Starting phenix.real_space_refine on Fri Mar 1 05:05:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfr_34725/03_2024/8hfr_34725.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfr_34725/03_2024/8hfr_34725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfr_34725/03_2024/8hfr_34725.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfr_34725/03_2024/8hfr_34725.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfr_34725/03_2024/8hfr_34725.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfr_34725/03_2024/8hfr_34725.pdb" } resolution = 2.64 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= 0.002 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 203 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3551 5.49 5 Mg 237 5.21 5 S 147 5.16 5 C 81640 2.51 5 N 28277 2.21 5 O 38522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "g2 GLU 87": "OE1" <-> "OE2" Residue "b3 ARG 40": "NH1" <-> "NH2" Residue "V5 PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "rA ARG 396": "NH1" <-> "NH2" Residue "rA GLU 459": "OE1" <-> "OE2" Residue "rA GLU 460": "OE1" <-> "OE2" Residue "rA PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CD TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CD GLU 180": "OE1" <-> "OE2" Residue "yE TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "eH GLU 30": "OE1" <-> "OE2" Residue "xI GLU 211": "OE1" <-> "OE2" Residue "DO GLU 54": "OE1" <-> "OE2" Residue "DO TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "vV GLU 317": "OE1" <-> "OE2" Residue "SZ GLU 34": "OE1" <-> "OE2" Residue "Ib TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Xc TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "xd GLU 22": "OE1" <-> "OE2" Residue "xd GLU 31": "OE1" <-> "OE2" Residue "Wg TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "li ARG 36": "NH1" <-> "NH2" Residue "Hj GLU 228": "OE1" <-> "OE2" Residue "Tl GLU 86": "OE1" <-> "OE2" Residue "sm GLU 126": "OE1" <-> "OE2" Residue "No TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Zq PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "kr GLU 4": "OE1" <-> "OE2" Residue "Gu GLU 54": "OE1" <-> "OE2" Residue "Gu GLU 59": "OE1" <-> "OE2" Residue "Gu PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ox GLU 29": "OE1" <-> "OE2" Residue "ox GLU 79": "OE1" <-> "OE2" Residue "Jy GLU 15": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 152374 Number of models: 1 Model: "" Number of chains: 69 Chain: "h1" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 961 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 114} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "g2" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 109} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Chain: "b3" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 422 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 51} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "B4" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1901 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 239} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "V5" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 128} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "O6" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1548 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 188} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "f7" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 847 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F8" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1241 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 165} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 11} Unresolved non-hydrogen planarities: 82 Chain: "v9" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 748 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 81 Chain: "rA" Number of atoms: 5044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5044 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 24, 'TRANS': 622} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 12, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 108 Chain: "tB" Number of atoms: 1246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1246 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 148} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "cC" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 689 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 1, 'TRANS': 95} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "CD" Number of atoms: 2968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2968 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 371} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 13, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 87 Chain: "yE" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1786 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 233} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 41 Chain: "UF" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 864 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 3, 'TRANS': 111} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 54 Chain: "dG" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 862 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 105} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "eH" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "xI" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 524 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain breaks: 1 Chain: "qJ" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1022 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain breaks: 3 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 28 Chain: "DK" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 816 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PTRANS': 9, 'TRANS': 155} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 527 Unresolved non-hydrogen angles: 679 Unresolved non-hydrogen dihedrals: 438 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 12, 'TYR:plan': 4, 'ASN:plan1': 15, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 11, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 298 Chain: "LL" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1492 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 188} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "KM" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 796 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'PTRANS': 9, 'TRANS': 149} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 421 Unresolved non-hydrogen angles: 527 Unresolved non-hydrogen dihedrals: 338 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 186 Chain: "AN" Number of atoms: 1843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 1843 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 346} Link IDs: {'PTRANS': 16, 'TRANS': 354} Chain breaks: 1 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1207 Unresolved non-hydrogen angles: 1538 Unresolved non-hydrogen dihedrals: 1004 Unresolved non-hydrogen chiralities: 108 Planarities with less than four sites: {'GLN:plan1': 22, 'HIS:plan': 5, 'TYR:plan': 12, 'ASN:plan1': 31, 'TRP:plan': 4, 'ASP:plan': 17, 'PHE:plan': 19, 'GLU:plan': 18, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 638 Chain: "DO" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2675 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "RP" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1374 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 2, 'TRANS': 185} Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ARG:plan': 9, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 107 Chain: "MQ" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1042 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 131} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "FR" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 816 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PTRANS': 9, 'TRANS': 155} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 527 Unresolved non-hydrogen angles: 679 Unresolved non-hydrogen dihedrals: 438 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 12, 'TYR:plan': 4, 'ASN:plan1': 15, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 11, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 298 Chain: "mS" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 711 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "pT" Number of atoms: 4285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4285 Classifications: {'peptide': 580} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 552} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 106 Chain: "YU" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 989 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "vV" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1875 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 8, 'TRANS': 236} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 48 Chain: "CW" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 2120 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 391} Link IDs: {'PTRANS': 17, 'TRANS': 409} Chain breaks: 3 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1375 Unresolved non-hydrogen angles: 1756 Unresolved non-hydrogen dihedrals: 1142 Unresolved non-hydrogen chiralities: 124 Planarities with less than four sites: {'GLN:plan1': 27, 'ASP:plan': 19, 'TYR:plan': 11, 'ASN:plan1': 36, 'TRP:plan': 6, 'HIS:plan': 6, 'PHE:plan': 22, 'GLU:plan': 21, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 740 Chain: "EX" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 1725 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 324} Link IDs: {'PTRANS': 16, 'TRANS': 330} Chain breaks: 2 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1120 Unresolved non-hydrogen angles: 1429 Unresolved non-hydrogen dihedrals: 928 Unresolved non-hydrogen chiralities: 106 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 4, 'TYR:plan': 9, 'ASN:plan1': 25, 'TRP:plan': 4, 'ASP:plan': 17, 'PHE:plan': 19, 'GLU:plan': 18, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 580 Chain: "nY" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 673 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 90} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "SZ" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1420 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 163} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "ia" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 718 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 92} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "Ib" Number of atoms: 1446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1446 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 52 Chain: "Xc" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 963 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 117} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "xd" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 601 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 71} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "1e" Number of atoms: 69952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3274, 69952 Classifications: {'RNA': 3274} Modifications used: {'rna2p_pur': 336, 'rna2p_pyr': 246, 'rna3p_pur': 1472, 'rna3p_pyr': 1220} Link IDs: {'rna2p': 582, 'rna3p': 2691} Chain breaks: 3 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {' C%rna3p_pyr:plan': 2, ' A%rna3p_pur:plan2': 3, ' A%rna2p_pur:plan': 1, ' U%rna3p_pyr:plan': 2, ' A%rna2p_pur:plan2': 1, ' C%rna3p_pyr:plan2': 2, ' U%rna2p_pyr:plan': 1, ' A%rna3p_pur:plan': 3} Unresolved non-hydrogen planarities: 90 Chain: "2f" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2579 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 57, 'rna3p_pyr': 51} Link IDs: {'rna2p': 12, 'rna3p': 108} Chain: "Wg" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1190 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 201} Link IDs: {'PTRANS': 9, 'TRANS': 223} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 719 Unresolved non-hydrogen angles: 915 Unresolved non-hydrogen dihedrals: 594 Unresolved non-hydrogen chiralities: 69 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 10, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 7, 'GLU:plan': 21, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 371 Chain: "jh" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 677 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "li" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 433 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Hj" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1660 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 12, 'TRANS': 217} Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 9, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 74 Chain: "Qk" Number of atoms: 1434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1434 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 175} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Tl" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1256 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 153} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "sm" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1036 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 5, 'TRANS': 144} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 6, 'GLU:plan': 3, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 137 Chain: "3n" Number of atoms: 3313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3313 Classifications: {'RNA': 156} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 12, 'rna3p_pur': 61, 'rna3p_pyr': 66} Link IDs: {'rna2p': 29, 'rna3p': 126} Chain: "No" 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: "zp" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 668 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'TRANS': 87} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 16 Chain: "Zq" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1052 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 128} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 16 Chain: "kr" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 573 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 73} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "As" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1089 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 193} Link IDs: {'PTRANS': 9, 'TRANS': 207} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 657 Unresolved non-hydrogen angles: 821 Unresolved non-hydrogen dihedrals: 548 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 12, 'TYR:plan': 4, 'ASN:plan1': 14, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 10, 'GLU:plan': 9, 'TYR%COO:plan': 1, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 305 Chain: "Bt" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 816 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PTRANS': 9, 'TRANS': 155} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 527 Unresolved non-hydrogen angles: 679 Unresolved non-hydrogen dihedrals: 438 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 12, 'TYR:plan': 4, 'ASN:plan1': 15, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 11, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 298 Chain: "Gu" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1784 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 212} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Pv" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1383 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 176} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "aw" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1170 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 140} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "ox" Number of atoms: 1147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1147 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 136} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Jy" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1270 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 161} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "Ez" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 1973 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 10, 'TRANS': 279} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'ASP:plan': 13, 'PHE:plan': 4, 'GLU:plan': 26, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 230 Chain: "g2" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "CD" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "1e" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 223 Unusual residues: {' MG': 223} Classifications: {'undetermined': 223} Link IDs: {None: 222} Chain: "2f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "3n" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "No" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "zp" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 197 residue: pdb=" N VALO6 3 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VALO6 3 " occ=0.50 residue: pdb=" N GLUO6 4 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLUO6 4 " occ=0.50 residue: pdb=" N PROO6 5 " occ=0.50 ... (5 atoms not shown) pdb=" CD PROO6 5 " occ=0.50 residue: pdb=" N VALO6 6 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VALO6 6 " occ=0.50 residue: pdb=" N VALO6 7 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VALO6 7 " occ=0.50 residue: pdb=" N VALO6 8 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VALO6 8 " occ=0.50 residue: pdb=" N ILEO6 9 " occ=0.50 ... (6 atoms not shown) pdb=" CD1 ILEO6 9 " occ=0.50 residue: pdb=" N ASPO6 10 " occ=0.50 ... (6 atoms not shown) pdb=" OD2 ASPO6 10 " occ=0.50 residue: pdb=" N GLYO6 11 " occ=0.50 ... (2 atoms not shown) pdb=" O GLYO6 11 " occ=0.50 residue: pdb=" N LYSO6 12 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYSO6 12 " occ=0.50 residue: pdb=" N GLYO6 13 " occ=0.50 ... (2 atoms not shown) pdb=" O GLYO6 13 " occ=0.50 residue: pdb=" N HISO6 14 " occ=0.50 ... (8 atoms not shown) pdb=" NE2 HISO6 14 " occ=0.50 ... (remaining 185 not shown) Time building chain proxies: 56.90, per 1000 atoms: 0.37 Number of scatterers: 152374 At special positions: 0 Unit cell: (311.956, 247.828, 289.912, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 147 16.00 P 3551 15.00 Mg 237 11.99 O 38522 8.00 N 28277 7.00 C 81640 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYSg2 44 " - pdb=" SG CYSg2 47 " distance=2.05 Simple disulfide: pdb=" SG CYSg2 44 " - pdb=" SG CYSg2 81 " distance=2.05 Simple disulfide: pdb=" SG CYSg2 47 " - pdb=" SG CYSg2 81 " distance=2.01 Simple disulfide: pdb=" SG CYSg2 47 " - pdb=" SG CYSg2 84 " distance=2.05 Simple disulfide: pdb=" SG CYStB 6 " - pdb=" SG CYStB 9 " distance=2.07 Simple disulfide: pdb=" SG CYStB 6 " - pdb=" SG CYStB 32 " distance=2.00 Simple disulfide: pdb=" SG CYStB 9 " - pdb=" SG CYStB 32 " distance=2.02 Simple disulfide: pdb=" SG CYStB 9 " - pdb=" SG CYStB 36 " distance=2.11 Simple disulfide: pdb=" SG CYStB 32 " - pdb=" SG CYStB 36 " distance=2.01 Simple disulfide: pdb=" SG CYSnY 39 " - pdb=" SG CYSnY 57 " distance=2.04 Simple disulfide: pdb=" SG CYSnY 42 " - pdb=" SG CYSnY 59 " distance=2.03 Simple disulfide: pdb=" SG CYSjh 22 " - pdb=" SG CYSjh 37 " distance=2.06 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: 51.79 Conformation dependent library (CDL) restraints added in 12.4 seconds 21256 Ramachandran restraints generated. 