restraints generated. 7086 Oldfield, 0 Emsley, 7086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1279 residues out of total 6052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1086 time to evaluate : 6.445 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: R 34 MET cc_start: 0.3911 (tpt) cc_final: 0.3235 (tpt) REVERT: R 352 LYS cc_start: 0.5381 (tttt) cc_final: 0.5046 (mttm) REVERT: R 376 ARG cc_start: 0.6454 (mtp-110) cc_final: 0.5671 (mtp180) REVERT: R 454 ASN cc_start: 0.4599 (m-40) cc_final: 0.4397 (t0) REVERT: X 35 TYR cc_start: 0.7160 (m-80) cc_final: 0.6653 (m-80) REVERT: X 50 HIS cc_start: 0.7831 (m-70) cc_final: 0.7284 (m-70) REVERT: X 200 ASN cc_start: 0.8215 (p0) cc_final: 0.7884 (p0) REVERT: i 51 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8770 (pp) REVERT: J 100 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7480 (ttt180) REVERT: j 60 GLU cc_start: 0.8268 (tt0) cc_final: 0.8043 (tt0) REVERT: k 90 MET cc_start: 0.8110 (mmp) cc_final: 0.7835 (mmm) REVERT: 7 102 ASN cc_start: 0.8182 (t0) cc_final: 0.7967 (t0) REVERT: l 17 THR cc_start: 0.7974 (OUTLIER) cc_final: 0.7566 (p) REVERT: M 92 ARG cc_start: 0.8126 (mtm-85) cc_final: 0.7914 (ptp-170) REVERT: N 23 LYS cc_start: 0.8105 (ttmt) cc_final: 0.7446 (tptp) REVERT: N 85 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7701 (pp) REVERT: N 102 GLN cc_start: 0.8471 (mm-40) cc_final: 0.8249 (mm-40) REVERT: N 186 ARG cc_start: 0.7910 (mpt-90) cc_final: 0.7546 (mpt-90) REVERT: O 77 ARG cc_start: 0.8601 (mtm-85) cc_final: 0.8324 (mtm-85) REVERT: p 94 TYR cc_start: 0.8106 (t80) cc_final: 0.7828 (t80) REVERT: p 127 TYR cc_start: 0.8258 (m-80) cc_final: 0.8025 (m-80) REVERT: p 142 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7833 (mt) REVERT: Q 56 ASP cc_start: 0.7034 (m-30) cc_final: 0.6678 (m-30) REVERT: 5 64 ASN cc_start: 0.8110 (p0) cc_final: 0.7883 (p0) REVERT: 5 173 ARG cc_start: 0.8678 (mtm110) cc_final: 0.8279 (mtm110) REVERT: s 143 ASN cc_start: 0.8962 (m-40) cc_final: 0.8573 (m-40) REVERT: s 184 ARG cc_start: 0.8573 (mmm160) cc_final: 0.8208 (tpt-90) REVERT: s 211 GLU cc_start: 0.8457 (tp30) cc_final: 0.8098 (mm-30) REVERT: T 5 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7784 (mtm110) REVERT: U 141 LYS cc_start: 0.8777 (ttmt) cc_final: 0.8418 (ttpp) REVERT: V 28 SER cc_start: 0.9037 (p) cc_final: 0.8648 (m) REVERT: V 48 ILE cc_start: 0.9162 (mm) cc_final: 0.8952 (mm) REVERT: W 35 LYS cc_start: 0.9121 (tmtt) cc_final: 0.8848 (tptm) REVERT: W 75 TYR cc_start: 0.8686 (t80) cc_final: 0.7351 (t80) REVERT: W 99 LYS cc_start: 0.8970 (ptpt) cc_final: 0.8708 (pttm) REVERT: Y 26 SER cc_start: 0.8688 (m) cc_final: 0.8193 (t) REVERT: Y 32 GLN cc_start: 0.9145 (tp40) cc_final: 0.8833 (tp40) REVERT: Y 38 SER cc_start: 0.8661 (OUTLIER) cc_final: 0.8290 (p) REVERT: Y 47 ARG cc_start: 0.8106 (mtp-110) cc_final: 0.7776 (mtp-110) REVERT: Y 60 LYS cc_start: 0.8860 (mppt) cc_final: 0.8560 (mtmt) REVERT: b 48 ARG cc_start: 0.8899 (ttm110) cc_final: 0.8308 (mtm180) REVERT: C 19 LYS cc_start: 0.8901 (pttt) cc_final: 0.8626 (pttp) REVERT: c 87 ARG cc_start: 0.8849 (ttm170) cc_final: 0.8600 (ttm170) REVERT: d 19 ASN cc_start: 0.8498 (m-40) cc_final: 0.8145 (m-40) REVERT: d 28 LYS cc_start: 0.7653 (tttp) cc_final: 0.7336 (mtpt) REVERT: E 28 LYS cc_start: 0.8767 (mttm) cc_final: 0.8237 (mttt) REVERT: E 68 LYS cc_start: 0.8362 (ttmm) cc_final: 0.7630 (tttp) REVERT: E 69 TYR cc_start: 0.8679 (t80) cc_final: 0.8405 (t80) REVERT: E 118 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7229 (mt-10) REVERT: E 245 LEU cc_start: 0.8767 (tp) cc_final: 0.8548 (tp) REVERT: e 61 MET cc_start: 0.8568 (tmm) cc_final: 0.8318 (tmm) REVERT: F 7 GLU cc_start: 0.6762 (mt-10) cc_final: 0.6110 (mt-10) REVERT: F 14 LEU cc_start: 0.8558 (mt) cc_final: 0.8314 (tp) REVERT: F 59 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7278 (t0) REVERT: F 70 ARG cc_start: 0.7145 (mtp180) cc_final: 0.6674 (mtt180) REVERT: F 112 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7944 (t0) REVERT: F 327 CYS cc_start: 0.7914 (p) cc_final: 0.7297 (m) REVERT: F 348 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.6833 (mtt180) REVERT: F 349 LYS cc_start: 0.8530 (tmtt) cc_final: 0.8291 (tptm) REVERT: f 64 VAL cc_start: 0.8587 (OUTLIER) cc_final: 0.8070 (p) REVERT: g 87 MET cc_start: 0.7422 (mpp) cc_final: 0.7152 (mpp) REVERT: H 14 SER cc_start: 0.8719 (t) cc_final: 0.8341 (p) REVERT: H 17 GLN cc_start: 0.8401 (tt0) cc_final: 0.7851 (tp40) REVERT: H 34 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.7854 (tptp) REVERT: H 69 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8069 (mt) REVERT: H 177 GLU cc_start: 0.7776 (pp20) cc_final: 0.6755 (pp20) REVERT: H 183 TRP cc_start: 0.8750 (t-100) cc_final: 0.8182 (t-100) REVERT: I 8 LYS cc_start: 0.7546 (mtmt) cc_final: 0.7139 (mptt) REVERT: I 108 LYS cc_start: 0.7195 (tmtt) cc_final: 0.6882 (tttm) REVERT: L 63 MET cc_start: -0.1105 (tmm) cc_final: -0.2340 (mmp) outliers start: 193 outliers final: 136 residues processed: 1203 average time/residue: 1.2614 time to fit residues: 2577.0515 Evaluate side-chains 1183 residues out of total 6052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1034 time to evaluate : 6.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 341 ILE Chi-restraints excluded: chain R residue 361 ASN Chi-restraints excluded: chain R residue 373 THR Chi-restraints excluded: chain R residue 380 LEU Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 447 LEU Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 94 ILE Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 73 SER Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain J residue 172 ASN Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 62 LYS Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 232 HIS Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 18 THR Chi-restraints excluded: chain k residue 34 SER Chi-restraints excluded: chain 7 residue 6 THR Chi-restraints excluded: chain 7 residue 17 THR Chi-restraints excluded: chain 7 residue 52 LEU Chi-restraints excluded: chain 7 residue 64 HIS Chi-restraints excluded: chain 7 residue 68 LEU Chi-restraints excluded: chain 7 residue 71 VAL Chi-restraints excluded: chain 7 residue 132 VAL Chi-restraints excluded: chain 7 residue 151 VAL Chi-restraints excluded: chain 7 residue 164 ILE Chi-restraints excluded: chain l residue 17 THR Chi-restraints excluded: chain l residue 68 LYS Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 159 THR Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain O residue 38 ILE Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain p residue 18 VAL Chi-restraints excluded: chain p residue 86 ASN Chi-restraints excluded: chain p residue 126 THR Chi-restraints excluded: chain p residue 138 GLN Chi-restraints excluded: chain p residue 142 ILE Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain Q residue 44 SER Chi-restraints excluded: chain 5 residue 16 SER Chi-restraints excluded: chain 5 residue 36 ILE Chi-restraints excluded: chain 5 residue 114 VAL Chi-restraints excluded: chain 5 residue 129 THR Chi-restraints excluded: chain 5 residue 137 ASN Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain s residue 21 TYR Chi-restraints excluded: chain s residue 137 VAL Chi-restraints excluded: chain s residue 174 ASN Chi-restraints excluded: chain s residue 189 VAL Chi-restraints excluded: chain s residue 196 VAL Chi-restraints excluded: chain T residue 5 ARG Chi-restraints excluded: chain T residue 59 SER Chi-restraints excluded: chain U residue 142 GLN Chi-restraints excluded: chain V residue 96 ILE Chi-restraints excluded: chain V residue 128 LEU Chi-restraints excluded: chain V residue 139 ARG Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 47 VAL Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain r residue 76 LEU Chi-restraints excluded: chain r residue 188 VAL Chi-restraints excluded: chain x residue 14 SER Chi-restraints excluded: chain x residue 56 ASP Chi-restraints excluded: chain x residue 93 LEU Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Z residue 59 SER Chi-restraints excluded: chain Z residue 64 GLU Chi-restraints excluded: chain Z residue 102 LEU Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 111 LEU Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 68 ILE Chi-restraints excluded: chain b residue 83 THR Chi-restraints excluded: chain b residue 98 THR Chi-restraints excluded: chain b residue 100 THR Chi-restraints excluded: chain