10628 Oldfield, 0 Emsley, 10628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 20274 Finding SS restraints... Secondary structure from input PDB file: 370 helices and 104 sheets defined 39.6% alpha, 14.0% beta 1078 base pairs and 1867 stacking pairs defined. Time for finding SS restraints: 47.81 Creating SS restraints... Processing helix chain 'h1' and resid 5 through 10 Processing helix chain 'h1' and resid 13 through 36 Processing helix chain 'h1' and resid 43 through 70 Processing helix chain 'h1' and resid 85 through 91 Processing helix chain 'h1' and resid 93 through 98 Processing helix chain 'h1' and resid 101 through 111 Processing helix chain 'g2' and resid 66 through 70 Processing helix chain 'g2' and resid 82 through 114 Processing helix chain 'b3' and resid 11 through 19 removed outlier: 4.457A pdb=" N ASNb3 19 " --> pdb=" O LYSb3 15 " (cutoff:3.500A) Processing helix chain 'b3' and resid 36 through 58 Processing helix chain 'B4' and resid 5 through 10 Processing helix chain 'B4' and resid 33 through 39 Processing helix chain 'B4' and resid 105 through 107 No H-bonds generated for 'chain 'B4' and resid 105 through 107' Processing helix chain 'B4' and resid 173 through 177 removed outlier: 3.537A pdb=" N ASPB4 176 " --> pdb=" O GLYB4 173 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYSB4 177 " --> pdb=" O ARGB4 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'B4' and resid 173 through 177' Processing helix chain 'B4' and resid 181 through 190 Processing helix chain 'B4' and resid 200 through 204 Processing helix chain 'V5' and resid 119 through 126 Processing helix chain 'V5' and resid 126 through 131 Processing helix chain 'O6' and resid 15 through 30 removed outlier: 3.757A pdb=" N VALO6 22 " --> pdb=" O ARGO6 18 " (cutoff:3.500A) Processing helix chain 'O6' and resid 37 through 40 Processing helix chain 'O6' and resid 46 through 59 Processing helix chain 'O6' and resid 75 through 88 Processing helix chain 'O6' and resid 92 through 100 Processing helix chain 'O6' and resid 111 through 115 removed outlier: 3.920A pdb=" N LYSO6 114 " --> pdb=" O PROO6 111 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYSO6 115 " --> pdb=" O TYRO6 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'O6' and resid 111 through 115' Processing helix chain 'O6' and resid 120 through 123 Processing helix chain 'O6' and resid 124 through 129 Processing helix chain 'O6' and resid 138 through 146 Processing helix chain 'O6' and resid 149 through 184 removed outlier: 3.667A pdb=" N VALO6 153 " --> pdb=" O TYRO6 149 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THRO6 184 " --> pdb=" O SERO6 180 " (cutoff:3.500A) Processing helix chain 'O6' and resid 188 through 198 Processing helix chain 'f7' and resid 37 through 42 Processing helix chain 'f7' and resid 43 through 45 No H-bonds generated for 'chain 'f7' and resid 43 through 45' Processing helix chain 'F8' and resid 110 through 114 removed outlier: 4.075A pdb=" N LYSF8 113 " --> pdb=" O LYSF8 110 " (cutoff:3.500A) Processing helix chain 'F8' and resid 131 through 150 removed outlier: 4.041A pdb=" N GLUF8 148 " --> pdb=" O ALAF8 144 " (cutoff:3.500A) Processing helix chain 'F8' and resid 154 through 161 Processing helix chain 'F8' and resid 170 through 174 removed outlier: 3.524A pdb=" N LEUF8 174 " --> pdb=" O PROF8 171 " (cutoff:3.500A) Processing helix chain 'v9' and resid 160 through 175 Processing helix chain 'v9' and resid 380 through 386 Processing helix chain 'v9' and resid 398 through 406 Processing helix chain 'v9' and resid 408 through 416 removed outlier: 4.281A pdb=" N LEUv9 412 " --> pdb=" O GLNv9 408 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLUv9 413 " --> pdb=" O VALv9 409 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ARGv9 414 " --> pdb=" O LYSv9 410 " (cutoff:3.500A) Processing helix chain 'v9' and resid 423 through 436 Processing helix chain 'v9' and resid 445 through 460 removed outlier: 3.840A pdb=" N VALv9 449 " --> pdb=" O ASPv9 445 " (cutoff:3.500A) Processing helix chain 'rA' and resid 13 through 29 Processing helix chain 'rA' and resid 38 through 68 removed outlier: 3.837A pdb=" N ILErA 64 " --> pdb=" O LYSrA 60 " (cutoff:3.500A) Processing helix chain 'rA' and resid 75 through 86 Processing helix chain 'rA' and resid 87 through 117 Processing helix chain 'rA' and resid 121 through 143 Processing helix chain 'rA' and resid 143 through 158 removed outlier: 3.827A pdb=" N LEUrA 147 " --> pdb=" O LEUrA 143 " (cutoff:3.500A) Processing helix chain 'rA' and resid 179 through 188 Processing helix chain 'rA' and resid 233 through 246 removed outlier: 3.721A pdb=" N SERrA 239 " --> pdb=" O ILErA 235 " (cutoff:3.500A) Processing helix chain 'rA' and resid 263 through 274 Processing helix chain 'rA' and resid 275 through 278 Processing helix chain 'rA' and resid 299 through 309 removed outlier: 3.918A pdb=" N GLNrA 304 " --> pdb=" O GLUrA 300 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LEUrA 305 " --> pdb=" O GLUrA 301 " (cutoff:3.500A) Processing helix chain 'rA' and resid 328 through 345 Processing helix chain 'rA' and resid 357 through 362 removed outlier: 3.619A pdb=" N HISrA 362 " --> pdb=" O LEUrA 358 " (cutoff:3.500A) Processing helix chain 'rA' and resid 379 through 384 removed outlier: 3.836A pdb=" N LYSrA 383 " --> pdb=" O PROrA 379 " (cutoff:3.500A) Processing helix chain 'rA' and resid 399 through 406 Processing helix chain 'rA' and resid 415 through 420 removed outlier: 3.657A pdb=" N ASPrA 418 " --> pdb=" O ASNrA 415 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYSrA 419 " --> pdb=" O LEUrA 416 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYRrA 420 " --> pdb=" O LYSrA 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'rA' and resid 415 through 420' Processing helix chain 'rA' and resid 440 through 445 removed outlier: 3.810A pdb=" N PHErA 444 " --> pdb=" O ASNrA 440 " (cutoff:3.500A) Processing helix chain 'rA' and resid 448 through 467 Processing helix chain 'rA' and resid 482 through 511 Processing helix chain 'rA' and resid 528 through 539 Processing helix chain 'rA' and resid 542 through 556 Processing helix chain 'rA' and resid 561 through 567 Processing helix chain 'rA' and resid 595 through 610 Processing helix chain 'rA' and resid 610 through 616 Processing helix chain 'rA' and resid 631 through 636 Processing helix chain 'tB' and resid 33 through 42 Processing helix chain 'tB' and resid 52 through 60 Processing helix chain 'tB' and resid 66 through 70 Processing helix chain 'tB' and resid 82 through 112 removed outlier: 3.981A pdb=" N ALAtB 94 " --> pdb=" O LEUtB 90 " (cutoff:3.500A) Processing helix chain 'tB' and resid 116 through 129 Processing helix chain 'tB' and resid 132 through 154 removed outlier: 3.572A pdb=" N ILEtB 136 " --> pdb=" O GLUtB 132 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARGtB 137 " --> pdb=" O LEUtB 133 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLUtB 148 " --> pdb=" O LYStB 144 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SERtB 154 " --> pdb=" O GLUtB 150 " (cutoff:3.500A) Processing helix chain 'cC' and resid 10 through 20 Processing helix chain 'cC' and resid 26 through 36 Processing helix chain 'cC' and resid 49 through 64 Processing helix chain 'cC' and resid 73 through 82 Processing helix chain 'CD' and resid 111 through 119 Processing helix chain 'CD' and resid 132 through 138 removed outlier: 3.688A pdb=" N TYRCD 137 " --> pdb=" O SERCD 134 " (cutoff:3.500A) Processing helix chain 'CD' and resid 142 through 154 Processing helix chain 'CD' and resid 165 through 169 Processing helix chain 'CD' and resid 187 through 198 Processing helix chain 'CD' and resid 204 through 208 removed outlier: 3.513A pdb=" N SERCD 207 " --> pdb=" O ALACD 204 " (cutoff:3.500A) Processing helix chain 'CD' and resid 228 through 234 Processing helix chain 'CD' and resid 372 through 381 Processing helix chain 'yE' and resid 12 through 16 removed outlier: 3.851A pdb=" N PHEyE 16 " --> pdb=" O GLUyE 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'yE' and resid 12 through 16' Processing helix chain 'yE' and resid 32 through 43 Processing helix chain 'yE' and resid 77 through 88 Processing helix chain 'yE' and resid 103 through 107 Processing helix chain 'yE' and resid 122 through 133 Processing helix chain 'yE' and resid 147 through 151 Processing helix chain 'yE' and resid 166 through 178 Processing helix chain 'yE' and resid 211 through 223 Processing helix chain 'yE' and resid 236 through 243 removed outlier: 3.562A pdb=" N LEUyE 240 " --> pdb=" O LEUyE 236 " (cutoff:3.500A) Processing helix chain 'UF' and resid 19 through 26 Processing helix chain 'UF' and resid 29 through 39 Processing helix chain 'UF' and resid 72 through 87 removed outlier: 3.686A pdb=" N LEUUF 76 " --> pdb=" O SERUF 72 " (cutoff:3.500A) Processing helix chain 'dG' and resid 24 through 26 No H-bonds generated for 'chain 'dG' and resid 24 through 26' Processing helix chain 'dG' and resid 27 through 45 removed outlier: 3.907A pdb=" N VALdG 33 " --> pdb=" O ALAdG 29 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYSdG 34 " --> pdb=" O PROdG 30 " (cutoff:3.500A) Processing helix chain 'dG' and resid 52 through 60 Processing helix chain 'eH' and resid 54 through 58 Processing helix chain 'eH' and resid 78 through 84 Processing helix chain 'eH' and resid 101 through 116 removed outlier: 4.185A pdb=" N VALeH 107 " --> pdb=" O LYSeH 103 " (cutoff:3.500A) Processing helix chain 'xI' and resid 109 through 138 Processing helix chain 'xI' and resid 144 through 159 Processing helix chain 'xI' and resid 202 through 206 removed outlier: 3.614A pdb=" N LEUxI 206 " --> pdb=" O PHExI 203 " (cutoff:3.500A) Processing helix chain 'qJ' and resid 11 through 34 Processing helix chain 'qJ' and resid 52 through 64 Processing helix chain 'qJ' and resid 90 through 120 Processing helix chain 'qJ' and resid 138 through 154 removed outlier: 3.798A pdb=" N VALqJ 150 " --> pdb=" O ALAqJ 146 " (cutoff:3.500A) Processing helix chain 'DK' and resid 12 through 32 removed outlier: 4.219A pdb=" N ALADK 16 " --> pdb=" O ASPDK 12 " (cutoff:3.500A) Processing helix chain 'DK' and resid 37 through 45 removed outlier: 3.608A pdb=" N PHEDK 41 " --> pdb=" O LYSDK 37 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VALDK 42 " --> pdb=" O LEUDK 38 " (cutoff:3.500A) Processing helix chain 'DK' and resid 61 through 73 removed outlier: 3.676A pdb=" N PHEDK 65 " --> pdb=" O GLNDK 61 " (cutoff:3.500A) Processing helix chain 'DK' and resid 156 through 160 removed outlier: 4.061A pdb=" N ARGDK 159 " --> pdb=" O ARGDK 156 " (cutoff:3.500A) Processing helix chain 'LL' and resid 17 through 20 removed outlier: 3.552A pdb=" N GLULL 20 " --> pdb=" O HISLL 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'LL' and resid 17 through 20' Processing helix chain 'LL' and resid 27 through 47 Processing helix chain 'LL' and resid 76 through 84 Processing helix chain 'LL' and resid 86 through 93 Processing helix chain 'LL' and resid 105 through 123 Processing helix chain 'LL' and resid 140 through 145 removed outlier: 3.856A pdb=" N THRLL 144 " --> pdb=" O SERLL 140 " (cutoff:3.500A) Processing helix chain 'LL' and resid 165 through 179 Processing helix chain 'LL' and resid 179 through 198 removed outlier: 3.789A pdb=" N LYSLL 185 " --> pdb=" O GLYLL 181 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALALL 187 " --> pdb=" O ARGLL 183 " (cutoff:3.500A) Processing helix chain 'KM' and resid 38 through 50 Processing helix chain 'KM' and resid 78 through 86 Processing helix chain 'KM' and resid 105 through 116 Processing helix chain 'KM' and resid 117 through 120 removed outlier: 3.883A pdb=" N SERKM 120 " --> pdb=" O ARGKM 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'KM' and resid 117 through 120' Processing helix chain 'KM' and resid 124 through 139 Processing helix chain 'KM' and resid 147 through 157 Processing helix chain 'AN' and resid 102 through 114 Processing helix chain 'AN' and resid 130 through 137 removed outlier: 3.591A pdb=" N ILEAN 134 " --> pdb=" O ASPAN 130 " (cutoff:3.500A) Processing helix chain 'AN' and resid 147 through 159 Processing helix chain 'AN' and resid 179 through 181 No H-bonds generated for 'chain 'AN' and resid 179 through 181' Processing helix chain 'AN' and resid 182 through 187 Processing helix chain 'AN' and resid 206 through 210 removed outlier: 3.595A pdb=" N TRPAN 209 " --> pdb=" O LEUAN 206 " (cutoff:3.500A) Processing helix chain 'AN' and resid 224 through 229 removed outlier: 4.260A pdb=" N THRAN 228 " --> pdb=" O PROAN 225 " (cutoff:3.500A) Processing helix chain 'AN' and resid 231 through 240 Processing helix chain 'AN' and resid 253 through 261 Processing helix chain 'AN' and resid 274 through 295 Processing helix chain 'AN' and resid 296 through 303 removed outlier: 3.783A pdb=" N LEUAN 299 " --> pdb=" O ARGAN 296 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEUAN 300 " --> pdb=" O GLUAN 297 " (cutoff:3.500A) Processing helix chain 'AN' and resid 333 through 337 removed outlier: 3.688A pdb=" N SERAN 336 " --> pdb=" O TYRAN 333 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SERAN 337 " --> pdb=" O TYRAN 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'AN' and resid 333 through 337' Processing helix chain 'AN' and resid 346 through 353 Processing helix chain 'AN' and resid 357 through 367 Processing helix chain 'AN' and resid 378 through 382 removed outlier: 3.928A pdb=" N GLUAN 381 " --> pdb=" O GLNAN 378 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYRAN 382 " --> pdb=" O PROAN 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'AN' and resid 378 through 382' Processing helix chain 'AN' and resid 432 through 436 removed outlier: 3.695A pdb=" N SERAN 436 " --> pdb=" O ASNAN 433 " (cutoff:3.500A) Processing helix chain 'DO' and resid 23 through 28 Processing helix chain 'DO' and resid 31 through 43 Processing helix chain 'DO' and resid 114 through 128 Processing helix chain 'DO' and resid 131 through 139 removed outlier: 3.525A pdb=" N GLYDO 139 " --> pdb=" O VALDO 135 " (cutoff:3.500A) Processing helix chain 'DO' and resid 154 through 159 removed outlier: 3.629A pdb=" N ILEDO 159 " --> pdb=" O LEUDO 156 " (cutoff:3.500A) Processing helix chain 'DO' and resid 161 through 173 Processing helix chain 'DO' and resid 174 through 184 Processing helix chain 'DO' and resid 214 through 219 Processing helix chain 'DO' and resid 234 through 239 Processing helix chain 'DO' and resid 240 through 243 removed outlier: 3.517A pdb=" N HISDO 243 " --> pdb=" O PRODO 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'DO' and resid 240 through 243' Processing helix chain 'DO' and resid 252 through 263 removed outlier: 4.746A pdb=" N ASPDO 259 " --> pdb=" O PHEDO 255 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLNDO 260 " --> pdb=" O THRDO 256 " (cutoff:3.500A) Processing helix chain 'DO' and resid 285 through 291 removed outlier: 3.668A pdb=" N ILEDO 289 " --> pdb=" O ASPDO 285 " (cutoff:3.500A) Processing helix chain 'DO' and resid 292 through 297 Processing helix chain 'DO' and resid 320 through 328 Processing helix chain 'DO' and resid 330 through 337 Processing helix chain 'DO' and resid 352 through 361 Processing helix chain 'RP' and resid 4 through 16 Processing helix chain 'RP' and resid 18 through 20 No H-bonds generated for 'chain 'RP' and resid 18 through 20' Processing helix chain 'RP' and resid 28 through 35 Processing helix chain 'RP' and resid 37 through 48 Processing helix chain 'RP' and resid 60 through 73 Processing helix chain 'RP' and resid 77 through 81 removed outlier: 3.898A pdb=" N ARGRP 81 " --> pdb=" O TYRRP 78 " (cutoff:3.500A) Processing helix chain 'RP' and resid 84 through 89 Processing helix chain 'RP' and resid 90 through 113 removed outlier: 3.653A pdb=" N VALRP 94 " --> pdb=" O PRORP 90 " (cutoff:3.500A) Processing helix chain 'RP' and resid 116 through 129 Processing helix chain 'RP' and resid 134 through 188 Processing helix chain 'MQ' and resid 77 through 89 Processing helix chain 'MQ' and resid 89 through 97 removed outlier: 4.138A pdb=" N LYSMQ 93 " --> pdb=" O ALAMQ 89 " (cutoff:3.500A) Processing helix chain 'MQ' and resid 97 through 111 Processing helix chain 'MQ' and resid 113 through 135 removed outlier: 3.779A pdb=" N THRMQ 130 " --> pdb=" O GLNMQ 126 " (cutoff:3.500A) Processing helix chain 'FR' and resid 13 through 31 Processing helix chain 'FR' and resid 39 through 45 Processing helix chain 'FR' and resid 61 through 72 removed outlier: 3.837A pdb=" N PHEFR 65 " --> pdb=" O GLNFR 61 " (cutoff:3.500A) Processing helix chain 'mS' and resid 37 through 48 removed outlier: 3.838A pdb=" N ARGmS 45 " --> pdb=" O ARGmS 41 " (cutoff:3.500A) Processing helix chain 'pT' and resid 21 through 51 Processing helix chain 'pT' and resid 60 through 77 Processing helix chain 'pT' and resid 110 through 119 Processing helix chain 'pT' and resid 125 through 131 Processing helix chain 'pT' and resid 178 through 201 Processing helix chain 'pT' and resid 203 through 207 removed outlier: 3.966A pdb=" N LEUpT 207 " --> pdb=" O PROpT 204 " (cutoff:3.500A) Processing helix chain 'pT' and resid 219 through 234 Processing helix chain 'pT' and resid 270 through 280 removed outlier: 3.790A pdb=" N GLNpT 274 " --> pdb=" O THRpT 270 " (cutoff:3.500A) Processing helix chain 'pT' and resid 372 through 386 removed outlier: 3.549A pdb=" N GLYpT 386 " --> pdb=" O ILEpT 382 " (cutoff:3.500A) Processing helix chain 'pT' and resid 405 through 429 removed outlier: 3.864A pdb=" N LEUpT 409 " --> pdb=" O ASNpT 405 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEUpT 421 " --> pdb=" O LYSpT 417 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLUpT 425 " --> pdb=" O LEUpT 421 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASNpT 428 " --> pdb=" O SERpT 424 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASNpT 429 " --> pdb=" O GLUpT 425 " (cutoff:3.500A) Processing helix chain 'pT' and resid 445 through 451 Processing helix chain 'pT' and resid 481 through 492 Processing helix chain 'pT' and resid 547 through 562 