b residue 128 GLN Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain c residue 8 THR Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 133 LEU Chi-restraints excluded: chain d residue 8 THR Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain e residue 33 SER Chi-restraints excluded: chain e residue 76 GLU Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 198 HIS Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 348 ARG Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain f residue 106 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain g residue 14 THR Chi-restraints excluded: chain g residue 51 SER Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 34 LYS Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 229 ASP Chi-restraints excluded: chain h residue 80 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 85 MET Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain L residue 174 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 926 optimal weight: 50.0000 chunk 976 optimal weight: 10.0000 chunk 890 optimal weight: 8.9990 chunk 949 optimal weight: 6.9990 chunk 975 optimal weight: 10.0000 chunk 571 optimal weight: 0.9980 chunk 413 optimal weight: 0.7980 chunk 745 optimal weight: 8.9990 chunk 291 optimal weight: 4.9990 chunk 857 optimal weight: 7.9990 chunk 897 optimal weight: 10.0000 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 170 GLN ** J 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 99 GLN j 108 GLN K 41 GLN K 45 ASN ** K 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 28 GLN N 120 GLN ** n 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 117 ASN ** 5 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 54 ASN T 34 GLN U 8 GLN ** U 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 103 GLN Z 53 HIS ** c 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 GLN d 42 ASN E 8 GLN F 279 ASN f 15 ASN ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 26 ASN I 4 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 142451 Z= 0.419 Angle : 0.727 12.128 209630 Z= 0.375 Chirality : 0.045 0.394 26316 Planarity : 0.005 0.070 13421 Dihedral : 23.515 179.800 62765 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.11 % Favored : 91.63 % Rotamer: Outliers : 3.72 % Allowed : 17.48 % Favored : 78.80 % 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: -1.42 (0.10), residues: 7086 helix: 0.27 (0.11), residues: 2272 sheet: -1.17 (0.16), residues: 1002 loop : -1.65 (0.10), residues: 3812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F 262 HIS 0.012 0.002 HIS F 163 PHE 0.024 0.002 PHE J 229 TYR 0.036 0.002 TYR p 30 ARG 0.011 0.001 ARG b 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14172 Ramachandran restraints generated. 7086 Oldfield, 0 Emsley, 7086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14172 Ramachandran restraints generated. 7086 Oldfield, 0 Emsley, 7086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1251 residues out of total 6052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1032 time to evaluate : 6.522 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: R 34 MET cc_start: 0.3925 (tpt) cc_final: 0.3233 (tpt) REVERT: R 352 LYS cc_start: 0.5655 (tttt) cc_final: 0.5298 (mttm) REVERT: R 454 ASN cc_start: 0.4683 (m-40) cc_final: 0.4476 (t0) REVERT: X 50 HIS cc_start: 0.7965 (m-70) cc_final: 0.7533 (m170) REVERT: X 129 ILE cc_start: 0.8942 (tt) cc_final: 0.8723 (mt) REVERT: X 200 ASN cc_start: 0.8496 (p0) cc_final: 0.8074 (p0) REVERT: i 51 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8839 (pp) REVERT: J 100 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7593 (ttt180) REVERT: K 155 ASN cc_start: 0.8508 (p0) cc_final: 0.8180 (p0) REVERT: 7 102 ASN cc_start: 0.8235 (t0) cc_final: 0.7993 (t0) REVERT: M 92 ARG cc_start: 0.8152 (mtm-85) cc_final: 0.7900 (ptp-170) REVERT: M 132 ASN cc_start: 0.7660 (p0) cc_final: 0.7329 (p0) REVERT: M 155 THR cc_start: 0.8253 (p) cc_final: 0.7446 (p) REVERT: N 23 LYS cc_start: 0.8125 (ttmt) cc_final: 0.7493 (tptp) REVERT: N 85 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8012 (pp) REVERT: N 102 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8315 (mm-40) REVERT: n 36 ARG cc_start: 0.7097 (mtp-110) cc_final: 0.6465 (mtp85) REVERT: p 127 TYR cc_start: 0.8467 (m-80) cc_final: 0.8245 (m-80) REVERT: p 142 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.7898 (mt) REVERT: p 175 ASN cc_start: 0.7810 (OUTLIER) cc_final: 0.7477 (m110) REVERT: Q 56 ASP cc_start: 0.7132 (m-30) cc_final: 0.6848 (m-30) REVERT: Q 58 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9113 (mp) REVERT: 5 72 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8662 (mt0) REVERT: 5 173 ARG cc_start: 0.8773 (mtm110) cc_final: 0.8063 (mtm-85) REVERT: S 50 LYS cc_start: 0.8594 (mttm) cc_final: 0.8275 (mmtt) REVERT: s 143 ASN cc_start: 0.9084 (m-40) cc_final: 0.8678 (m-40) REVERT: s 184 ARG cc_start: 0.8614 (mmm160) cc_final: 0.8206 (tpt-90) REVERT: s 211 GLU cc_start: 0.8275 (tp30) cc_final: 0.7799 (mm-30) REVERT: T 5 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7455 (mtt90) REVERT: U 110 MET cc_start: 0.9105 (mmt) cc_final: 0.8889 (mmp) REVERT: U 141 LYS cc_start: 0.8854 (ttmt) cc_final: 0.8555 (ttpp) REVERT: V 48 ILE cc_start: 0.9239 (mm) cc_final: 0.8995 (mm) REVERT: V 139 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8248 (mtp85) REVERT: W 35 LYS cc_start: 0.9117 (tmtt) cc_final: 0.8844 (tptm) REVERT: W 75 TYR cc_start: 0.8850 (t80) cc_final: 0.8239 (t80) REVERT: Y 26 SER cc_start: 0.8869 (m) cc_final: 0.8294 (t) REVERT: Y 47 ARG cc_start: 0.8125 (mtp-110) cc_final: 0.7682 (mtp-110) REVERT: Y 60 LYS cc_start: 0.8935 (mppt) cc_final: 0.8656 (mtmt) REVERT: C 19 LYS cc_start: 0.8977 (pttt) cc_final: 0.8703 (pttp) REVERT: d 28 LYS cc_start: 0.7891 (tttp) cc_final: 0.7448 (mtpt) REVERT: E 68 LYS cc_start: 0.8434 (ttmm) cc_final: 0.8015 (ttmm) REVERT: E 69 TYR cc_start: 0.8771 (t80) cc_final: 0.8568 (t80) REVERT: E 118 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7375 (mt-10) REVERT: e 53 LYS cc_start: 0.8508 (tttt) cc_final: 0.8209 (ttmt) REVERT: e 61 MET cc_start: 0.8639 (tmm) cc_final: 0.8345 (tmm) REVERT: F 7 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6507 (mt-10) REVERT: F 112 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.8120 (t0) REVERT: F 348 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7030 (mtt180) REVERT: F 349 LYS cc_start: 0.8618 (tmtt) cc_final: 0.8330 (tptm) REVERT: g 87 MET cc_start: 0.7499 (mpp) cc_final: 0.7253 (mpp) REVERT: H 17 GLN cc_start: 0.8543 (tt0) cc_final: 0.8114 (tp40) REVERT: H 34 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.7965 (tptp) REVERT: H 69 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8025 (mt) REVERT: H 177 GLU cc_start: 0.7852 (pp20) cc_final: 0.7554 (pp20) REVERT: I 8 LYS cc_start: 0.7586 (mtmt) cc_final: 0.7185 (mptt) REVERT: I 108 LYS cc_start: 0.7353 (tmtt) cc_final: 0.7043 (tttm) REVERT: L 63 MET cc_start: -0.0796 (tmm) cc_final: -0.2034 (mmp) outliers start: 219 outliers final: 175 residues processed: 1168 average time/residue: 1.2571 time to fit residues: 2502.2392 Evaluate side-chains 1189 residues out of total 6052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1001 time to evaluate : 6.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 348 VAL Chi-restraints excluded: chain R residue 361 ASN Chi-restraints excluded: chain R residue 373 THR Chi-restraints excluded: chain R residue 380 LEU Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 447 LEU Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 94 ILE Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 64 THR Chi-restraints excluded: chain i residue 68 THR Chi-restraints excluded: chain i residue 73 SER Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain j residue 69 LEU Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 18 THR Chi-restraints excluded: chain k residue 34 SER Chi-restraints excluded: chain k residue 79 SER Chi-restraints excluded: chain 7 residue 6 THR Chi-restraints excluded: chain 7 residue 17 THR Chi-restraints excluded: chain 7 residue 68 LEU Chi-restraints excluded: chain 7 residue 71 VAL Chi-restraints excluded: chain 7 residue 132 VAL Chi-restraints excluded: chain 7 residue 151 VAL Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 17 THR Chi-restraints excluded: chain l residue 68 LYS Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 159 THR Chi-restraints excluded: chain m residue 53 