Processing helix chain 'YU' and resid 11 through 21 Processing helix chain 'YU' and resid 23 through 31 removed outlier: 4.153A pdb=" N VALYU 29 " --> pdb=" O SERYU 25 " (cutoff:3.500A) Processing helix chain 'YU' and resid 36 through 44 Processing helix chain 'YU' and resid 100 through 102 No H-bonds generated for 'chain 'YU' and resid 100 through 102' Processing helix chain 'YU' and resid 112 through 123 Processing helix chain 'vV' and resid 168 through 182 Processing helix chain 'vV' and resid 203 through 215 removed outlier: 4.107A pdb=" N ALAvV 207 " --> pdb=" O GLNvV 203 " (cutoff:3.500A) Processing helix chain 'vV' and resid 260 through 267 Processing helix chain 'vV' and resid 297 through 304 removed outlier: 4.152A pdb=" N ALAvV 304 " --> pdb=" O VALvV 300 " (cutoff:3.500A) Processing helix chain 'vV' and resid 381 through 386 Processing helix chain 'CW' and resid 34 through 43 Processing helix chain 'CW' and resid 66 through 79 Processing helix chain 'CW' and resid 103 through 114 removed outlier: 4.116A pdb=" N GLYCW 109 " --> pdb=" O SERCW 105 " (cutoff:3.500A) Processing helix chain 'CW' and resid 126 through 129 Processing helix chain 'CW' and resid 130 through 135 removed outlier: 3.622A pdb=" N GLNCW 135 " --> pdb=" O PROCW 131 " (cutoff:3.500A) Processing helix chain 'CW' and resid 147 through 160 removed outlier: 4.105A pdb=" N LYSCW 154 " --> pdb=" O PROCW 150 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LYSCW 160 " --> pdb=" O ALACW 156 " (cutoff:3.500A) Processing helix chain 'CW' and resid 182 through 187 Processing helix chain 'CW' and resid 206 through 210 removed outlier: 3.996A pdb=" N LYSCW 210 " --> pdb=" O GLUCW 207 " (cutoff:3.500A) Processing helix chain 'CW' and resid 235 through 240 Processing helix chain 'CW' and resid 253 through 261 removed outlier: 4.249A pdb=" N GLNCW 258 " --> pdb=" O GLUCW 254 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N THRCW 259 " --> pdb=" O GLNCW 255 " (cutoff:3.500A) Processing helix chain 'CW' and resid 274 through 295 Processing helix chain 'CW' and resid 298 through 303 Processing helix chain 'CW' and resid 347 through 354 Processing helix chain 'CW' and resid 357 through 366 Processing helix chain 'EX' and resid 102 through 114 Processing helix chain 'EX' and resid 130 through 136 Processing helix chain 'EX' and resid 148 through 159 Processing helix chain 'EX' and resid 182 through 187 Processing helix chain 'EX' and resid 206 through 210 removed outlier: 3.854A pdb=" N TRPEX 209 " --> pdb=" O LEUEX 206 " (cutoff:3.500A) Processing helix chain 'EX' and resid 232 through 240 Processing helix chain 'EX' and resid 253 through 262 Processing helix chain 'EX' and resid 274 through 295 Processing helix chain 'EX' and resid 296 through 300 Processing helix chain 'EX' and resid 346 through 353 Processing helix chain 'EX' and resid 357 through 368 Processing helix chain 'nY' and resid 8 through 15 removed outlier: 3.812A pdb=" N THRnY 11 " --> pdb=" O VALnY 8 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYSnY 13 " --> pdb=" O ILEnY 10 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYRnY 14 " --> pdb=" O THRnY 11 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLYnY 15 " --> pdb=" O GLYnY 12 " (cutoff:3.500A) Processing helix chain 'nY' and resid 19 through 35 removed outlier: 4.382A pdb=" N LYSnY 28 " --> pdb=" O ARGnY 24 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEUnY 29 " --> pdb=" O GLNnY 25 " (cutoff:3.500A) Processing helix chain 'nY' and resid 73 through 92 Processing helix chain 'SZ' and resid 33 through 49 Processing helix chain 'SZ' and resid 98 through 115 removed outlier: 3.569A pdb=" N ARGSZ 115 " --> pdb=" O ALASZ 111 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 117 through 119 No H-bonds generated for 'chain 'SZ' and resid 117 through 119' Processing helix chain 'SZ' and resid 137 through 142 Processing helix chain 'ia' and resid 25 through 30 removed outlier: 3.622A pdb=" N TYRia 28 " --> pdb=" O LYSia 25 " (cutoff:3.500A) Processing helix chain 'ia' and resid 34 through 49 Processing helix chain 'ia' and resid 51 through 64 Processing helix chain 'ia' and resid 65 through 78 removed outlier: 3.670A pdb=" N LYSia 75 " --> pdb=" O LYSia 71 " (cutoff:3.500A) Processing helix chain 'ia' and resid 79 through 98 Processing helix chain 'Ib' and resid 61 through 66 Processing helix chain 'Ib' and resid 67 through 84 Processing helix chain 'Ib' and resid 116 through 120 removed outlier: 3.705A pdb=" N GLYIb 119 " --> pdb=" O ASNIb 116 " (cutoff:3.500A) Processing helix chain 'Ib' and resid 150 through 164 Processing helix chain 'Xc' and resid 57 through 61 Processing helix chain 'Xc' and resid 68 through 79 removed outlier: 3.711A pdb=" N VALXc 75 " --> pdb=" O ALAXc 71 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLUXc 76 " --> pdb=" O METXc 72 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASNXc 79 " --> pdb=" O VALXc 75 " (cutoff:3.500A) Processing helix chain 'Xc' and resid 90 through 103 Processing helix chain 'Xc' and resid 130 through 139 removed outlier: 3.640A pdb=" N ILEXc 134 " --> pdb=" O ASPXc 130 " (cutoff:3.500A) Processing helix chain 'xd' and resid 6 through 15 Processing helix chain 'xd' and resid 19 through 42 removed outlier: 4.319A pdb=" N SERxd 32 " --> pdb=" O GLUxd 28 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N HISxd 33 " --> pdb=" O ALAxd 29 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SERxd 36 " --> pdb=" O SERxd 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEUxd 42 " --> pdb=" O ARGxd 38 " (cutoff:3.500A) Processing helix chain 'xd' and resid 44 through 73 removed outlier: 4.048A pdb=" N LYSxd 48 " --> pdb=" O GLYxd 44 " (cutoff:3.500A) Processing helix chain 'Wg' and resid 19 through 37 removed outlier: 3.937A pdb=" N LYSWg 23 " --> pdb=" O GLYWg 19 " (cutoff:3.500A) Processing helix chain 'Wg' and resid 49 through 60 removed outlier: 3.612A pdb=" N GLUWg 55 " --> pdb=" O PROWg 51 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THRWg 58 " --> pdb=" O GLNWg 54 " (cutoff:3.500A) Processing helix chain 'Wg' and resid 69 through 77 Processing helix chain 'Wg' and resid 89 through 95 Processing helix chain 'Wg' and resid 110 through 114 Processing helix chain 'Wg' and resid 158 through 160 No H-bonds generated for 'chain 'Wg' and resid 158 through 160' Processing helix chain 'Wg' and resid 161 through 168 Processing helix chain 'Wg' and resid 196 through 206 Processing helix chain 'jh' and resid 6 through 11 removed outlier: 3.550A pdb=" N LYSjh 10 " --> pdb=" O SERjh 7 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARGjh 11 " --> pdb=" O PHEjh 8 " (cutoff:3.500A) Processing helix chain 'jh' and resid 50 through 58 removed outlier: 3.800A pdb=" N LYSjh 54 " --> pdb=" O GLYjh 50 " (cutoff:3.500A) Processing helix chain 'jh' and resid 66 through 68 No H-bonds generated for 'chain 'jh' and resid 66 through 68' Processing helix chain 'jh' and resid 69 through 77 Processing helix chain 'li' and resid 6 through 19 Processing helix chain 'li' and resid 24 through 28 Processing helix chain 'Hj' and resid 46 through 50 removed outlier: 3.898A pdb=" N VALHj 50 " --> pdb=" O SERHj 47 " (cutoff:3.500A) Processing helix chain 'Hj' and resid 53 through 69 removed outlier: 3.678A pdb=" N LEUHj 69 " --> pdb=" O LEUHj 65 " (cutoff:3.500A) Processing helix chain 'Hj' and resid 72 through 77 Processing helix chain 'Hj' and resid 83 through 96 Processing helix chain 'Hj' and resid 101 through 119 removed outlier: 3.637A pdb=" N GLUHj 118 " --> pdb=" O ALAHj 114 " (cutoff:3.500A) Processing helix chain 'Hj' and resid 135 through 143 Processing helix chain 'Hj' and resid 159 through 163 Processing helix chain 'Hj' and resid 165 through 174 Processing helix chain 'Hj' and resid 182 through 191 Processing helix chain 'Hj' and resid 207 through 220 Processing helix chain 'Hj' and resid 225 through 230 Processing helix chain 'Hj' and resid 239 through 253 Processing helix chain 'Qk' and resid 23 through 40 Processing helix chain 'Qk' and resid 42 through 52 removed outlier: 4.269A pdb=" N LYSQk 46 " --> pdb=" O ALAQk 42 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VALQk 47 " --> pdb=" O PROQk 43 " (cutoff:3.500A) Processing helix chain 'Qk' and resid 64 through 72 Processing helix chain 'Qk' and resid 107 through 118 Processing helix chain 'Qk' and resid 123 through 131 Processing helix chain 'Qk' and resid 149 through 153 Processing helix chain 'Tl' and resid 54 through 58 removed outlier: 3.742A pdb=" N GLNTl 58 " --> pdb=" O LYSTl 55 " (cutoff:3.500A) Processing helix chain 'Tl' and resid 99 through 123 removed outlier: 3.930A pdb=" N GLNTl 103 " --> pdb=" O SERTl 99 " (cutoff:3.500A) Processing helix chain 'sm' and resid 28 through 58 Processing helix chain 'sm' and resid 58 through 71 removed outlier: 3.859A pdb=" N LYSsm 62 " --> pdb=" O LEUsm 58 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VALsm 67 " --> pdb=" O PHEsm 63 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VALsm 68 " --> pdb=" O METsm 64 " (cutoff:3.500A) Processing helix chain 'sm' and resid 72 through 74 No H-bonds generated for 'chain 'sm' and resid 72 through 74' Processing helix chain 'sm' and resid 82 through 93 Processing helix chain 'sm' and resid 95 through 106 removed outlier: 3.610A pdb=" N LEUsm 99 " --> pdb=" O ASPsm 95 " (cutoff:3.500A) Processing helix chain 'sm' and resid 113 through 134 removed outlier: 3.679A pdb=" N GLUsm 129 " --> pdb=" O GLNsm 125 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHEsm 134 " --> pdb=" O PHEsm 130 " (cutoff:3.500A) Processing helix chain 'sm' and resid 143 through 150 Processing helix chain 'sm' and resid 156 through 161 Processing helix chain 'No' and resid 3 through 12 Processing helix chain 'No' and resid 16 through 32 removed outlier: 3.842A pdb=" N TRPNo 28 " --> pdb=" O ARGNo 24 " (cutoff:3.500A) Processing helix chain 'No' and resid 44 through 52 Processing helix chain 'No' and resid 75 through 79 removed outlier: 3.819A pdb=" N GLYNo 78 " --> pdb=" O VALNo 75 " (cutoff:3.500A) Processing helix chain 'No' and resid 83 through 87 removed outlier: 3.566A pdb=" N GLNNo 87 " --> pdb=" O PRONo 84 " (cutoff:3.500A) Processing helix chain 'No' and resid 97 through 110 Processing helix chain 'No' and resid 139 through 144 Processing helix chain 'No' and resid 153 through 157 removed outlier: 4.098A pdb=" N LYSNo 157 " --> pdb=" O PRONo 154 " (cutoff:3.500A) Processing helix chain 'No' and resid 158 through 163 Processing helix chain 'No' and resid 165 through 173 Processing helix chain 'No' and resid 177 through 181 removed outlier: 4.000A pdb=" N ASNNo 181 " --> pdb=" O HISNo 178 " (cutoff:3.500A) Processing helix chain 'No' and resid 186 through 194 Processing helix chain 'zp' and resid 7 through 20 Processing helix chain 'zp' and resid 20 through 56 Processing helix chain 'zp' and resid 83 through 93 Processing helix chain 'zp' and resid 94 through 99 Processing helix chain 'Zq' and resid 58 through 65 Processing helix chain 'Zq' and resid 103 through 123 removed outlier: 3.662A pdb=" N ARGZq 107 " --> pdb=" O GLNZq 103 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VALZq 113 " --> pdb=" O GLUZq 109 " (cutoff:3.500A) Processing helix chain 'Zq' and resid 124 through 126 No H-bonds generated for 'chain 'Zq' and resid 124 through 126' Processing helix chain 'kr' and resid 7 through 16 Processing helix chain 'kr' and resid 58 through 69 removed outlier: 3.954A pdb=" N ALAkr 62 " --> pdb=" O ASPkr 58 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYSkr 63 " --> pdb=" O ALAkr 59 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYSkr 64 " --> pdb=" O GLYkr 60 " (cutoff:3.500A) Processing helix chain 'As' and resid 6 through 20 Processing helix chain 'As' and resid 71 through 80 Processing helix chain 'As' and resid 86 through 96 Processing helix chain 'As' and resid 96 through 107 removed outlier: 3.786A pdb=" N ILEAs 100 " --> pdb=" O ASNAs 96 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYSAs 101 " --> pdb=" O LYSAs 97 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYSAs 102 " --> pdb=" O LYSAs 98 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYSAs 105 " --> pdb=" O LYSAs 101 " (cutoff:3.500A) Processing helix chain 'As' and resid 143 through 154 Processing helix chain 'As' and resid 175 through 194 Processing helix chain 'Bt' and resid 13 through 32 Processing helix chain 'Bt' and resid 38 through 45 Processing helix chain 'Bt' and resid 61 through 72 Processing helix chain 'Gu' and resid 27 through 73 Processing helix chain 'Gu' and resid 96 through 106 Processing helix chain 'Gu' and resid 120 through 130 Processing helix chain 'Gu' and resid 140 through 152 Processing helix chain 'Gu' and resid 165 through 174 removed outlier: 4.299A pdb=" N ILEGu 169 " --> pdb=" O ASPGu 165 " (cutoff:3.500A) Processing helix chain 'Gu' and resid 175 through 177 No H-bonds generated for 'chain 'Gu' and resid 175 through 177' Processing helix chain 'Gu' and resid 180 through 190 Processing helix chain 'Gu' and resid 194 through 202 Processing helix chain 'Gu' and resid 235 through 244 Processing helix chain 'Pv' and resid 10 through 12 No H-bonds generated for 'chain 'Pv' and resid 10 through 12' Processing helix chain 'Pv' and resid 25 through 35 Processing helix chain 'Pv' and resid 40 through 53 Processing helix chain 'Pv' and resid 70 through 74 removed outlier: 3.747A pdb=" N GLYPv 73 " --> pdb=" O THRPv 70 " (cutoff:3.500A) Processing helix chain 'Pv' and resid 84 through 106 Processing helix chain 'Pv' and resid 108 through 110 No H-bonds generated for 'chain 'Pv' and resid 108 through 110' Processing helix chain 'Pv' and resid 169 through 183 Processing helix chain 'aw' and resid 2 through 6 Processing helix chain 'aw' and resid 41 through 49 Processing helix chain 'aw' and resid 64 through 69 removed outlier: 3.946A pdb=" N TRPaw 69 " --> pdb=" O ALAaw 66 " (cutoff:3.500A) Processing helix chain 'aw' and resid 74 through 82 removed outlier: 4.939A pdb=" N TRPaw 79 " --> pdb=" O ASPaw 76 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THRaw 80 " --> pdb=" O LYSaw 77 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILEaw 82 " --> pdb=" O TRPaw 79 " (cutoff:3.500A) Processing helix chain 'aw' and resid 83 through 93 removed outlier: 4.075A pdb=" N ASPaw 88 " --> pdb=" O GLUaw 84 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLNaw 89 " --> pdb=" O ASPaw 85 " (cutoff:3.500A) Processing helix chain 'aw' and resid 104 through 108 Processing helix chain 'aw' and resid 131 through 142 Processing helix chain 'ox' and resid 3 through 9 Processing helix chain 'ox' and resid 10 through 14 Processing helix chain 'ox' and resid 17 through 26 Processing helix chain 'ox' and resid 27 through 36 Processing helix chain 'ox' and resid 60 through 70 removed outlier: 3.810A pdb=" N LEUox 64 " --> pdb=" O THRox 60 " (cutoff:3.500A) Processing helix chain 'ox' and resid 71 through 80 Processing helix chain 'ox' and resid 86 through 95 removed outlier: 3.864A pdb=" N SERox 90 " --> pdb=" O THRox 86 " (cutoff:3.500A) Processing helix chain 'ox' and resid 97 through 111 Processing helix chain 'ox' and resid 111 through 131 removed outlier: 3.630A pdb=" N GLUox 115 " --> pdb=" O SERox 111 " (cutoff:3.500A) Processing helix chain 'Jy' and resid 28 through 41 Processing helix chain 'Jy' and resid 73 through 87 removed outlier: 3.953A pdb=" N GLUJy 77 " --> pdb=" O GLYJy 73 " (cutoff:3.500A) Processing helix chain 'Jy' and resid 135 through 140 removed outlier: 3.829A pdb=" N VALJy 138 " --> pdb=" O GLYJy 135 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THRJy 139 " --> pdb=" O ALAJy 136 " (cutoff:3.500A) Processing helix chain 'Jy' and resid 155 through 166 Processing helix chain 'Ez' and resid 9 through 16 Processing helix chain 'Ez' and resid 20 through 25 Processing helix chain 'Ez' and resid 29 through 38 Processing helix chain 'Ez' and resid 81 through 86 Proline residue: Ez 84 - end of helix No H-bonds generated for 'chain 'Ez' and resid 81 through 86' Processing helix chain 'Ez' and resid 94 through 114 Processing helix chain 'Ez' and resid 157 through 170 Processing helix chain 'Ez' and resid 191 through 200 removed outlier: 3.941A pdb=" N LEUEz 195 " --> pdb=" O ASPEz 191 " (cutoff:3.500A) Processing helix chain 'Ez' and resid 201 through 214 removed outlier: 3.771A pdb=" N SEREz 205 " --> pdb=" O GLYEz 201 " (cutoff:3.500A) Processing helix chain 'Ez' and resid 215 through 223 removed outlier: 3.748A pdb=" N PHEEz 219 " --> pdb=" O ASPEz 215 " (cutoff:3.500A) Processing helix chain 'Ez' and resid 223 through 230 Processing helix chain 'Ez' and resid 232 through 234 No H-bonds generated for 'chain 'Ez' and resid 232 through 234' Processing helix chain 'Ez' and resid 235 through 250 Processing helix chain 'Ez' and resid 261 through 273 Processing helix chain 'Ez' and resid 278 through 295 Processing sheet with id=AA1, first strand: chain 'h1' and resid 116 through 117 Processing sheet with id=AA2, first strand: chain 'g2' and resid 19 through 24 removed outlier: 4.685A pdb=" N LYSg2 19 " --> pdb=" O VALg2 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B4' and resid 71 through 77 removed outlier: 6.337A pdb=" N LEUB4 58 " --> pdb=" O ILEB4 48 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILEB4 48 " --> pdb=" O LEUB4 58 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LYSB4 60 " --> pdb=" O LYSB4 46 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ARGB4 64 " --> pdb=" O ARGB4 42 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ARGB4 42 " --> pdb=" O ARGB4 64 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B4' and resid 101 through 103 removed outlier: 5.749A pdb=" N ARGB4 147 " --> pdb=" O ILEB4 137 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N HISB4 139 " --> pdb=" O LYSB4 145 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYSB4 145 " --> pdb=" O HISB4 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'V5' and resid 17 through 18 Processing sheet with id=AA6, first strand: chain 'V5' and resid 22 through 25 removed outlier: 6.707A pdb=" N METV5 59 " --> pdb=" O ILEV5 37 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N VALV5 39 " --> pdb=" O METV5 57 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N METV5 57 " --> pdb=" O VALV5 39 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALAV5 99 " --> pdb=" O VALV5 79 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N GLYV5 100 " --> pdb=" O ILEV5 22 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ASNV5 24 " --> pdb=" O GLYV5 100 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ILEV5 102 " --> pdb=" O ASNV5 24 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'V5' and resid 85 through 87 removed outlier: 3.970A pdb=" N VALV5 91 " --> pdb=" O ARGV5 87 