THR Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain n residue 4 GLN Chi-restraints excluded: chain O residue 38 ILE Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain p residue 66 VAL Chi-restraints excluded: chain p residue 89 VAL Chi-restraints excluded: chain p residue 90 ASN Chi-restraints excluded: chain p residue 101 THR Chi-restraints excluded: chain p residue 126 THR Chi-restraints excluded: chain p residue 138 GLN Chi-restraints excluded: chain p residue 142 ILE Chi-restraints excluded: chain p residue 175 ASN Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 44 SER Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain Q residue 175 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain 5 residue 16 SER Chi-restraints excluded: chain 5 residue 36 ILE Chi-restraints excluded: chain 5 residue 72 GLN 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 5 residue 144 SER Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 150 VAL Chi-restraints excluded: chain s residue 21 TYR Chi-restraints excluded: chain s residue 174 ASN Chi-restraints excluded: chain s residue 196 VAL Chi-restraints excluded: chain s residue 200 SER Chi-restraints excluded: chain T residue 5 ARG Chi-restraints excluded: chain T residue 59 SER Chi-restraints excluded: chain T residue 143 ILE Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 39 SER Chi-restraints excluded: chain U residue 74 ASN Chi-restraints excluded: chain U residue 142 GLN Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain V residue 139 ARG Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 47 VAL Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain r residue 76 LEU Chi-restraints excluded: chain r residue 188 VAL Chi-restraints excluded: chain x residue 14 SER Chi-restraints excluded: chain x residue 56 ASP Chi-restraints excluded: chain x residue 93 LEU Chi-restraints excluded: chain x residue 131 SER Chi-restraints excluded: chain Y residue 9 SER Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Z residue 48 SER Chi-restraints excluded: chain Z residue 59 SER Chi-restraints excluded: chain Z residue 102 LEU Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 97 ILE Chi-restraints excluded: chain a residue 111 LEU Chi-restraints excluded: chain b residue 26 VAL Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 68 ILE Chi-restraints excluded: chain b residue 83 THR Chi-restraints excluded: chain b residue 98 THR Chi-restraints excluded: chain b residue 100 THR Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain c residue 8 THR Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain d residue 8 THR Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain d residue 42 ASN Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 76 GLU Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 198 HIS Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 318 LYS Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 348 ARG Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain f residue 106 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 51 SER Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 34 LYS Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 229 ASP Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 80 VAL Chi-restraints excluded: chain I residue 4 GLN Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 162 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 946 optimal weight: 7.9990 chunk 623 optimal weight: 5.9990 chunk 1003 optimal weight: 10.0000 chunk 612 optimal weight: 0.8980 chunk 476 optimal weight: 4.9990 chunk 697 optimal weight: 20.0000 chunk 1053 optimal weight: 10.0000 chunk 969 optimal weight: 8.9990 chunk 838 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 647 optimal weight: 2.