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHEV5 92 " --> pdb=" O METtB 20 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N VALtB 22 " --> pdb=" O PHEV5 92 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TYRV5 94 " --> pdb=" O VALtB 22 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O6' and resid 6 through 10 Processing sheet with id=AA9, first strand: chain 'O6' and resid 42 through 44 Processing sheet with id=AB1, first strand: chain 'f7' and resid 8 through 18 removed outlier: 9.813A pdb=" N VALf7 9 " --> pdb=" O ILEf7 32 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ILEf7 32 " --> pdb=" O VALf7 9 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N GLYf7 11 " --> pdb=" O ILEf7 30 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N ILEf7 30 " --> pdb=" O GLYf7 11 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N HISf7 13 " --> pdb=" O SERf7 28 " (cutoff:3.500A) removed outlier: 9.842A pdb=" N SERf7 28 " --> pdb=" O HISf7 13 " (cutoff:3.500A) removed outlier: 11.390A pdb=" N SERf7 15 " --> pdb=" O ASNf7 26 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N ASNf7 26 " --> pdb=" O SERf7 15 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLNf7 17 " --> pdb=" O ASNf7 24 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ASNf7 26 " --> pdb=" O PHEf7 85 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N PHEf7 85 " --> pdb=" O ASNf7 26 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VALf7 80 " --> pdb=" O HISf7 75 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARGf7 73 " --> pdb=" O ARGf7 82 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N THRf7 84 " --> pdb=" O VALf7 71 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N VALf7 71 " --> pdb=" O THRf7 84 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ARGf7 48 " --> pdb=" O PHEf7 101 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VALf7 52 " --> pdb=" O SERf7 97 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N SERf7 97 " --> pdb=" O VALf7 52 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F8' and resid 77 through 80 removed outlier: 6.865A pdb=" N SERF8 66 " --> pdb=" O TYRF8 54 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N TYRF8 54 " --> pdb=" O SERF8 66 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THRF8 38 " --> pdb=" O TYRF8 54 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N VALF8 39 " --> pdb=" O THRF8 87 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'rA' and resid 205 through 210 removed outlier: 3.569A pdb=" N TYRrA 205 " --> pdb=" O ASPrA 220 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THRrA 169 " --> pdb=" O CYSrA 249 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N LEUrA 251 " --> pdb=" O THRrA 169 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEUrA 171 " --> pdb=" O LEUrA 251 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N PHErA 253 " --> pdb=" O LEUrA 171 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N CYSrA 173 " --> pdb=" O PHErA 253 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N ASPrA 255 " --> pdb=" O CYSrA 173 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VALrA 250 " --> pdb=" O METrA 284 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N VALrA 286 " --> pdb=" O VALrA 250 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N TYRrA 252 " --> pdb=" O VALrA 286 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASNrA 288 " --> pdb=" O TYRrA 252 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N METrA 254 " --> pdb=" O ASNrA 288 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'rA' and resid 526 through 527 removed outlier: 6.696A pdb=" N LYSrA 526 " --> pdb=" O THRUF 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'tB' and resid 4 through 5 Processing sheet with id=AB6, first strand: chain 'cC' and resid 21 through 25 removed outlier: 6.213A pdb=" N LYScC 22 " --> pdb=" O LEUcC 93 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEUcC 41 " --> pdb=" O ILEcC 92 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'CD' and resid 356 through 359 removed outlier: 6.449A pdb=" N VALCD 57 " --> pdb=" O LYSCD 357 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ILECD 359 " --> pdb=" O THRCD 55 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N THRCD 55 " --> pdb=" O ILECD 359 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILECD 335 " --> pdb=" O VALCD 220 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N VALCD 220 " --> pdb=" O ILECD 335 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ILECD 215 " --> pdb=" O ASNCD 279 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LYSCD 281 " --> pdb=" O LYSCD 325 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N METCD 323 " --> pdb=" O TYRCD 283 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VALCD 285 " --> pdb=" O PHECD 321 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N PHECD 321 " --> pdb=" O VALCD 285 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARGCD 70 " --> pdb=" O LEUCD 60 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLYCD 52 " --> pdb=" O VALCD 78 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ASPCD 80 " --> pdb=" O LYSCD 50 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LYSCD 50 " --> pdb=" O ASPCD 80 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'CD' and resid 98 through 106 removed outlier: 6.883A pdb=" N GLYCD 91 " --> pdb=" O LEUCD 102 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THRCD 104 " --> pdb=" O VALCD 89 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VALCD 89 " --> pdb=" O THRCD 104 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N TRPCD 106 " --> pdb=" O VALCD 87 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VALCD 87 " --> pdb=" O TRPCD 106 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEUCD 161 " --> pdb=" O VALCD 87 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VALCD 89 " --> pdb=" O ARGCD 159 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ARGCD 159 " --> pdb=" O VALCD 89 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLYCD 91 " --> pdb=" O VALCD 157 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VALCD 157 " --> pdb=" O GLYCD 91 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'CD' and resid 98 through 106 removed outlier: 6.883A pdb=" N GLYCD 91 " --> pdb=" O LEUCD 102 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THRCD 104 " --> pdb=" O VALCD 89 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VALCD 89 " --> pdb=" O THRCD 104 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N TRPCD 106 " --> pdb=" O VALCD 87 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VALCD 87 " --> pdb=" O TRPCD 106 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'CD' and resid 225 through 227 removed outlier: 3.589A pdb=" N GLYCD 225 " --> pdb=" O ARGCD 270 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'yE' and resid 3 through 5 removed outlier: 3.725A pdb=" N LEUyE 203 " --> pdb=" O ASNyE 200 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'yE' and resid 17 through 19 removed outlier: 6.576A pdb=" N CYSyE 24 " --> pdb=" O VALyE 49 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N THRyE 51 " --> pdb=" O CYSyE 24 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VALyE 26 " --> pdb=" O THRyE 51 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'yE' and resid 64 through 65 removed outlier: 6.251A pdb=" N LEUyE 70 " --> pdb=" O GLNyE 95 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'yE' and resid 108 through 110 Processing sheet with id=AC6, first strand: chain 'yE' and resid 152 through 154 Processing sheet with id=AC7, first strand: chain 'UF' and resid 54 through 58 removed outlier: 8.503A pdb=" N TYRUF 103 " --> pdb=" O THRUF 14 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N THRUF 16 " --> pdb=" O TYRUF 103 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N LEUUF 105 " --> pdb=" O THRUF 16 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASPUF 18 " --> pdb=" O LEUUF 105 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N PHEUF 107 " --> pdb=" O ASPUF 18 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLUUF 102 " --> pdb=" O THRUF 98 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'UF' and resid 42 through 43 Processing sheet with id=AC9, first strand: chain 'dG' and resid 49 through 51 removed outlier: 6.714A pdb=" N ARGdG 50 " --> pdb=" O VALdG 93 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'eH' and resid 72 through 76 Processing sheet with id=AD2, first strand: chain 'qJ' and resid 84 through 85 Processing sheet with id=AD3, first strand: chain 'qJ' and resid 167 through 169 Processing sheet with id=AD4, first strand: chain 'DK' and resid 51 through 54 removed outlier: 6.698A pdb=" N ARGDK 51 " --> pdb=" O PHEDK 169 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N TYRDK 171 " --> pdb=" O ARGDK 51 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILEDK 53 " --> pdb=" O TYRDK 171 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHEDK 104 " --> pdb=" O PRODK 143 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'DK' and resid 78 through 80 removed outlier: 4.133A pdb=" N PHEDK 104 " --> pdb=" O PRODK 143 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLYDK 146 " --> pdb=" O VALDK 174 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'LL' and resid 22 through 24 removed outlier: 6.415A pdb=" N LYSLL 23 " --> pdb=" O LEUNo 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'LL' and resid 57 through 59 Processing sheet with id=AD8, first strand: chain 'KM' and resid 17 through 18 removed outlier: 3.625A pdb=" N ALAKM 17 " --> pdb=" O VALKM 58 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'KM' and resid 60 through 64 Processing sheet with id=AE1, first strand: chain 'KM' and resid 103 through 104 Processing sheet with id=AE2, first strand: chain 'AN' and resid 115 through 116 removed outlier: 3.794A pdb=" N ASPAN 116 " --> pdb=" O LEUAN 121 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEUAN 122 " --> pdb=" O ASNAN 168 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEUAN 219 " --> pdb=" O VALAN 245 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'AN' and resid 309 through 314 removed outlier: 6.323A pdb=" N SERAN 310 " --> pdb=" O LEUAN 465 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VALAN 467 " --> pdb=" O SERAN 310 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SERAN 312 " --> pdb=" O VALAN 467 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILEAN 460 " --> pdb=" O VALAN 452 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VALAN 452 " --> pdb=" O ILEAN 460 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEUAN 464 " --> pdb=" O THRAN 448 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'DO' and resid 15 through 21 removed outlier: 5.937A pdb=" N ASNDO 18 " --> pdb=" O VALDO 8 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VALDO 8 " --> pdb=" O ASNDO 18 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VALDO 151 " --> pdb=" O THRDO 7 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEUDO 150 " --> pdb=" O VALDO 248 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEUDO 206 " --> pdb=" O ILEDO 249 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N THRDO 251 " --> pdb=" O LEUDO 206 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VALDO 208 " --> pdb=" O THRDO 251 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'DO' and resid 62 through 64 Processing sheet with id=AE6, first strand: chain 'DO' and resid 186 through 187 Processing sheet with id=AE7, first strand: chain 'RP' and resid 22 through 24 Processing sheet with id=AE8, first strand: chain 'MQ' and resid 6 through 7 removed outlier: 6.650A pdb=" N ILEMQ 6 " --> pdb=" O ILEIb 20 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLYIb 32 " --> pdb=" O GLYIb 29 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'MQ' and resid 14 through 15 removed outlier: 3.613A pdb=" N PHESZ 150 " --> pdb=" O VALMQ 15 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'MQ' and resid 53 through 59 removed outlier: 4.799A pdb=" N GLYMQ 48 " --> pdb=" O PROMQ 54 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LYSMQ 43 " --> pdb=" O ILEMQ 38 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILEMQ 38 " --> pdb=" O LYSMQ 43 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEUMQ 45 " --> pdb=" O VALMQ 36 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ARGMQ 19 " --> pdb=" O ILEMQ 35 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VALMQ 20 " --> pdb=" O THRMQ 66 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THRMQ 66 " --> pdb=" O VALMQ 20 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'FR' and resid 52 through 53 removed outlier: 6.315A pdb=" N ILEFR 53 " --> pdb=" O TYRFR 171 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N METFR 173 " --> pdb=" O ILEFR 53 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLYFR 146 " --> pdb=" O VALFR 174 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLYFR 82 " --> pdb=" O ASNFR 99 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N LYSFR 101 " --> pdb=" O LEUFR 80 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEUFR 80 " --> pdb=" O LYSFR 101 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ARGFR 103 " --> pdb=" O HISFR 78 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N HISFR 78 " --> pdb=" O ARGFR 103 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'mS' and resid 7 through 12 removed outlier: 3.513A pdb=" N LYSmS 19 " --> pdb=" O CYSmS 12 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LYSmS 66 " --> pdb=" O ARGmS 87 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ARGmS 87 " --> pdb=" O LYSmS 66 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VALmS 68 " --> pdb=" O LEUmS 85 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'pT' and resid 87 through 96 removed outlier: 6.080A pdb=" N ALApT 90 " --> pdb=" O HISpT 146 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N HISpT 146 " --> pdb=" O ALApT 90 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLYpT 144 " --> pdb=" O PROpT 92 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'pT' and resid 100 through 102 removed outlier: 6.670A pdb=" N ILEpT 100 " --> pdb=" O ALApT 440 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALApT 440 " --> pdb=" O ILEpT 100 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLYpT 102 " --> pdb=" O GLNpT 438 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'pT' and resid 100 through 102 removed outlier: 6.670A pdb=" N ILEpT 100 " --> pdb=" O ALApT 440 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALApT 440 " --> pdb=" O ILEpT 100 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLYpT 102 " --> pdb=" O GLNpT 438 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILEpT 496 " --> pdb=" O TRPpT 442 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'pT' and resid 236 through 238 Processing sheet with id=AF8, first strand: chain 'pT' and resid 236 through 238 Processing sheet with id=AF9, first strand: chain 'pT' and resid 360 through 362 Processing sheet with id=AG1, first strand: chain 'YU' and resid 32 through 34 Processing sheet with id=AG2, first strand: chain 'YU' and resid 79 through 82 removed outlier: 6.680A pdb=" N ALAYU 79 " --> pdb=" O VALYU 73 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N VALYU 73 " --> pdb=" O ALAYU 79 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLNYU 81 " --> pdb=" O SERYU 71 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLYYU 68 " --> pdb=" O VALYU 56 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLUYU 55 " --> pdb=" O THRYU 107 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'YU' and resid 86 through 88 Processing sheet with id=AG4, first strand: chain 'vV' and resid 190 through 192 removed outlier: 6.928A pdb=" N THRvV 158 " --> pdb=" O TYRvV 244 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N VALvV 246 " --> pdb=" O THRvV 158 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLNvV 160 " --> pdb=" O VALvV 246 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ILEvV 248 " --> pdb=" O GLNvV 160 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ARGvV 162 " --> pdb=" O ILEvV 248 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'vV' and resid 256 through 258 removed outlier: 6.998A pdb=" N GLNvV 284 " --> pdb=" O SERvV 277 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLNvV 292 " --> pdb=" O ASPvV 287 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'vV' and resid 353 through 357 removed outlier: 6.953A pdb=" N ASPvV 337 " --> pdb=" O VALvV 323 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VALvV 323 " --> pdb=" O ASPvV 337 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THRvV 339 " --> pdb=" O LEUvV 321 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYSvV 399 " --> pdb=" O METvV 370 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TYRvV 372 " --> pdb=" O LEUvV 397 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEUvV 397 " --> pdb=" O TYRvV 372 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'CW' and resid 115 through 116 removed outlier: 3.825A pdb=" N ASPCW 116 " --> pdb=" O LEUCW 121 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEUCW 121 " --> pdb=" O ASPCW 116 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'CW' and resid 193 through 194 removed outlier: 7.517A pdb=" N LEUCW 193 " --> pdb=" O LEUCW 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'CW' and resid 270 through 271 removed outlier: 3.914A pdb=" N GLUCW 404 " --> pdb=" O LYSCW 372 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYSCW 372 " --> pdb=" O GLUCW 404 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'CW' and resid 270 through 271 Processing sheet with id=AH2, first strand: chain 'CW' and resid 310 through 313 removed outlier: 6.639A pdb=" N SERCW 310 " --> pdb=" O LEUCW 465 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N VALCW 467 " --> pdb=" O SERCW 310 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N SERCW 312 " --> pdb=" O VALCW 467 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'EX' and resid 115 through 116 removed outlier: 3.650A pdb=" N LEUEX 121 " --> pdb=" O ASPEX 116 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'EX' and resid 166 through 168 removed outlier: 6.685A pdb=" N VALEX 167 " --> pdb=" O CYSEX 194 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'EX' and resid 312 through 313 removed outlier: 6.325A pdb=" N SEREX 312 " --> pdb=" O VALEX 467 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SEREX 444 " --> pdb=" O ARGEX 468 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'nY' and resid 37 through 38 removed outlier: 3.993A pdb=" N ILEnY 54 " --> pdb=" O GLYnY 50 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'SZ' and resid 57 through 64 removed outlier: 5.453A pdb=" N ILESZ 58 " --> pdb=" O ARGSZ 12 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ARGSZ 12 " --> pdb=" O ILESZ 58 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLUSZ 6 " --> pdb=" O ILESZ 64 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'SZ' and resid 87 through 96 removed outlier: 7.192A pdb=" N ASNSZ 74 " --> pdb=" O GLUSZ 128 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLUSZ 128 " --> pdb=" O ASNSZ 74 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLYSZ 76 " --> pdb=" O VALSZ 126 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VALSZ 126 " --> pdb=" O GLYSZ 76 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TRPSZ 78 " --> pdb=" O LEUSZ 124 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Ib' and resid 3 through 11 removed outlier: 6.976A pdb=" N ILEIb 4 " --> pdb=" O ASNIb 59 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEUIb 52 " --> pdb=" O VALIb 48 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Ib' and resid 133 through 135 removed outlier: 6.851A pdb=" N LYSIb 87 " --> pdb=" O LYSIb 184 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYSIb 184 " --> pdb=" O LYSIb 87 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LYSIb 89 " --> pdb=" O SERIb 182 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Ib' and resid 100 through 104 Processing sheet with id=AI3, first strand: chain 'Xc' and resid 62 through 65 removed outlier: 3.601A pdb=" N GLNXc 64 " --> pdb=" O GLNXc 84 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYSXc 119 " --> pdb=" O VALXc 85 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYSXc 120 " --> pdb=" O THRXc 111 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THRXc 111 " --> pdb=" O LYSXc 120 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TYRXc 122 " --> pdb=" O VALXc 109 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VALXc 109 " --> pdb=" O TYRXc 122 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARGXc 124 " --> pdb=" O LEUXc 107 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Wg' and resid 64 through 66 removed outlier: 6.571A pdb=" N HISWg 44 " --> pdb=" O VALWg 217 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N VALWg 217 " --> pdb=" O HISWg 44 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N SERWg 218 " --> pdb=" O THRWg 231 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Wg' and resid 130 through 131 removed outlier: 3.904A pdb=" N ALAWg 131 " --> pdb=" O GLUWg 193 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLUWg 193 " --> pdb=" O ALAWg 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI5 Processing sheet with id=AI6, first strand: chain 'Wg' and resid 136 through 137 Processing sheet with id=AI7, first strand: chain 'jh' and resid 16 through 17 Processing sheet with id=AI8, first strand: chain 'Hj' and resid 177 through 180 removed outlier: 6.572A pdb=" N VALHj 151 " --> pdb=" O ALAHj 178 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VALHj 180 " --> pdb=" O VALHj 151 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ILEHj 153 " --> pdb=" O VALHj 180 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'Qk' and resid 62 through 63 removed outlier: 6.314A pdb=" N VALQk 81 " --> pdb=" O ALAQk 102 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N LEUQk 104 " --> pdb=" O VALQk 81 " (cutoff:3.500A) removed outlier: 9.591A pdb=" N VALQk 83 " --> pdb=" O LEUQk 104 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N PHEQk 106 " --> pdb=" O VALQk 83 " (cutoff:3.500A) removed outlier: 10.811A pdb=" N GLYQk 85 " --> pdb=" O PHEQk 106 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'Qk' and resid 62 through 63 Processing sheet with id=AJ2, first strand: chain 'Tl' and resid 83 through 92 removed outlier: 3.502A pdb=" N ARGTl 83 " --> pdb=" O VALTl 80 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASNTl 66 " --> pdb=" O GLYTl 73 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILETl 75 " --> pdb=" O VALTl 64 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VALTl 64 " --> pdb=" O ILETl 75 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N ASNTl 77 " --> pdb=" O GLYTl 62 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N GLYTl 62 " --> pdb=" O ASNTl 77 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'Tl' and resid 139 through 141 Processing sheet with id=AJ4, first strand: chain 'No' and resid 36 through 39 removed outlier: 4.674A pdb=" N ILENo 61 " --> pdb=" O ALANo 39 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TYRNo 127 " --> pdb=" O GLNNo 123 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLNNo 123 " --> pdb=" O TYRNo 127 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TYRNo 129 " --> pdb=" O VALNo 121 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASNNo 117 " --> pdb=" O ILENo 133 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VALNo 135 " --> pdb=" O VALNo 115 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N VALNo 115 " --> pdb=" O VALNo 135 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'Zq' and resid 69 through 76 removed outlier: 6.757A pdb=" N LYSZq 69 " --> pdb=" O GLUZq 47 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N HISZq 40 " --> pdb=" O PROZq 28 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEUZq 42 " --> pdb=" O VALZq 26 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILEZq 46 " --> pdb=" O LYSZq 22 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LYSZq 22 " --> pdb=" O ILEZq 46 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LYSZq 9 " --> pdb=" O ILEZq 25 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N VALZq 10 " --> pdb=" O THRZq 83 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'kr' and resid 3 through 5 removed outlier: 4.716A pdb=" N VALkr 55 " --> pdb=" O ILEkr 5 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THRkr 22 " --> pdb=" O ARGkr 46 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALAkr 23 " --> pdb=" O LYSkr 74 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'As' and resid 164 through 167 Processing sheet with id=AJ8, first strand: chain 'As' and resid 50 through 52 Processing sheet with id=AJ9, first strand: chain 'As' and resid 67 through 68 removed outlier: 6.806A pdb=" N ILEAs 67 " --> pdb=" O METAs 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ9 Processing sheet with id=AK1, first strand: chain 'As' and resid 111 through 113 Processing sheet with id=AK2, first strand: chain 'Bt' and resid 58 through 59 removed outlier: 3.792A pdb=" N ILEBt 52 " --> pdb=" O PHEBt 59 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARGBt 51 " --> pdb=" O PHEBt 169 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N TYRBt 171 " --> pdb=" O ARGBt 51 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILEBt 53 " --> pdb=" O TYRBt 171 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N METBt 173 " --> pdb=" O ILEBt 53 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLYBt 146 " --> pdb=" O VALBt 174 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ASNBt 99 " --> pdb=" O THRBt 81 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'Gu' and resid 205 through 206 removed outlier: 4.270A pdb=" N SERGu 113 " --> pdb=" O ARGGu 88 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'Gu' and resid 153 through 156 Processing sheet with id=AK5, first strand: chain 'Pv' and resid 14 through 22 removed outlier: 3.640A pdb=" N TYRPv 21 " --> pdb=" O SERPv 144 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N SERPv 144 " --> pdb=" O TYRPv 21 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THRPv 151 " --> pdb=" O VALPv 114 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N VALPv 114 " --> pdb=" O THRPv 151 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'Pv' and resid 58 through 59 Processing sheet with id=AK7, first strand: chain 'Pv' and resid 128 through 131 removed outlier: 3.550A pdb=" N ARGPv 135 " --> pdb=" O ARGPv 131 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'aw' and resid 72 through 73 Processing sheet with id=AK9, first strand: chain 'aw' and resid 101 through 103 removed outlier: 6.052A pdb=" N VALaw 125 " --> pdb=" O GLUaw 146 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'ox' and resid 50 through 51 removed outlier: 3.637A pdb=" N LYSox 56 " --> pdb=" O CYSox 51 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'Jy' and resid 46 through 49 removed outlier: 6.629A pdb=" N VALJy 46 " --> pdb=" O VALJy 67 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VALJy 67 " --> pdb=" O VALJy 46 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N SERJy 48 " --> pdb=" O ILEJy 65 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ILEJy 14 " --> pdb=" O ASNJy 132 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASNJy 132 " --> pdb=" O ILEJy 14 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N SERJy 22 " --> pdb=" O GLYJy 124 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLYJy 124 " --> pdb=" O SERJy 22 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'Jy' and resid 90 through 91 Processing sheet with id=AL4, first strand: chain 'Ez' and resid 72 through 79 removed outlier: 5.342A pdb=" N VALEz 74 " --> pdb=" O SEREz 66 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N SEREz 66 " --> pdb=" O VALEz 74 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALAEz 76 " --> pdb=" O ILEEz 64 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LEUEz 51 " --> pdb=" O ASPEz 147 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'Ez' and resid 183 through 184 removed outlier: 3.589A pdb=" N GLUEz 189 " --> pdb=" O ASPEz 184 " (cutoff:3.500A) 3492 hydrogen bonds defined for protein. 10023 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2656 hydrogen bonds 4256 hydrogen bond angles 0 basepair planarities 1078 basepair parallelities 1867 stacking parallelities Total time for adding SS restraints: 312.57 Time building geometry restraints manager: 56.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 33652 1.33 - 1.49: 73936 1.49 - 1.64: 54459 1.64 - 1.79: 105 1.79 - 1.94: 126 Bond restraints: 162278 Sorted by residual: bond pdb=" CB CYStB 36 " pdb=" SG CYStB 36 " ideal model delta sigma weight residual 1.808 1.943 -0.135 3.30e-02 9.18e+02 1.67e+01 bond pdb=" N GLYAs 69 " pdb=" CA GLYAs 69 " ideal model delta sigma weight residual 1.450 1.481 -0.031 9.10e-03 1.21e+04 1.16e+01 bond pdb=" CA ILEv9 168 " pdb=" CB ILEv9 168 " ideal model delta sigma weight residual 1.538 1.504 0.035 1.06e-02 8.90e+03 1.09e+01 bond pdb=" N GLYKM 102 " pdb=" CA GLYKM 102 " ideal model delta sigma weight residual 1.443 1.481 -0.038 1.17e-02 7.31e+03 1.04e+01 bond pdb=" CA VALKM 18 " pdb=" CB VALKM 18 " ideal model delta sigma weight residual 1.540 1.507 0.032 1.01e-02 9.80e+03 1.02e+01 ... (remaining 162273 not shown) Histogram of bond angle deviations from ideal: 94.99 - 103.85: 10974 103.85 - 112.71: 97925 112.71 - 121.56: 87080 121.56 - 130.42: 39377 130.42 - 139.28: 1836 Bond angle restraints: 237192 Sorted by residual: angle pdb=" N PROBt 119 " pdb=" CA PROBt 119 " pdb=" CB PROBt 119 " ideal model delta sigma weight residual 102.65 110.73 -8.08 6.80e-01 2.16e+00 1.41e+02 angle pdb=" N PRODK 139 " pdb=" CA PRODK 139 " pdb=" CB PRODK 139 " ideal model delta sigma weight residual 102.65 110.49 -7.84 6.80e-01 2.16e+00 1.33e+02 angle pdb=" N PRODK 58 " pdb=" CA PRODK 58 " pdb=" CB PRODK 58 " ideal model delta sigma weight residual 102.65 110.49 -7.84 6.80e-01 2.16e+00 1.33e+02 angle pdb=" N PROsm 77 " pdb=" CA PROsm 77 " pdb=" CB PROsm 77 " ideal model delta sigma weight residual 102.81 109.48 -6.67 6.70e-01 2.23e+00 9.90e+01 angle pdb=" N PROFR 33 " pdb=" CA PROFR 33 " pdb=" CB PROFR 33 " ideal model delta sigma weight residual 101.83 109.93 -8.10 8.40e-01 1.42e+00 9.29e+01 ... (remaining 237187 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 92858 35.96 - 71.92: 8340 71.92 - 107.88: 870 107.88 - 143.85: 24 143.85 - 179.81: 60 Dihedral angle restraints: 102152 sinusoidal: 70913 harmonic: 31239 Sorted by residual: dihedral pdb=" CA TYRrA 558 " pdb=" C TYRrA 558 " pdb=" N VALrA 559 " pdb=" CA VALrA 559 " ideal model delta harmonic sigma weight residual -180.00 -127.97 -52.03 0 5.00e+00 4.00e-02 1.08e+02 dihedral pdb=" CA ARGrA 353 " pdb=" C ARGrA 353 " pdb=" N ILErA 354 " pdb=" CA ILErA 354 " ideal model delta harmonic sigma weight residual 180.00 -130.86 -49.14 0 5.00e+00 4.00e-02 9.66e+01 dihedral pdb=" CB CYStB 9 " pdb=" SG CYStB 9 " pdb=" SG CYStB 32 " pdb=" CB CYStB 32 " ideal model delta sinusoidal sigma weight residual 93.00 178.24 -85.24 1 1.00e+01 1.00e-02 8.80e+01 ... (remaining 102149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 26870 0.082 - 0.165: 2800 0.165 - 0.247: 311 0.247 - 0.330: 59 0.330 - 0.412: 11 Chirality restraints: 30051 Sorted by residual: chirality pdb=" CB ILEyE 142 " pdb=" CA ILEyE 142 " pdb=" CG1 ILEyE 142 " pdb=" CG2 ILEyE 142 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" CB VALHj 190 " pdb=" CA VALHj 190 " pdb=" CG1 VALHj 190 " pdb=" CG2 VALHj 190 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" C3' G1e1097 " pdb=" C4' G1e1097 " pdb=" O3' G1e1097 " pdb=" C2' G1e1097 " both_signs ideal model delta sigma weight residual False -2.74 -2.36 -0.38 2.00e-01 2.50e+01 3.63e+00 ... (remaining 30048 not shown) Planarity restraints: 17198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G1e 406 " -0.075 2.00e-02 2.50e+03 3.07e-02 2.83e+01 pdb=" N9 G1e 406 " 0.064 2.00e-02 2.50e+03 pdb=" C8 G1e 406 " 0.008 2.00e-02 2.50e+03 pdb=" N7 G1e 406 " 0.004 2.00e-02 2.50e+03 pdb=" C5 G1e 406 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G1e 406 " -0.015 2.00e-02 2.50e+03 pdb=" O6 G1e 406 " -0.016 2.00e-02 2.50e+03 pdb=" N1 G1e 406 " -0.012 2.00e-02 2.50e+03 pdb=" C2 G1e 406 " 0.004 2.00e-02 2.50e+03 pdb=" N2 G1e 406 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G1e 406 " 0.024 2.00e-02 2.50e+03 pdb=" C4 G1e 406 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G1e 835 " -0.070 2.00e-02 2.50e+03 2.97e-02 2.64e+01 pdb=" N9 G1e 835 " 0.069 2.00e-02 2.50e+03 pdb=" C8 G1e 835 " 0.008 2.00e-02 2.50e+03 pdb=" N7 G1e 835 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G1e 835 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G1e 835 " -0.013 2.00e-02 2.50e+03 pdb=" O6 G1e 835 " -0.012 2.00e-02 2.50e+03 pdb=" N1 G1e 835 " -0.009 2.00e-02 2.50e+03 pdb=" C2 G1e 835 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G1e 835 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G1e 835 " 0.020 2.00e-02 2.50e+03 pdb=" C4 G1e 835 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G1e1973 " -0.030 2.00e-02 2.50e+03 2.86e-02 2.46e+01 pdb=" N9 G1e1973 " 0.021 2.00e-02 2.50e+03 pdb=" C8 G1e1973 " 0.023 2.00e-02 2.50e+03 pdb=" N7 G1e1973 " 0.007 2.00e-02 2.50e+03 pdb=" C5 G1e1973 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G1e1973 " -0.020 2.00e-02 2.50e+03 pdb=" O6 G1e1973 " -0.000 2.00e-02 2.50e+03 pdb=" N1 G1e1973 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G1e1973 " -0.068 2.00e-02 2.50e+03 pdb=" N2 G1e1973 " 0.054 2.00e-02 2.50e+03 pdb=" N3 G1e1973 " 0.008 2.00e-02 2.50e+03 pdb=" C4 G1e1973 " 0.003 2.00e-02 2.50e+03 ... (remaining 17195 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 50 2.26 - 2.92: 57273 2.92 - 3.58: 207496 3.58 - 4.24: 426499 4.24 - 4.90: 601507 Nonbonded interactions: 1292825 Sorted by model distance: nonbonded pdb=" N6 A1e1129 " pdb="MG MG1e3465 " model vdw 1.596 2.250 nonbonded pdb=" OP2 C1e2913 " pdb="MG MG1e3432 " model vdw 1.722 2.170 nonbonded pdb=" OP1 G1e2658 " pdb="MG MG1e3584 " model vdw 1.793 2.170 nonbonded pdb=" OP2 A1e1454 " pdb="MG MG1e3567 " model vdw 1.818 2.170 nonbonded pdb=" OP2 G1e 104 " pdb="MG MG1e3625 " model vdw 1.846 2.170 ... (remaining 1292820 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'AN' and (resid 101 through 412 or resid 437 through 477)) selection = (chain 'CW' and resid 101 through 477) selection = chain 'EX' } ncs_group { reference = chain 'Bt' selection = chain 'DK' selection = chain 'FR' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 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: 38.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 97.320 Check model and map are aligned: 1.720 Set scattering table: 1.060 Process input model: 583.950 Find NCS groups from input model: 4.310 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:9.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 736.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 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 0.135 162278 Z= 0.447 Angle : 0.946 17.868 237192 Z= 0.518 Chirality : 0.053 0.412 30051 Planarity : 0.006 0.080 17198 Dihedral : 22.166 179.807 81842 Min Nonbonded Distance : 1.596 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.41 % Allowed : 7.94 % Favored : 91.64 % Rotamer: Outliers : 0.60 % Allowed : 8.25 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.24 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.07), residues: 10628 helix: -1.89 (0.06), residues: 3992 sheet: -1.10 (0.13), residues: 1386 loop : -2.84 (0.07), residues: 5250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRPMQ 85 HIS 0.022 0.002 HISeH 21 PHE 0.050 0.003 PHEGu 229 TYR 0.039 0.003 TYRSZ 172 ARG 0.017 0.001 ARGeH 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21256 Ramachandran restraints generated. 10628 Oldfield, 0 Emsley, 10628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21256 Ramachandran restraints generated. 10628 Oldfield, 0 Emsley, 10628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1031 residues out of total 9273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 992 time to evaluate : 8.653 Fit side-chains REVERT: rA 79 ARG cc_start: 0.8034 (ttp-110) cc_final: 0.7781 (ptp90) REVERT: rA 396 ARG cc_start: 0.6655 (ptp-170) cc_final: 0.6346 (tmm-80) REVERT: rA 564 ASP cc_start: 0.7946 (m-30) cc_final: 0.7744 (m-30) REVERT: tB 104 GLU cc_start: 0.7556 (tm-30) cc_final: 0.7320 (tm-30) REVERT: cC 66 LYS cc_start: 0.7779 (mttp) cc_final: 0.7547 (ptpt) REVERT: CD 37 ARG cc_start: 0.8363 (mmt90) cc_final: 0.8148 (mmt90) REVERT: UF 102 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7502 (mm-30) REVERT: LL 180 ARG cc_start: 0.7426 (ttp-170) cc_final: 0.6920 (ttt180) REVERT: pT 8 GLU cc_start: 0.4554 (tp30) cc_final: 0.4013 (mp0) REVERT: pT 134 ARG cc_start: 0.8307 (ptp90) cc_final: 0.7618 (ptp90) REVERT: vV 370 MET cc_start: 0.7418 (mmm) cc_final: 0.7171 (mmp) REVERT: ia 91 ASN cc_start: 0.8050 (m-40) cc_final: 0.7846 (m110) REVERT: Hj 67 ILE cc_start: 0.7959 (tp) cc_final: 0.7577 (mp) REVERT: sm 48 LYS cc_start: 0.7212 (ttpt) cc_final: 0.6810 (pttt) REVERT: sm 49 LEU cc_start: 0.7823 (tt) cc_final: 0.7414 (tp) REVERT: sm 62 LYS cc_start: 0.7053 (mtpt) cc_final: 0.6210 (mptt) REVERT: No 5 LYS cc_start: 0.8011 (mmmt) cc_final: 0.7811 (mmtp) REVERT: zp 29 ARG cc_start: 0.8330 (ttm170) cc_final: 0.8037 (ttp-110) REVERT: aw 136 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7810 (mt-10) REVERT: ox 124 LYS cc_start: 0.8538 (ttmt) cc_final: 0.8038 (tmtm) REVERT: Jy 19 LEU cc_start: 0.8446 (mp) cc_final: 0.8196 (mp) REVERT: Jy 30 LEU cc_start: 0.7093 (mp) cc_final: 0.6826 (mp) REVERT: Jy 84 LEU cc_start: 0.6413 (mt) cc_final: 0.6103 (mt) outliers start: 39 outliers final: 22 residues processed: 1028 average time/residue: 2.2066 time to fit residues: 3273.6159 Evaluate side-chains 775 residues out of total 9273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 753 time to evaluate : 8.