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 106 ASN X 170 GLN ** J 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 108 GLN K 41 GLN K 45 ASN ** K 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 150 ASN N 120 GLN n 32 ASN ** n 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 54 ASN T 34 GLN ** U 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 103 GLN W 87 ASN Z 53 HIS ** c 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 42 ASN F 279 ASN F 319 ASN ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 142451 Z= 0.400 Angle : 0.717 12.318 209630 Z= 0.371 Chirality : 0.045 0.410 26316 Planarity : 0.005 0.066 13421 Dihedral : 23.548 179.724 62765 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.20 % Favored : 91.59 % Rotamer: Outliers : 3.65 % Allowed : 17.58 % Favored : 78.77 % 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: -1.48 (0.10), residues: 7086 helix: 0.21 (0.11), residues: 2275 sheet: -1.22 (0.16), residues: 1000 loop : -1.69 (0.10), residues: 3811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 262 HIS 0.016 0.002 HIS d 43 PHE 0.026 0.002 PHE J 229 TYR 0.034 0.002 TYR p 30 ARG 0.012 0.001 ARG b 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14172 Ramachandran restraints generated. 7086 Oldfield, 0 Emsley, 7086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14172 Ramachandran restraints generated. 7086 Oldfield, 0 Emsley, 7086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1218 residues out of total 6052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 1003 time to evaluate : 6.478 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: R 34 MET cc_start: 0.3936 (tpt) cc_final: 0.3217 (tpt) REVERT: R 313 ARG cc_start: 0.4101 (ptm160) cc_final: 0.3552 (mtp180) REVERT: R 352 LYS cc_start: 0.5640 (tttt) cc_final: 0.5291 (mttm) REVERT: R 454 ASN cc_start: 0.4594 (m-40) cc_final: 0.4370 (t0) REVERT: X 35 TYR cc_start: 0.7443 (m-80) cc_final: 0.7087 (m-80) REVERT: X 200 ASN cc_start: 0.8513 (p0) cc_final: 0.8125 (p0) REVERT: i 51 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8835 (pp) REVERT: J 100 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7643 (ttt180) REVERT: K 155 ASN cc_start: 0.8488 (p0) cc_final: 0.8143 (p0) REVERT: 7 102 ASN cc_start: 0.8260 (t0) cc_final: 0.8008 (t0) REVERT: M 132 ASN cc_start: 0.7662 (p0) cc_final: 0.7346 (p0) REVERT: N 23 LYS cc_start: 0.8133 (ttmt) cc_final: 0.7485 (tptp) REVERT: N 102 GLN cc_start: 0.8485 (mm-40) cc_final: 0.8276 (mm-40) REVERT: N 153 ASP cc_start: 0.7198 (t0) cc_final: 0.6925 (t0) REVERT: n 36 ARG cc_start: 0.7108 (mtp-110) cc_final: 0.6479 (mtp85) REVERT: p 127 TYR cc_start: 0.8468 (m-80) cc_final: 0.8252 (m-80) REVERT: p 142 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7921 (mt) REVERT: p 175 ASN cc_start: 0.7818 (OUTLIER) cc_final: 0.7505 (m110) REVERT: p 187 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7903 (ttt90) REVERT: Q 56 ASP cc_start: 0.7152 (m-30) cc_final: 0.6858 (m-30) REVERT: Q 58 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9183 (mp) REVERT: 5 72 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8669 (mt0) REVERT: 5 173 ARG cc_start: 0.8747 (mtm110) cc_final: 0.8016 (mtm-85) REVERT: S 50 LYS cc_start: 0.8583 (mttm) cc_final: 0.8271 (mmtt) REVERT: s 143 ASN cc_start: 0.9088 (m-40) cc_final: 0.8712 (m-40) REVERT: s 202 LYS cc_start: 0.7349 (mttt) cc_final: 0.7094 (ptmt) REVERT: s 211 GLU cc_start: 0.8336 (tp30) cc_final: 0.7880 (mm-30) REVERT: T 5 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7452 (mtt90) REVERT: U 110 MET cc_start: 0.9065 (mmt) cc_final: 0.8855 (mmp) REVERT: V 48 ILE cc_start: 0.9218 (mm) cc_final: 0.9005 (mm) REVERT: V 139 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8263 (mtp85) REVERT: W 75 TYR cc_start: 0.8876 (t80) cc_final: 0.8289 (t80) REVERT: Y 26 SER cc_start: 0.8837 (m) cc_final: 0.8267 (t) REVERT: Y 32 GLN cc_start: 0.9207 (tp40) cc_final: 0.8864 (tp40) REVERT: Y 38 SER cc_start: 0.8790 (OUTLIER) cc_final: 0.8366 (p) REVERT: Y 60 LYS cc_start: 0.8892 (mppt) cc_final: 0.8613 (mtmt) REVERT: Z 131 ASP cc_start: 0.8348 (p0) cc_final: 0.8009 (p0) REVERT: b 48 ARG cc_start: 0.8969 (ttm110) cc_final: 0.8559 (mtm110) REVERT: C 19 LYS cc_start: 0.8966 (pttt) cc_final: 0.8711 (pttp) REVERT: d 28 LYS cc_start: 0.7860 (tttp) cc_final: 0.7423 (mtpt) REVERT: E 68 LYS cc_start: 0.8447 (ttmm) cc_final: 0.8023 (ttmm) REVERT: E 69 TYR cc_start: 0.8784 (t80) cc_final: 0.8582 (t80) REVERT: E 118 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7408 (mt-10) REVERT: e 61 MET cc_start: 0.8657 (tmm) cc_final: 0.8360 (tmm) REVERT: F 7 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6540 (mt-10) REVERT: F 112 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.8151 (t0) REVERT: F 348 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.7102 (mtt180) REVERT: F 349 LYS cc_start: 0.8602 (tmtt) cc_final: 0.8301 (tptm) REVERT: f 70 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7671 (mtt90) REVERT: g 87 MET cc_start: 0.7484 (mpp) cc_final: 0.7246 (mpp) REVERT: H 17 GLN cc_start: 0.8508 (tt0) cc_final: 0.8167 (tt0) REVERT: H 34 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.7966 (tptp) REVERT: H 69 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8003 (mt) REVERT: H 79 TYR cc_start: 0.8831 (m-80) cc_final: 0.8526 (m-80) REVERT: H 177 GLU cc_start: 0.7852 (pp20) cc_final: 0.7552 (pp20) REVERT: I 8 LYS cc_start: 0.7572 (mtmt) cc_final: 0.7205 (mptt) REVERT: I 108 LYS cc_start: 0.7460 (tmtt) cc_final: 0.7133 (tttm) REVERT: L 63 MET cc_start: -0.0990 (tmm) cc_final: -0.2061 (mmp) outliers start: 215 outliers final: 183 residues processed: 1139 average time/residue: 1.2381 time to fit residues: 2402.0598 Evaluate side-chains 1183 residues out of total 6052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 985 time to evaluate : 6.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 348 VAL Chi-restraints excluded: chain R residue 361 ASN Chi-restraints excluded: chain R residue 373 THR Chi-restraints excluded: chain R residue 380 LEU Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain R residue 447 LEU Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 94 ILE Chi-restraints excluded: chain i residue 51 LEU Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 64 THR Chi-restraints excluded: chain i residue 73 SER Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 93 ASN Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain j residue 69 LEU Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 232 HIS Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 18 THR Chi-restraints excluded: chain k residue 34 SER Chi-restraints excluded: chain k residue 79 SER Chi-restraints excluded: chain 7 residue 6 THR Chi-restraints excluded: chain 7 residue 17 THR Chi-restraints excluded: chain 7 residue 52 LEU Chi-restraints excluded: chain 7 residue 68 LEU Chi-restraints excluded: chain 7 residue 71 VAL Chi-restraints excluded: chain 7 residue 132 VAL Chi-restraints excluded: chain 7 residue 151 VAL Chi-restraints excluded: chain 7 residue 164 ILE Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 17 THR Chi-restraints excluded: chain l residue 68 LYS Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 159 THR Chi-restraints excluded: chain m residue 53 THR Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain n residue 4 GLN Chi-restraints excluded: chain O residue 38 ILE Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain p residue 18 VAL Chi-restraints excluded: chain p residue 89 VAL Chi-restraints excluded: chain p residue 90 ASN Chi-restraints excluded: chain p residue 101 THR Chi-restraints excluded: chain p residue 126 THR Chi-restraints excluded: chain p residue 138 GLN Chi-restraints excluded: chain p residue 142 ILE Chi-restraints excluded: chain p residue 175 ASN Chi-restraints excluded: chain p residue 183 THR Chi-restraints excluded: chain p residue 187 ARG Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 44 SER Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 62 THR Chi-restraints excluded: chain Q residue 118 VAL Chi-restraints excluded: chain Q residue 175 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain 5 residue 16 SER Chi-restraints excluded: chain 5 residue 36 ILE Chi-restraints excluded: chain 5 residue 72 GLN Chi-restraints excluded: chain 5 residue 114 VAL Chi-restraints excluded: chain 5 residue 119 VAL Chi-restraints excluded: chain 5 residue 144 SER Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 175 ARG Chi-restraints excluded: chain S residue 22 ASP Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 150 VAL Chi-restraints excluded: chain s residue 21 TYR Chi-restraints excluded: chain s residue 110 LEU Chi-restraints excluded: chain s residue 174 ASN Chi-restraints excluded: chain s residue 196 VAL Chi-restraints excluded: chain s residue 200 SER Chi-restraints excluded: chain T residue 5 ARG Chi-restraints excluded: chain T residue 59 SER Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 