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B4 residue 45 VAL Chi-restraints excluded: chain F8 residue 65 ILE Chi-restraints excluded: chain rA residue 93 ILE Chi-restraints excluded: chain CD residue 85 VAL Chi-restraints excluded: chain CD residue 110 LEU Chi-restraints excluded: chain CD residue 114 VAL Chi-restraints excluded: chain CD residue 382 THR Chi-restraints excluded: chain yE residue 92 VAL Chi-restraints excluded: chain UF residue 43 VAL Chi-restraints excluded: chain xI residue 202 ARG Chi-restraints excluded: chain LL residue 58 VAL Chi-restraints excluded: chain LL residue 159 VAL Chi-restraints excluded: chain KM residue 80 LEU Chi-restraints excluded: chain DO residue 230 VAL Chi-restraints excluded: chain MQ residue 15 VAL Chi-restraints excluded: chain MQ residue 20 VAL Chi-restraints excluded: chain MQ residue 21 VAL Chi-restraints excluded: chain Ib residue 20 ILE Chi-restraints excluded: chain Ib residue 22 SER Chi-restraints excluded: chain Ib residue 65 VAL Chi-restraints excluded: chain Ib residue 101 VAL Chi-restraints excluded: chain Zq residue 23 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1406 random chunks: chunk 1187 optimal weight: 5.9990 chunk 1065 optimal weight: 9.9990 chunk 591 optimal weight: 20.0000 chunk 364 optimal weight: 20.0000 chunk 718 optimal weight: 7.9990 chunk 569 optimal weight: 1.9990 chunk 1102 optimal weight: 3.9990 chunk 426 optimal weight: 8.9990 chunk 670 optimal weight: 7.9990 chunk 820 optimal weight: 5.9990 chunk 1276 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h1 99 GLN g2 98 GLN B4 140 ASN O6 42 ASN v9 435 GLN rA 195 GLN ** rA 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** rA 549 GLN tB 24 ASN yE 21 ASN yE 50 HIS ** yE 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UF 25 ASN UF 109 GLN qJ 17 HIS ** DO 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** RP 68 GLN mS 59 HIS pT 26 ASN pT 146 HIS pT 540 GLN vV 163 GLN vV 176 GLN vV 292 GLN SZ 46 GLN Ib 49 ASN Ib 157 ASN Wg 54 GLN jh 12 HIS li 33 ASN Hj 38 GLN Hj 59 GLN Qk 45 ASN Tl 103 GLN Tl 112 ASN Tl 134 GLN sm 120 GLN No 11 GLN ** Gu 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Gu 225 GLN Pv 10 ASN aw 25 HIS aw 120 ASN ox 36 ASN Jy 95 ASN ** Jy 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ez 57 ASN Ez 151 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.176 162278 Z= 0.355 Angle : 0.687 13.474 237192 Z= 0.359 Chirality : 0.044 0.311 30051 Planarity : 0.006 0.094 17198 Dihedral : 22.636 179.978 66677 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.21 % Favored : 92.68 % Rotamer: Outliers : 4.38 % Allowed : 13.98 % Favored : 81.64 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.90 (0.08), residues: 10628 helix: -0.06 (0.08), residues: 3989 sheet: -0.93 (0.13), residues: 1400 loop : -2.38 (0.08), residues: 5239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRPMQ 85 HIS 0.012 0.001 HISeH 21 PHE 0.039 0.002 PHEtB 31 TYR 0.034 0.002 TYRaw 60 ARG 0.009 0.001 ARGLL 101 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21256 Ramachandran restraints generated. 10628 Oldfield, 0 Emsley, 10628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21256 Ramachandran restraints generated. 10628 Oldfield, 0 Emsley, 10628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1057 residues out of total 9273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 772 time to evaluate : 8.403 Fit side-chains REVERT: g2 94 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8785 (mp) REVERT: b3 25 LYS cc_start: 0.7315 (OUTLIER) cc_final: 0.6327 (mttm) REVERT: B4 72 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7438 (mmp-170) REVERT: V5 108 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6839 (mp0) REVERT: O6 84 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8130 (mt) REVERT: F8 12 SER cc_start: 0.8892 (m) cc_final: 0.8408 (p) REVERT: rA 79 ARG cc_start: 0.7986 (ttp-110) cc_final: 0.7704 (ptp-170) REVERT: rA 237 MET cc_start: 0.9023 (mmp) cc_final: 0.8529 (mmp) REVERT: rA 269 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.7057 (ttpp) REVERT: rA 396 ARG cc_start: 0.6850 (ptp-170) cc_final: 0.6341 (ttp-170) REVERT: rA 464 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.6979 (tt0) REVERT: rA 530 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7892 (mttm) REVERT: rA 549 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8204 (tm-30) REVERT: tB 138 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7908 (tt0) REVERT: cC 66 LYS cc_start: 0.7734 (mttp) cc_final: 0.7479 (ptpt) REVERT: CD 110 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8772 (mp) REVERT: CD 342 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8809 (mp) REVERT: UF 89 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8487 (mt) REVERT: UF 102 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7381 (mm-30) REVERT: DO 63 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7251 (tt0) REVERT: DO 194 TYR cc_start: 0.8308 (OUTLIER) cc_final: 0.7271 (m-10) REVERT: DO 361 HIS cc_start: 0.5951 (OUTLIER) cc_final: 0.5588 (m90) REVERT: RP 126 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7656 (mm-30) REVERT: MQ 16 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.7924 (pm20) REVERT: pT 8 GLU cc_start: 0.4283 (tp30) cc_final: 0.3902 (mp0) REVERT: pT 134 ARG cc_start: 0.8261 (ptp90) cc_final: 0.7601 (ptp90) REVERT: YU 55 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6400 (mm-30) REVERT: SZ 128 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7166 (tt0) REVERT: ia 11 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8209 (mt) REVERT: ia 91 ASN cc_start: 0.7985 (m-40) cc_final: 0.7731 (m110) REVERT: Xc 141 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.7892 (mp) REVERT: xd 23 ARG cc_start: 0.8015 (mtp85) cc_final: 0.7127 (mmp-170) REVERT: Hj 67 ILE cc_start: 0.7984 (tp) cc_final: 0.7613 (mp) REVERT: Tl 89 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8589 (mt) REVERT: Tl 104 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7120 (mp0) REVERT: Tl 128 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7891 (mp) REVERT: sm 48 LYS cc_start: 0.6939 (ttpt) cc_final: 0.6510 (pttt) REVERT: sm 62 LYS cc_start: 0.6961 (mtpt) cc_final: 0.6172 (mmtt) REVERT: Pv 13 LYS cc_start: 0.8397 (mtmm) cc_final: 0.7993 (mtpt) REVERT: ox 124 LYS cc_start: 0.8563 (ttmt) cc_final: 0.8041 (tmtm) REVERT: Jy 12 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7137 (tt) REVERT: Jy 19 LEU cc_start: 0.8310 (mp) cc_final: 0.8047 (mp) REVERT: Jy 30 LEU cc_start: 0.7200 (mp) cc_final: 0.6881 (mp) REVERT: Jy 59 ILE cc_start: 0.5940 (OUTLIER) cc_final: 0.5557 (pt) REVERT: Jy 84 LEU cc_start: 0.6410 (mt) cc_final: 0.6081 (mt) REVERT: Jy 141 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.6993 (ptm160) REVERT: Ez 35 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7290 (mtm-85) outliers start: 285 outliers final: 128 residues processed: 959 average time/residue: 2.0301 time to fit residues: 2890.5910 Evaluate side-chains 889 residues out of total 9273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 732 time to evaluate : 8.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g2 residue 71 THR Chi-restraints excluded: chain g2 residue 94 LEU Chi-restraints excluded: chain g2 residue 104 VAL Chi-restraints excluded: chain g2 residue 105 VAL Chi-restraints excluded: chain b3 residue 25 LYS Chi-restraints excluded: chain b3 residue 26 THR Chi-restraints excluded: chain B4 residue 31 THR Chi-restraints excluded: chain B4 residue 45 VAL Chi-restraints excluded: chain B4 residue 72 ARG Chi-restraints excluded: chain V5 residue 56 ASP Chi-restraints excluded: chain V5 residue 61 THR Chi-restraints excluded: chain V5 residue 74 MET Chi-restraints excluded: chain V5 residue 108 GLU Chi-restraints excluded: chain V5 residue 115 THR Chi-restraints excluded: chain O6 residue 84 LEU Chi-restraints excluded: chain F8 residue 15 VAL Chi-restraints excluded: chain F8 residue 79 VAL Chi-restraints excluded: chain F8 residue 84 VAL Chi-restraints excluded: chain F8 residue 91 VAL Chi-restraints excluded: chain F8 residue 145 LEU Chi-restraints excluded: chain v9 residue 430 ILE Chi-restraints excluded: chain rA residue 11 VAL Chi-restraints excluded: chain rA residue 233 ASN Chi-restraints excluded: chain rA residue 263 THR Chi-restraints excluded: chain rA residue 269 LYS Chi-restraints excluded: chain rA residue 385 LEU Chi-restraints excluded: chain rA residue 398 LEU Chi-restraints excluded: chain rA residue 459 GLU Chi-restraints excluded: chain rA residue 464 GLU Chi-restraints excluded: chain rA residue 530 LYS Chi-restraints excluded: chain rA residue 549 GLN Chi-restraints excluded: chain rA residue 595 ASP Chi-restraints excluded: chain tB residue 79 VAL Chi-restraints excluded: chain tB residue 124 LYS Chi-restraints excluded: chain tB residue 132 GLU Chi-restraints excluded: chain tB residue 135 ARG Chi-restraints excluded: chain tB residue 138 GLU Chi-restraints excluded: chain cC residue 75 ASN Chi-restraints excluded: chain CD residue 85 VAL Chi-restraints excluded: chain CD residue 110 LEU Chi-restraints excluded: chain CD residue 114 VAL Chi-restraints excluded: chain CD residue 210 GLU Chi-restraints excluded: chain CD residue 261 MET Chi-restraints excluded: chain CD residue 342 LEU Chi-restraints excluded: chain CD residue 382 THR Chi-restraints excluded: chain yE residue 3 THR Chi-restraints excluded: chain yE residue 90 ASP Chi-restraints excluded: chain yE residue 92 VAL Chi-restraints excluded: chain yE residue 108 ILE Chi-restraints excluded: chain yE residue 146 ILE Chi-restraints excluded: chain yE residue 164 GLN Chi-restraints excluded: chain yE residue 167 VAL Chi-restraints excluded: chain yE residue 169 ASP Chi-restraints excluded: chain yE residue 209 ASP Chi-restraints excluded: chain yE residue 235 ASN Chi-restraints excluded: chain UF residue 16 THR Chi-restraints excluded: chain UF residue 38 ILE Chi-restraints excluded: chain UF residue 43 VAL Chi-restraints excluded: chain UF residue 67 SER Chi-restraints excluded: chain UF residue 89 LEU Chi-restraints excluded: chain UF residue 96 VAL Chi-restraints excluded: chain dG residue 13 THR Chi-restraints excluded: chain dG residue 96 VAL Chi-restraints excluded: chain eH residue 31 ASN Chi-restraints excluded: chain eH residue 111 ARG Chi-restraints excluded: chain xI residue 147 SER Chi-restraints excluded: chain xI residue 150 GLU Chi-restraints excluded: chain xI residue 154 LYS Chi-restraints excluded: chain xI residue 202 ARG Chi-restraints excluded: chain qJ residue 50 ILE Chi-restraints excluded: chain qJ residue 53 VAL Chi-restraints excluded: chain qJ residue 110 LEU Chi-restraints excluded: chain LL residue 58 VAL Chi-restraints excluded: chain LL residue 121 SER Chi-restraints excluded: chain LL residue 124 ILE Chi-restraints excluded: chain LL residue 159 VAL Chi-restraints excluded: chain LL residue 182 ILE Chi-restraints excluded: chain KM residue 80 LEU Chi-restraints excluded: chain DO residue 63 GLU Chi-restraints excluded: chain DO residue 194 TYR Chi-restraints excluded: chain DO residue 227 THR Chi-restraints excluded: chain DO residue 230 VAL Chi-restraints excluded: chain DO residue 267 VAL Chi-restraints excluded: chain DO residue 333 VAL Chi-restraints excluded: chain DO residue 354 VAL Chi-restraints excluded: chain DO residue 359 LEU Chi-restraints excluded: chain DO residue 361 HIS Chi-restraints excluded: chain RP residue 14 VAL Chi-restraints excluded: chain RP residue 126 GLU Chi-restraints excluded: chain MQ residue 15 VAL Chi-restraints excluded: chain MQ residue 16 GLU Chi-restraints excluded: chain MQ residue 20 VAL Chi-restraints excluded: chain MQ residue 21 VAL Chi-restraints excluded: chain MQ residue 69 THR Chi-restraints excluded: chain mS residue 7 THR Chi-restraints excluded: chain pT residue 48 ASP Chi-restraints excluded: chain pT residue 177 LEU Chi-restraints excluded: chain pT residue 200 CYS Chi-restraints excluded: chain pT residue 291 ASP Chi-restraints excluded: chain pT residue 340 VAL Chi-restraints excluded: chain pT residue 387 VAL Chi-restraints excluded: chain pT residue 402 VAL Chi-restraints excluded: chain pT residue 514 VAL Chi-restraints excluded: chain pT residue 518 ASP Chi-restraints excluded: chain YU residue 55 GLU Chi-restraints excluded: chain YU residue 105 VAL Chi-restraints excluded: chain vV residue 155 TRP Chi-restraints excluded: chain vV residue 338 ILE Chi-restraints excluded: chain vV residue 345 ASP Chi-restraints excluded: chain nY residue 59 CYS Chi-restraints excluded: chain nY residue 72 SER Chi-restraints excluded: chain SZ residue 87 THR Chi-restraints excluded: chain SZ residue 128 GLU Chi-restraints excluded: chain SZ residue 160 THR Chi-restraints excluded: chain ia residue 11 LEU Chi-restraints excluded: chain ia residue 64 SER Chi-restraints excluded: chain Ib residue 12 VAL Chi-restraints excluded: chain Ib residue 50 ASN Chi-restraints excluded: chain Ib residue 101 VAL Chi-restraints excluded: chain Xc residue 25 VAL Chi-restraints excluded: chain Xc residue 70 THR Chi-restraints excluded: chain Xc residue 75 VAL Chi-restraints excluded: chain Xc residue 141 ILE Chi-restraints excluded: chain xd residue 36 SER Chi-restraints excluded: chain Hj residue 164 VAL Chi-restraints excluded: chain Hj residue 190 VAL Chi-restraints excluded: chain Hj residue 203 VAL Chi-restraints excluded: chain Hj residue 217 THR Chi-restraints excluded: chain Hj residue 227 ASP Chi-restraints excluded: chain Qk residue 41 ASP Chi-restraints excluded: chain Qk residue 186 VAL Chi-restraints excluded: chain Tl residue 25 VAL Chi-restraints excluded: chain Tl residue 72 VAL Chi-restraints excluded: chain Tl residue 89 LEU Chi-restraints excluded: chain Tl residue 104 GLU Chi-restraints excluded: chain Tl residue 128 LEU Chi-restraints excluded: chain sm residue 103 LYS Chi-restraints excluded: chain No residue 18 VAL Chi-restraints excluded: chain No residue 167 THR Chi-restraints excluded: chain No residue 196 THR Chi-restraints excluded: chain zp residue 42 LEU Chi-restraints excluded: chain Zq residue 23 VAL Chi-restraints excluded: chain Zq residue 46 ILE Chi-restraints excluded: chain Zq residue 60 LYS Chi-restraints excluded: chain kr residue 41 THR Chi-restraints excluded: chain Pv residue 24 VAL Chi-restraints excluded: chain ox residue 19 ASP Chi-restraints excluded: chain ox residue 118 SER Chi-restraints excluded: chain Jy residue 12 LEU Chi-restraints excluded: chain Jy residue 34 SER Chi-restraints excluded: chain Jy residue 46 VAL Chi-restraints excluded: chain Jy residue 59 ILE Chi-restraints excluded: chain Jy residue 107 ASP Chi-restraints excluded: chain Jy residue 141 ARG Chi-restraints excluded: chain Ez residue 35 ARG Chi-restraints excluded: chain Ez residue 93 THR Chi-restraints excluded: chain Ez residue 159 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1406 random chunks: chunk 709 optimal weight: 0.5980 chunk 396 optimal weight: 8.9990 chunk 1062 optimal weight: 30.0000 chunk 869 optimal weight: 10.0000 chunk 352 optimal weight: 6.9990 chunk 1279 optimal weight: 5.9990 chunk 1381 optimal weight: 8.9990 chunk 1139 optimal weight: 7.9990 chunk 1268 optimal weight: 20.0000 chunk 436 optimal weight: 1.9990 chunk 1026 optimal weight: 10.0000 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B4 140 ASN rA 26 GLN rA 267 GLN rA 362 HIS tB 24 ASN CD 211 GLN yE 50 HIS ** yE 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UF 25 ASN UF 109 GLN ** DO 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** RP 68 GLN mS 59 HIS pT 26 ASN pT 255 ASN vV 176 GLN vV 292 GLN Wg 54 GLN Hj 191 ASN Tl 112 ASN No 11 GLN kr 76 ASN ** Gu 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** aw 25 HIS aw 120 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.211 162278 Z= 0.325 Angle : 0.657 13.519 237192 Z= 0.344 Chirality : 0.043 0.312 30051 Planarity : 0.005 0.081 17198 Dihedral : 22.573 179.855 66669 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.59 % Favored : 92.33 % Rotamer: Outliers : 4.84 % Allowed : 15.98 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.08), residues: 10628 helix: 0.53 (0.08), residues: 3984 sheet: -0.78 (0.14), residues: 1390 loop : -2.23 (0.08), residues: 5254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRPMQ 85 HIS 0.009 0.001 HISDO 311 PHE 0.036 0.002 PHEGu 229 TYR 0.022 0.002 TYRaw 60 ARG 0.006 0.000 ARGLL 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21256 Ramachandran restraints generated. 10628 Oldfield, 0 Emsley, 10628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21256 Ramachandran restraints generated. 10628 Oldfield, 0 Emsley, 10628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1077 residues out of total 9273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 762 time to evaluate : 8.690 Fit side-chains REVERT: b3 25 LYS cc_start: 0.7343 (OUTLIER) cc_final: 0.6286 (mttm) REVERT: B4 72 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7375 (mmp-170) REVERT: O6 84 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8116 (mt) REVERT: O6 100 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7508 (mt-10) REVERT: F8 12 SER cc_start: 0.8902 (m) cc_final: 0.8381 (p) REVERT: v9 431 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8405 (mm) REVERT: v9 446 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7561 (mp0) REVERT: rA 79 ARG cc_start: 0.7983 (ttp-110) cc_final: 0.7691 (ptp-170) REVERT: rA 269 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6982 (ttpp) REVERT: rA 287 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7574 (mp) REVERT: rA 396 ARG cc_start: 0.6824 (ptp-170) cc_final: 0.6440 (ttp-170) REVERT: rA 464 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.6926 (tt0) REVERT: rA 535 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8020 (mpt) REVERT: tB 124 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8401 (ptmm) REVERT: tB 138 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7570 (tt0) REVERT: cC 66 LYS cc_start: 0.7748 (mttp) cc_final: 0.7468 (ptpt) REVERT: cC 71 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7633 (mt0) REVERT: CD 102 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8473 (pt) REVERT: CD 244 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7688 (mtp180) REVERT: CD 342 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8814 (mp) REVERT: UF 89 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8445 (mt) REVERT: UF 102 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7330 (mm-30) REVERT: eH 113 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.7997 (tttp) REVERT: xI 142 LYS cc_start: 0.8579 (mptt) cc_final: 0.8335 (mmtp) REVERT: xI 153 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7606 (tptm) REVERT: KM 80 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7388 (mp) REVERT: DO 194 TYR cc_start: 0.8288 (OUTLIER) cc_final: 0.6990 (m-10) REVERT: DO 361 HIS cc_start: 0.5910 (OUTLIER) cc_final: 0.5490 (m90) REVERT: MQ 16 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7895 (pm20) REVERT: mS 59 HIS cc_start: 0.7788 (OUTLIER) cc_final: 0.7542 (p-80) REVERT: pT 8 GLU cc_start: 0.4320 (tp30) cc_final: 0.4026 (mp0) REVERT: pT 87 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7601 (mtp180) REVERT: pT 134 ARG cc_start: 0.8210 (ptp90) cc_final: 0.7560 (ptp90) REVERT: YU 55 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6422 (mm-30) REVERT: vV 370 MET cc_start: 0.7286 (mmp) cc_final: 0.6698 (mmt) REVERT: vV 374 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7607 (mp) REVERT: nY 85 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7687 (ttm110) REVERT: SZ 61 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8818 (tp) REVERT: SZ 96 ASP cc_start: 0.7264 (OUTLIER) cc_final: 0.6908 (m-30) REVERT: SZ 104 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7618 (tt0) REVERT: SZ 128 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7141 (tt0) REVERT: ia 11 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8206 (mt) REVERT: ia 91 ASN cc_start: 0.7967 (m-40) cc_final: 0.7713 (m110) REVERT: Xc 141 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.7827 (mp) REVERT: xd 23 ARG cc_start: 0.8031 (mtp85) cc_final: 0.7110 (mmp-170) REVERT: Hj 67 ILE cc_start: 0.7964 (tp) cc_final: 0.7599 (mp) REVERT: Tl 89 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8581 (mt) REVERT: Tl 104 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: sm 42 LYS cc_start: 0.5453 (ttmt) cc_final: 0.4954 (pttt) REVERT: sm 48 LYS cc_start: 0.6914 (ttpt) cc_final: 0.6600 (pttt) REVERT: sm 49 LEU cc_start: 0.7878 (tt) cc_final: 0.7386 (tp) REVERT: sm 62 LYS cc_start: 0.6947 (mtpt) cc_final: 0.6150 (mptt) REVERT: Pv 13 LYS cc_start: 0.8345 (mtmm) cc_final: 0.8069 (mtpt) REVERT: ox 124 LYS cc_start: 0.8564 (ttmt) cc_final: 0.8040 (tmtm) REVERT: Jy 19 LEU cc_start: 0.8290 (mp) cc_final: 0.8020 (mp) REVERT: Jy 30 LEU cc_start: 0.7189 (mp) cc_final: 0.6869 (mp) REVERT: Jy 84 LEU cc_start: 0.6471 (mt) cc_final: 0.6147 (mt) REVERT: Jy 141 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.6933 (ptm160) REVERT: Ez 35 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7281 (mtm-85) outliers start: 315 outliers final: 163 residues processed: 974 average time/residue: 2.0240 time to fit residues: 2939.1765 Evaluate side-chains 944 residues out of total 9273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 743 time to evaluate : 8.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h1 residue 30 GLU Chi-restraints excluded: chain g2 residue 71 THR Chi-restraints excluded: chain g2 residue 104 VAL Chi-restraints excluded: chain g2 residue 105 VAL Chi-restraints excluded: chain b3 residue 25 LYS Chi-restraints excluded: chain b3 residue 26 THR Chi-restraints excluded: chain B4 residue 31 THR Chi-restraints excluded: chain B4 residue 45 VAL Chi-restraints excluded: chain B4 residue 47 GLN Chi-restraints excluded: chain B4 residue 72 ARG Chi-restraints excluded: chain V5 residue 56 ASP Chi-restraints excluded: chain V5 residue 61 THR Chi-restraints excluded: chain V5 residue 74 MET Chi-restraints excluded: chain V5 residue 115 THR Chi-restraints excluded: chain O6 residue 3 VAL Chi-restraints excluded: chain O6 residue 84 LEU Chi-restraints excluded: chain O6 residue 100 GLU Chi-restraints excluded: chain F8 residue 15 VAL Chi-restraints excluded: chain F8 residue 65 ILE Chi-restraints excluded: chain F8 residue 84 VAL Chi-restraints excluded: chain F8 residue 145 LEU Chi-restraints excluded: chain v9 residue 404 LEU Chi-restraints excluded: chain v9 residue 430 ILE Chi-restraints excluded: chain v9 residue 431 LEU Chi-restraints excluded: chain v9 residue 446 GLU Chi-restraints excluded: chain v9 residue 447 SER Chi-restraints excluded: chain rA residue 11 VAL Chi-restraints excluded: chain rA residue 178 VAL Chi-restraints excluded: chain rA residue 221 THR Chi-restraints excluded: chain rA residue 233 ASN Chi-restraints excluded: chain rA residue 263 THR Chi-restraints excluded: chain rA residue 269 LYS Chi-restraints excluded: chain rA residue 287 ILE Chi-restraints excluded: chain rA residue 312 VAL Chi-restraints excluded: chain rA residue 328 VAL Chi-restraints excluded: chain rA residue 385 LEU Chi-restraints excluded: chain rA residue 398 LEU Chi-restraints excluded: chain rA residue 464 GLU Chi-restraints excluded: chain rA residue 535 MET Chi-restraints excluded: chain tB residue 9 CYS Chi-restraints excluded: chain tB residue 32 CYS Chi-restraints excluded: chain tB residue 79 VAL Chi-restraints excluded: chain tB residue 124 LYS Chi-restraints excluded: chain tB residue 132 GLU Chi-restraints excluded: chain tB residue 138 GLU Chi-restraints excluded: chain cC residue 71 GLN Chi-restraints excluded: chain cC residue 75 ASN Chi-restraints excluded: chain CD residue 85 VAL Chi-restraints excluded: chain CD residue 102 LEU Chi-restraints excluded: chain CD residue 114 VAL Chi-restraints excluded: chain CD residue 160 VAL Chi-restraints excluded: chain CD residue 210 GLU Chi-restraints excluded: chain CD residue 242 THR Chi-restraints excluded: chain CD residue 244 ARG Chi-restraints excluded: chain CD residue 261 MET Chi-restraints excluded: chain CD residue 308 MET Chi-restraints excluded: chain CD residue 342 LEU Chi-restraints excluded: chain CD residue 382 THR Chi-restraints excluded: chain yE residue 3 THR Chi-restraints excluded: chain yE residue 50 HIS Chi-restraints excluded: chain yE residue 90 ASP Chi-restraints excluded: chain yE residue 92 VAL Chi-restraints excluded: chain yE residue 108 ILE Chi-restraints excluded: chain yE residue 146 ILE Chi-restraints excluded: chain yE residue 167 VAL Chi-restraints excluded: chain yE residue 169 ASP Chi-restraints excluded: chain yE residue 209 ASP Chi-restraints excluded: chain yE residue 235 ASN Chi-restraints excluded: chain UF residue 16 THR Chi-restraints excluded: chain UF residue 38 ILE Chi-restraints excluded: chain UF residue 43 VAL Chi-restraints excluded: chain UF residue 67 SER Chi-restraints excluded: chain UF residue 89 LEU Chi-restraints excluded: chain UF residue 96 VAL Chi-restraints excluded: chain dG residue 13 THR Chi-restraints excluded: chain dG residue 96 VAL Chi-restraints excluded: chain eH residue 31 ASN Chi-restraints excluded: chain eH residue 111 ARG Chi-restraints excluded: chain eH residue 113 LYS Chi-restraints excluded: chain xI residue 135 LYS Chi-restraints excluded: chain xI residue 147 SER Chi-restraints excluded: chain xI residue 150 GLU Chi-restraints excluded: chain xI residue 153 LYS Chi-restraints excluded: chain xI residue 202 ARG Chi-restraints excluded: chain qJ residue 50 ILE Chi-restraints excluded: chain qJ residue 53 VAL Chi-restraints excluded: chain qJ residue 167 THR Chi-restraints excluded: chain LL residue 58 VAL Chi-restraints excluded: chain LL residue 63 VAL Chi-restraints excluded: chain LL residue 121 SER Chi-restraints excluded: chain LL residue 124 ILE Chi-restraints excluded: chain LL residue 125 VAL Chi-restraints excluded: chain LL residue 159 VAL Chi-restraints excluded: chain KM residue 80 LEU Chi-restraints excluded: chain DO residue 6 VAL Chi-restraints excluded: chain DO residue 177 ASP Chi-restraints excluded: chain DO residue 194 TYR Chi-restraints excluded: chain DO residue 227 THR Chi-restraints excluded: chain DO residue 230 VAL Chi-restraints excluded: chain DO residue 267 VAL Chi-restraints excluded: chain DO residue 333 VAL Chi-restraints excluded: chain DO residue 354 VAL Chi-restraints excluded: chain DO residue 359 LEU Chi-restraints excluded: chain DO residue 361 HIS Chi-restraints excluded: chain RP residue 14 VAL Chi-restraints excluded: chain RP residue 22 VAL Chi-restraints excluded: chain MQ residue 15 VAL Chi-restraints excluded: chain MQ residue 16 GLU Chi-restraints excluded: chain MQ residue 20 VAL Chi-restraints excluded: chain MQ residue 21 VAL Chi-restraints excluded: chain MQ residue 69 THR Chi-restraints excluded: chain MQ residue 90 VAL Chi-restraints excluded: chain MQ residue 130 THR Chi-restraints excluded: chain mS residue 34 SER Chi-restraints excluded: chain mS residue 59 HIS Chi-restraints excluded: chain pT residue 48 ASP Chi-restraints excluded: chain pT residue 87 ARG Chi-restraints excluded: chain pT residue 111 THR Chi-restraints excluded: chain pT residue 177 LEU Chi-restraints excluded: chain pT residue 200 CYS Chi-restraints excluded: chain pT residue 291 ASP Chi-restraints excluded: chain pT residue 340 VAL Chi-restraints excluded: chain pT residue 402 VAL Chi-restraints excluded: chain pT residue 412 LEU Chi-restraints excluded: chain pT residue 511 ASP Chi-restraints excluded: chain pT residue 514 VAL Chi-restraints excluded: chain pT residue 518 ASP Chi-restraints excluded: chain YU residue 55 GLU Chi-restraints excluded: chain YU residue 74 TYR Chi-restraints excluded: chain YU residue 105 VAL Chi-restraints excluded: chain vV residue 155 TRP Chi-restraints excluded: chain vV residue 286 MET Chi-restraints excluded: chain vV residue 312 VAL Chi-restraints excluded: chain vV residue 338 ILE Chi-restraints excluded: chain vV residue 374 ILE Chi-restraints excluded: chain nY residue 46 THR Chi-restraints excluded: chain nY residue 59 CYS Chi-restraints excluded: chain nY residue 63 THR Chi-restraints excluded: chain nY residue 72 SER Chi-restraints excluded: chain nY residue 85 ARG Chi-restraints excluded: chain SZ residue 19 VAL Chi-restraints excluded: chain SZ residue 45 LEU Chi-restraints excluded: chain SZ residue 48 LEU Chi-restraints excluded: chain SZ residue 61 ILE Chi-restraints excluded: chain SZ residue 87 THR Chi-restraints excluded: chain SZ residue 96 ASP Chi-restraints excluded: chain SZ residue 104 GLU Chi-restraints excluded: chain SZ residue 128 GLU Chi-restraints excluded: chain SZ residue 160 THR Chi-restraints excluded: chain ia residue 11 LEU Chi-restraints excluded: chain ia residue 35 ASN Chi-restraints excluded: chain ia residue 64 SER Chi-restraints excluded: chain Ib residue 12 VAL Chi-restraints excluded: chain Ib residue 65 VAL Chi-restraints excluded: chain Ib residue 82 VAL Chi-restraints excluded: chain Ib residue 101 VAL Chi-restraints excluded: chain Ib residue 147 SER Chi-restraints excluded: chain Xc residue 25 VAL Chi-restraints excluded: chain Xc residue 58 SER Chi-restraints excluded: chain Xc residue 70 THR Chi-restraints excluded: chain Xc residue 72 MET Chi-restraints excluded: chain Xc residue 75 VAL Chi-restraints excluded: chain Xc residue 141 ILE Chi-restraints excluded: chain jh residue 5 THR Chi-restraints excluded: chain Hj residue 190 VAL Chi-restraints excluded: chain Hj residue 203 VAL Chi-restraints excluded: chain Hj residue 218 ILE Chi-restraints excluded: chain Hj residue 227 ASP Chi-restraints excluded: chain Qk residue 186 VAL Chi-restraints excluded: chain Tl residue 25 VAL Chi-restraints excluded: chain Tl residue 52 MET Chi-restraints excluded: chain Tl residue 72 VAL Chi-restraints excluded: chain Tl residue 89 LEU Chi-restraints excluded: chain Tl residue 104 GLU Chi-restraints excluded: chain sm residue 97 THR Chi-restraints excluded: chain sm residue 102 LEU Chi-restraints excluded: chain No residue 18 VAL Chi-restraints excluded: chain No residue 167 THR Chi-restraints excluded: chain No residue 196 THR Chi-restraints excluded: chain zp residue 42 LEU Chi-restraints excluded: chain zp residue 101 THR Chi-restraints excluded: chain Zq residue 23 VAL Chi-restraints excluded: chain Zq residue 46 ILE Chi-restraints excluded: chain Zq residue 60 LYS Chi-restraints excluded: chain kr residue 28 ASN Chi-restraints excluded: chain kr residue 41 THR Chi-restraints excluded: chain Pv residue 24 VAL Chi-restraints excluded: chain Pv residue 148 LEU Chi-restraints excluded: chain ox residue 19 ASP Chi-restraints excluded: chain ox residue 54 CYS Chi-restraints excluded: chain ox residue 110 GLN Chi-restraints excluded: chain ox residue 118 SER Chi-restraints excluded: chain Jy residue 31 THR Chi-restraints excluded: chain Jy residue 34 SER Chi-restraints excluded: chain Jy residue 46 VAL Chi-restraints excluded: chain Jy residue 67 VAL Chi-restraints excluded: chain Jy residue 107 ASP Chi-restraints excluded: chain Jy residue 141 ARG Chi-restraints excluded: chain Ez residue 35 ARG Chi-restraints excluded: chain Ez residue 68 THR Chi-restraints excluded: chain Ez residue 159 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1406 random chunks: chunk 1263 optimal weight: 0.0970 chunk 961 optimal weight: 10.0000 chunk 663 optimal weight: 50.0000 chunk 141 optimal weight: 6.9990 chunk 610 optimal weight: 0.6980 chunk 858 optimal weight: 8.9990 chunk 1283 optimal weight: 20.0000 chunk 1359 optimal weight: 9.9990 chunk 670 optimal weight: 10.0000 chunk 1216 optimal weight: 0.9990 chunk 366 optimal weight: 5.9990 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h1 34 GLN B4 140 ASN V5 98 ASN v9 395 HIS tB 24 ASN yE 50 HIS ** yE 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UF 25 ASN UF 109 GLN ** DO 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** RP 68 GLN pT 26 ASN vV 176 GLN vV 292 GLN Ib 49 ASN Wg 54 GLN Hj 191 ASN Tl 112 ASN No 11 GLN kr 76 ASN ** Gu 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** aw 25 HIS aw 120 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.173 162278 Z= 0.216 Angle : 0.578 12.607 237192 Z= 0.306 Chirality : 0.039 0.319 30051 Planarity : 0.004 0.058 17198 Dihedral : 22.461 179.761 66667 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.64 % Favored : 93.29 % Rotamer: Outliers : 4.52 % Allowed : 17.19 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.01 (0.08), residues: 10628 helix: 1.00 (0.08), residues: 3987 sheet: -0.64 (0.14), residues: 1407 loop : -2.09 (0.08), residues: 5234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPMQ 85 HIS 0.035 0.001 HISmS 59 PHE 0.028 0.002 PHEGu 229 TYR 0.018 0.001 TYRrA 91 ARG 0.004 0.000 ARGIb 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21256 Ramachandran restraints generated. 10628 Oldfield, 0 Emsley, 10628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21256 Ramachandran restraints generated. 10628 Oldfield, 0 Emsley, 10628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1074 residues out of total 9273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 780 time to evaluate : 8.813 Fit side-chains REVERT: V5 108 GLU cc_start: 0.7247 (mp0) cc_final: 0.6934 (mp0) REVERT: O6 100 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7459 (mt-10) REVERT: F8 12 SER cc_start: 0.8923 (m) cc_final: 0.8413 (p) REVERT: v9 426 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.6647 (mm-30) REVERT: v9 431 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8426 (mm) REVERT: v9 434 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8466 (tttp) REVERT: rA 79 ARG cc_start: 0.7968 (ttp-110) cc_final: 0.7646 (ptp-170) REVERT: rA 396 ARG cc_start: 0.6717 (ptp-170) cc_final: 0.6322 (ttp-170) REVERT: rA 464 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.6989 (tt0) REVERT: rA 535 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.7936 (mpt) REVERT: tB 123 ASP cc_start: 0.8194 (m-30) cc_final: 0.7893 (m-30) REVERT: tB 124 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8368 (ptmm) REVERT: tB 138 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7555 (tt0) REVERT: cC 66 LYS cc_start: 0.7729 (mttp) cc_final: 0.7442 (ptpt) REVERT: cC 71 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7901 (mt0) REVERT: UF 89 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8389 (mt) REVERT: UF 102 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7228 (mm-30) REVERT: eH 111 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7817 (tpm170) REVERT: xI 117 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8450 (mp) REVERT: xI 142 LYS cc_start: 0.8565 (mptt) cc_final: 0.8319 (mmtp) REVERT: qJ 31 GLU cc_start: 0.7703 (tp30) cc_final: 0.7500 (tp30) REVERT: qJ 108 LYS cc_start: 0.7620 (tptp) cc_final: 0.7327 (tttm) REVERT: KM 80 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7254 (mp) REVERT: DO 6 VAL cc_start: 0.8683 (OUTLIER) cc_final: 0.8390 (t) REVERT: DO 361 HIS cc_start: 0.5861 (OUTLIER) cc_final: 0.5443 (m90) REVERT: pT 87 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7529 (mtp180) REVERT: pT 134 ARG cc_start: 0.8170 (ptp90) cc_final: 0.7517 (ptp90) REVERT: YU 55 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6415 (mm-30) REVERT: SZ 61 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8776 (tp) REVERT: SZ 96 ASP cc_start: 0.7197 (OUTLIER) cc_final: 0.6780 (m-30) REVERT: SZ 172 TYR cc_start: 0.9021 (OUTLIER) cc_final: 0.7639 (t80) REVERT: ia 11 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8213 (mt) REVERT: ia 91 ASN cc_start: 0.7908 (m-40) cc_final: 0.7652 (m110) REVERT: Xc 69 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: Xc 141 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.7736 (mp) REVERT: xd 23 ARG cc_start: 0.8007 (mtp85) cc_final: 0.7066 (mmp-170) REVERT: xd 37 GLU cc_start: 0.7867 (pp20) cc_final: 0.7616 (mm-30) REVERT: Hj 67 ILE cc_start: 0.7843 (tp) cc_final: 0.7476 (mp) REVERT: Tl 89 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8541 (mt) REVERT: Tl 104 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7150 (mp0) REVERT: Tl 128 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7824 (mp) REVERT: sm 42 LYS cc_start: 0.5389 (ttmt) cc_final: 0.4889 (pttt) REVERT: sm 46 LYS cc_start: 0.6131 (OUTLIER) cc_final: 0.5527 (mttm) REVERT: sm 48 LYS cc_start: 0.6921 (ttpt) cc_final: 0.6713 (pttt) REVERT: sm 49 LEU cc_start: 0.7876 (tt) cc_final: 0.7390 (tp) REVERT: sm 62 LYS cc_start: 0.6962 (mtpt) cc_final: 0.6146 (mptt) REVERT: Pv 13 LYS cc_start: 0.8259 (mtmm) cc_final: 0.8048 (mtpt) REVERT: ox 124 LYS cc_start: 0.8565 (ttmt) cc_final: 0.8029 (tmtm) REVERT: Jy 19 LEU cc_start: 0.8212 (mp) cc_final: 0.7943 (mp) REVERT: Jy 84 LEU cc_start: 0.6506 (mt) cc_final: 0.6153 (mt) REVERT: Ez 35 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7329 (mtm-85) REVERT: Ez 88 ILE cc_start: 0.7452 (OUTLIER) cc_final: 0.6758 (tt) outliers start: 294 outliers final: 155 residues processed: 981 average time/residue: 2.0241 time to fit residues: 2967.2492 Evaluate side-chains 934 residues out of total 9273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 750 time to evaluate : 8.