39 SER Chi-restraints excluded: chain U residue 74 ASN Chi-restraints excluded: chain U residue 142 GLN Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 139 ARG Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 47 VAL Chi-restraints excluded: chain W residue 55 THR Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain r residue 30 VAL Chi-restraints excluded: chain r residue 76 LEU Chi-restraints excluded: chain r residue 188 VAL Chi-restraints excluded: chain x residue 14 SER Chi-restraints excluded: chain x residue 56 ASP Chi-restraints excluded: chain x residue 93 LEU Chi-restraints excluded: chain x residue 131 SER Chi-restraints excluded: chain Y residue 9 SER Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Z residue 48 SER Chi-restraints excluded: chain Z residue 59 SER Chi-restraints excluded: chain Z residue 102 LEU Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 97 ILE Chi-restraints excluded: chain a residue 111 LEU Chi-restraints excluded: chain b residue 26 VAL Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 68 ILE Chi-restraints excluded: chain b residue 83 THR Chi-restraints excluded: chain b residue 98 THR Chi-restraints excluded: chain b residue 100 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain c residue 8 THR Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain d residue 8 THR Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 76 GLU Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 198 HIS Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 318 LYS Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 348 ARG Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 70 ARG Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain f residue 106 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 51 SER Chi-restraints excluded: chain g residue 59 SER Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 108 ILE Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 34 LYS Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 229 ASP Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain H residue 275 THR Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 80 VAL Chi-restraints excluded: chain I residue 4 GLN Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 162 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 514 optimal weight: 1.9990 chunk 666 optimal weight: 0.8980 chunk 893 optimal weight: 10.0000 chunk 256 optimal weight: 0.7980 chunk 773 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 233 optimal weight: 2.9990 chunk 839 optimal weight: 5.9990 chunk 351 optimal weight: 3.9990 chunk 862 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 106 ASN X 170 GLN ** J 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 34 GLN ** j 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 108 GLN K 41 GLN K 45 ASN ** K 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 28 GLN n 32 ASN ** n 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 117 ASN ** 5 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 54 ASN Z 53 HIS ** c 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 GLN ** G 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 GLN L 158 GLN L 200 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.160328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.109863 restraints weight = 176943.321| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.32 r_work: 0.2915 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 142451 Z= 0.184 Angle : 0.599 12.664 209630 Z= 0.314 Chirality : 0.038 0.369 26316 Planarity : 0.004 0.058 13421 Dihedral : 23.496 179.917 62763 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.37 % Favored : 92.45 % Rotamer: Outliers : 3.05 % Allowed : 18.36 % Favored : 78.58 % 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: -1.22 (0.10), residues: 7086 helix: 0.50 (0.11), residues: 2273 sheet: -1.09 (0.16), residues: 959 loop : -1.57 (0.10), residues: 3854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 262 HIS 0.009 0.001 HIS H 90 PHE 0.023 0.001 PHE M 163 TYR 0.031 0.001 TYR p 30 ARG 0.012 0.001 ARG b 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 39618.18 seconds wall clock time: 689 minutes 32.38 seconds (41372.38 seconds total)