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h1 residue 30 GLU Chi-restraints excluded: chain g2 residue 71 THR Chi-restraints excluded: chain g2 residue 94 LEU Chi-restraints excluded: chain g2 residue 104 VAL Chi-restraints excluded: chain g2 residue 105 VAL Chi-restraints excluded: chain b3 residue 26 THR Chi-restraints excluded: chain B4 residue 45 VAL Chi-restraints excluded: chain V5 residue 56 ASP Chi-restraints excluded: chain V5 residue 74 MET Chi-restraints excluded: chain V5 residue 115 THR Chi-restraints excluded: chain O6 residue 3 VAL Chi-restraints excluded: chain O6 residue 100 GLU Chi-restraints excluded: chain F8 residue 15 VAL Chi-restraints excluded: chain F8 residue 71 VAL Chi-restraints excluded: chain F8 residue 84 VAL Chi-restraints excluded: chain F8 residue 145 LEU Chi-restraints excluded: chain v9 residue 404 LEU Chi-restraints excluded: chain v9 residue 409 VAL Chi-restraints excluded: chain v9 residue 426 GLU Chi-restraints excluded: chain v9 residue 428 ILE Chi-restraints excluded: chain v9 residue 430 ILE Chi-restraints excluded: chain v9 residue 431 LEU Chi-restraints excluded: chain v9 residue 434 LYS Chi-restraints excluded: chain v9 residue 447 SER Chi-restraints excluded: chain rA residue 73 ASP Chi-restraints excluded: chain rA residue 178 VAL Chi-restraints excluded: chain rA residue 201 THR Chi-restraints excluded: chain rA residue 221 THR Chi-restraints excluded: chain rA residue 233 ASN Chi-restraints excluded: chain rA residue 263 THR Chi-restraints excluded: chain rA residue 327 ASN Chi-restraints excluded: chain rA residue 328 VAL Chi-restraints excluded: chain rA residue 374 ARG Chi-restraints excluded: chain rA residue 385 LEU Chi-restraints excluded: chain rA residue 464 GLU Chi-restraints excluded: chain rA residue 486 VAL Chi-restraints excluded: chain rA residue 535 MET Chi-restraints excluded: chain tB residue 9 CYS Chi-restraints excluded: chain tB residue 32 CYS Chi-restraints excluded: chain tB residue 79 VAL Chi-restraints excluded: chain tB residue 124 LYS Chi-restraints excluded: chain tB residue 135 ARG Chi-restraints excluded: chain tB residue 138 GLU Chi-restraints excluded: chain cC residue 71 GLN Chi-restraints excluded: chain cC residue 75 ASN Chi-restraints excluded: chain CD residue 85 VAL Chi-restraints excluded: chain CD residue 114 VAL Chi-restraints excluded: chain CD residue 160 VAL Chi-restraints excluded: chain CD residue 210 GLU Chi-restraints excluded: chain CD residue 308 MET Chi-restraints excluded: chain CD residue 382 THR Chi-restraints excluded: chain yE residue 3 THR Chi-restraints excluded: chain yE residue 90 ASP Chi-restraints excluded: chain yE residue 92 VAL Chi-restraints excluded: chain yE residue 108 ILE Chi-restraints excluded: chain yE residue 146 ILE Chi-restraints excluded: chain yE residue 164 GLN Chi-restraints excluded: chain yE residue 169 ASP Chi-restraints excluded: chain UF residue 16 THR Chi-restraints excluded: chain UF residue 38 ILE Chi-restraints excluded: chain UF residue 43 VAL Chi-restraints excluded: chain UF residue 55 THR Chi-restraints excluded: chain UF residue 58 GLU Chi-restraints excluded: chain UF residue 67 SER Chi-restraints excluded: chain UF residue 89 LEU Chi-restraints excluded: chain UF residue 96 VAL Chi-restraints excluded: chain dG residue 13 THR Chi-restraints excluded: chain dG residue 96 VAL Chi-restraints excluded: chain eH residue 31 ASN Chi-restraints excluded: chain eH residue 111 ARG Chi-restraints excluded: chain xI residue 117 LEU Chi-restraints excluded: chain xI residue 147 SER Chi-restraints excluded: chain xI residue 150 GLU Chi-restraints excluded: chain xI residue 154 LYS Chi-restraints excluded: chain xI residue 202 ARG Chi-restraints excluded: chain qJ residue 29 GLN Chi-restraints excluded: chain qJ residue 50 ILE Chi-restraints excluded: chain qJ residue 53 VAL Chi-restraints excluded: chain LL residue 58 VAL Chi-restraints excluded: chain LL residue 63 VAL Chi-restraints excluded: chain LL residue 121 SER Chi-restraints excluded: chain LL residue 124 ILE Chi-restraints excluded: chain LL residue 159 VAL Chi-restraints excluded: chain KM residue 80 LEU Chi-restraints excluded: chain DO residue 6 VAL Chi-restraints excluded: chain DO residue 177 ASP Chi-restraints excluded: chain DO residue 230 VAL Chi-restraints excluded: chain DO residue 267 VAL Chi-restraints excluded: chain DO residue 333 VAL Chi-restraints excluded: chain DO residue 354 VAL Chi-restraints excluded: chain DO residue 361 HIS Chi-restraints excluded: chain RP residue 116 ASP Chi-restraints excluded: chain MQ residue 15 VAL Chi-restraints excluded: chain MQ residue 20 VAL Chi-restraints excluded: chain MQ residue 21 VAL Chi-restraints excluded: chain MQ residue 69 THR Chi-restraints excluded: chain MQ residue 90 VAL Chi-restraints excluded: chain mS residue 34 SER Chi-restraints excluded: chain pT residue 87 ARG Chi-restraints excluded: chain pT residue 111 THR Chi-restraints excluded: chain pT residue 177 LEU Chi-restraints excluded: chain pT residue 200 CYS Chi-restraints excluded: chain pT residue 211 LEU Chi-restraints excluded: chain pT residue 267 VAL Chi-restraints excluded: chain pT residue 327 GLU Chi-restraints excluded: chain pT residue 340 VAL Chi-restraints excluded: chain pT residue 387 VAL Chi-restraints excluded: chain pT residue 402 VAL Chi-restraints excluded: chain pT residue 412 LEU Chi-restraints excluded: chain pT residue 511 ASP Chi-restraints excluded: chain pT residue 531 THR Chi-restraints excluded: chain YU residue 55 GLU Chi-restraints excluded: chain YU residue 74 TYR Chi-restraints excluded: chain YU residue 105 VAL Chi-restraints excluded: chain vV residue 155 TRP Chi-restraints excluded: chain vV residue 314 GLN Chi-restraints excluded: chain vV residue 338 ILE Chi-restraints excluded: chain nY residue 46 THR Chi-restraints excluded: chain nY residue 59 CYS Chi-restraints excluded: chain nY residue 63 THR Chi-restraints excluded: chain nY residue 72 SER Chi-restraints excluded: chain SZ residue 19 VAL Chi-restraints excluded: chain SZ residue 45 LEU Chi-restraints excluded: chain SZ residue 61 ILE Chi-restraints excluded: chain SZ residue 87 THR Chi-restraints excluded: chain SZ residue 96 ASP Chi-restraints excluded: chain SZ residue 160 THR Chi-restraints excluded: chain SZ residue 172 TYR Chi-restraints excluded: chain ia residue 11 LEU Chi-restraints excluded: chain ia residue 35 ASN Chi-restraints excluded: chain ia residue 64 SER Chi-restraints excluded: chain Ib residue 12 VAL Chi-restraints excluded: chain Ib residue 65 VAL Chi-restraints excluded: chain Ib residue 82 VAL Chi-restraints excluded: chain Ib residue 101 VAL Chi-restraints excluded: chain Ib residue 132 VAL Chi-restraints excluded: chain Ib residue 147 SER Chi-restraints excluded: chain Xc residue 25 VAL Chi-restraints excluded: chain Xc residue 58 SER Chi-restraints excluded: chain Xc residue 69 GLU Chi-restraints excluded: chain Xc residue 70 THR Chi-restraints excluded: chain Xc residue 75 VAL Chi-restraints excluded: chain Xc residue 100 GLU Chi-restraints excluded: chain Xc residue 132 LEU Chi-restraints excluded: chain Xc residue 141 ILE Chi-restraints excluded: chain jh residue 5 THR Chi-restraints excluded: chain Hj residue 30 THR Chi-restraints excluded: chain Hj residue 132 VAL Chi-restraints excluded: chain Hj residue 164 VAL Chi-restraints excluded: chain Hj residue 203 VAL Chi-restraints excluded: chain Hj residue 217 THR Chi-restraints excluded: chain Hj residue 218 ILE Chi-restraints excluded: chain Hj residue 227 ASP Chi-restraints excluded: chain Qk residue 186 VAL Chi-restraints excluded: chain Tl residue 52 MET Chi-restraints excluded: chain Tl residue 89 LEU Chi-restraints excluded: chain Tl residue 104 GLU Chi-restraints excluded: chain Tl residue 128 LEU Chi-restraints excluded: chain sm residue 46 LYS Chi-restraints excluded: chain sm residue 97 THR Chi-restraints excluded: chain sm residue 102 LEU Chi-restraints excluded: chain No residue 18 VAL Chi-restraints excluded: chain No residue 196 THR Chi-restraints excluded: chain zp residue 42 LEU Chi-restraints excluded: chain zp residue 101 THR Chi-restraints excluded: chain zp residue 103 PHE Chi-restraints excluded: chain Zq residue 23 VAL Chi-restraints excluded: chain Zq residue 46 ILE Chi-restraints excluded: chain kr residue 14 LEU Chi-restraints excluded: chain kr residue 28 ASN Chi-restraints excluded: chain kr residue 41 THR Chi-restraints excluded: chain kr residue 48 SER Chi-restraints excluded: chain Pv residue 24 VAL Chi-restraints excluded: chain ox residue 19 ASP Chi-restraints excluded: chain Jy residue 18 VAL Chi-restraints excluded: chain Jy residue 31 THR Chi-restraints excluded: chain Jy residue 67 VAL Chi-restraints excluded: chain Jy residue 107 ASP Chi-restraints excluded: chain Jy residue 148 VAL Chi-restraints excluded: chain Jy residue 161 SER Chi-restraints excluded: chain Ez residue 35 ARG Chi-restraints excluded: chain Ez residue 88 ILE Chi-restraints excluded: chain Ez residue 93 THR Chi-restraints excluded: chain Ez residue 159 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1406 random chunks: chunk 1131 optimal weight: 10.0000 chunk 771 optimal weight: 30.0000 chunk 19 optimal weight: 0.8980 chunk 1011 optimal weight: 10.0000 chunk 560 optimal weight: 8.9990 chunk 1159 optimal weight: 1.9990 chunk 939 optimal weight: 30.0000 chunk 1 optimal weight: 1.9990 chunk 693 optimal weight: 10.0000 chunk 1219 optimal weight: 0.9990 chunk 342 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B4 140 ASN tB 24 ASN tB 130 ASN CD 182 GLN CD 184 ASN ** yE 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UF 25 ASN UF 109 GLN ** xI 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DO 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** RP 68 GLN mS 27 GLN mS 59 HIS vV 292 GLN SZ 46 GLN Ib 157 ASN Wg 54 GLN Hj 191 ASN Tl 112 ASN Tl 131 GLN No 11 GLN kr 76 ASN ** Gu 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** aw 25 HIS aw 120 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.165 162278 Z= 0.220 Angle : 0.574 12.255 237192 Z= 0.303 Chirality : 0.038 0.315 30051 Planarity : 0.004 0.059 17198 Dihedral : 22.404 179.985 66667 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.94 % Favored : 92.99 % Rotamer: Outliers : 4.84 % Allowed : 17.66 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.08), residues: 10628 helix: 1.24 (0.08), residues: 3980 sheet: -0.57 (0.14), residues: 1429 loop : -1.98 (0.08), residues: 5219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPDO 106 HIS 0.009 0.001 HISaw 25 PHE 0.029 0.002 PHEGu 229 TYR 0.019 0.001 TYRrA 91 ARG 0.004 0.000 ARGkr 3 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21256 Ramachandran restraints generated. 10628 Oldfield, 0 Emsley, 10628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21256 Ramachandran restraints generated. 10628 Oldfield, 0 Emsley, 10628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 9273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 773 time to evaluate : 8.763 Fit side-chains REVERT: g2 94 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8681 (mp) REVERT: V5 108 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6825 (mp0) REVERT: O6 100 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7472 (mt-10) REVERT: F8 12 SER cc_start: 0.8912 (m) cc_final: 0.8405 (p) REVERT: v9 426 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.6677 (mm-30) REVERT: v9 431 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8410 (mm) REVERT: v9 434 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8449 (tttp) REVERT: rA 79 ARG cc_start: 0.7966 (ttp-110) cc_final: 0.7676 (ptp-170) REVERT: rA 396 ARG cc_start: 0.6656 (ptp-170) cc_final: 0.6315 (ttp-170) REVERT: rA 464 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.6966 (tt0) REVERT: tB 123 ASP cc_start: 0.8192 (m-30) cc_final: 0.7909 (m-30) REVERT: tB 124 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8375 (ptmm) REVERT: tB 138 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7383 (tt0) REVERT: cC 40 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8188 (mppt) REVERT: cC 71 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7888 (mt0) REVERT: CD 102 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8399 (pt) REVERT: CD 110 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8817 (mp) REVERT: CD 342 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8805 (mp) REVERT: UF 89 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8357 (mt) REVERT: UF 102 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7243 (mm-30) REVERT: eH 111 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7822 (tpm170) REVERT: eH 113 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.7891 (tttp) REVERT: qJ 31 GLU cc_start: 0.7714 (tp30) cc_final: 0.7498 (tp30) REVERT: LL 178 LYS cc_start: 0.8299 (tttp) cc_final: 0.8021 (tttp) REVERT: KM 80 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7239 (mp) REVERT: DO 6 VAL cc_start: 0.8694 (OUTLIER) cc_final: 0.8430 (t) REVERT: DO 307 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8185 (mt0) REVERT: DO 361 HIS cc_start: 0.5865 (OUTLIER) cc_final: 0.5444 (m90) REVERT: MQ 16 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.7884 (pm20) REVERT: pT 87 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7546 (mtp180) REVERT: pT 134 ARG cc_start: 0.8143 (ptp90) cc_final: 0.7485 (ptp90) REVERT: YU 55 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6402 (mm-30) REVERT: vV 374 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7606 (mp) REVERT: SZ 61 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8783 (tp) REVERT: SZ 96 ASP cc_start: 0.7232 (OUTLIER) cc_final: 0.6822 (m-30) REVERT: SZ 128 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7150 (tt0) REVERT: SZ 172 TYR cc_start: 0.9019 (OUTLIER) cc_final: 0.7636 (t80) REVERT: ia 11 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8243 (mt) REVERT: ia 91 ASN cc_start: 0.7883 (m-40) cc_final: 0.7634 (m110) REVERT: Xc 69 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: Xc 141 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.7745 (mp) REVERT: xd 23 ARG cc_start: 0.8003 (mtp85) cc_final: 0.7066 (mmp-170) REVERT: xd 37 GLU cc_start: 0.7870 (pp20) cc_final: 0.7620 (mm-30) REVERT: jh 25 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.7208 (tmm-80) REVERT: Hj 67 ILE cc_start: 0.7833 (tp) cc_final: 0.7467 (mp) REVERT: Hj 98 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8218 (mtt-85) REVERT: Tl 89 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8541 (mt) REVERT: Tl 104 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7141 (mp0) REVERT: Tl 128 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7826 (mp) REVERT: sm 42 LYS cc_start: 0.5305 (ttmt) cc_final: 0.4826 (pttt) REVERT: sm 46 LYS cc_start: 0.6019 (OUTLIER) cc_final: 0.5489 (mttm) REVERT: sm 49 LEU cc_start: 0.7843 (tt) cc_final: 0.7353 (tp) REVERT: sm 62 LYS cc_start: 0.6983 (mtpt) cc_final: 0.6168 (mptt) REVERT: zp 38 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.7716 (mtmt) REVERT: ox 124 LYS cc_start: 0.8559 (ttmt) cc_final: 0.8030 (tmtm) REVERT: Jy 19 LEU cc_start: 0.8177 (mp) cc_final: 0.7905 (mp) REVERT: Jy 59 ILE cc_start: 0.5872 (OUTLIER) cc_final: 0.5534 (pt) REVERT: Jy 84 LEU cc_start: 0.6482 (mt) cc_final: 0.6149 (mt) REVERT: Jy 131 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.7330 (mtm) REVERT: Jy 141 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.6817 (ptm160) REVERT: Ez 88 ILE cc_start: 0.7480 (OUTLIER) cc_final: 0.6802 (tt) outliers start: 315 outliers final: 175 residues processed: 989 average time/residue: 2.0142 time to fit residues: 2973.5865 Evaluate side-chains 965 residues out of total 9273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 747 time to evaluate : 8.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g2 residue 71 THR Chi-restraints excluded: chain g2 residue 94 LEU Chi-restraints excluded: chain g2 residue 104 VAL Chi-restraints excluded: chain g2 residue 105 VAL Chi-restraints excluded: chain b3 residue 26 THR Chi-restraints excluded: chain B4 residue 31 THR Chi-restraints excluded: chain B4 residue 47 GLN Chi-restraints excluded: chain B4 residue 169 ILE Chi-restraints excluded: chain V5 residue 56 ASP Chi-restraints excluded: chain V5 residue 61 THR Chi-restraints excluded: chain V5 residue 74 MET Chi-restraints excluded: chain V5 residue 108 GLU Chi-restraints excluded: chain V5 residue 115 THR Chi-restraints excluded: chain O6 residue 3 VAL Chi-restraints excluded: chain O6 residue 41 LEU Chi-restraints excluded: chain O6 residue 100 GLU Chi-restraints excluded: chain F8 residue 15 VAL Chi-restraints excluded: chain F8 residue 71 VAL Chi-restraints excluded: chain F8 residue 84 VAL Chi-restraints excluded: chain F8 residue 91 VAL Chi-restraints excluded: chain v9 residue 404 LEU Chi-restraints excluded: chain v9 residue 409 VAL Chi-restraints excluded: chain v9 residue 426 GLU Chi-restraints excluded: chain v9 residue 430 ILE Chi-restraints excluded: chain v9 residue 431 LEU Chi-restraints excluded: chain v9 residue 434 LYS Chi-restraints excluded: chain rA residue 11 VAL Chi-restraints excluded: chain rA residue 73 ASP Chi-restraints excluded: chain rA residue 178 VAL Chi-restraints excluded: chain rA residue 201 THR Chi-restraints excluded: chain rA residue 221 THR Chi-restraints excluded: chain rA residue 233 ASN Chi-restraints excluded: chain rA residue 263 THR Chi-restraints excluded: chain rA residue 287 ILE Chi-restraints excluded: chain rA residue 327 ASN Chi-restraints excluded: chain rA residue 328 VAL Chi-restraints excluded: chain rA residue 374 ARG Chi-restraints excluded: chain rA residue 398 LEU Chi-restraints excluded: chain rA residue 464 GLU Chi-restraints excluded: chain rA residue 486 VAL Chi-restraints excluded: chain rA residue 595 ASP Chi-restraints excluded: chain tB residue 9 CYS Chi-restraints excluded: chain tB residue 79 VAL Chi-restraints excluded: chain tB residue 124 LYS Chi-restraints excluded: chain tB residue 130 ASN Chi-restraints excluded: chain tB residue 135 ARG Chi-restraints excluded: chain tB residue 138 GLU Chi-restraints excluded: chain cC residue 40 LYS Chi-restraints excluded: chain cC residue 71 GLN Chi-restraints excluded: chain cC residue 75 ASN Chi-restraints excluded: chain CD residue 85 VAL Chi-restraints excluded: chain CD residue 102 LEU Chi-restraints excluded: chain CD residue 110 LEU Chi-restraints excluded: chain CD residue 114 VAL Chi-restraints excluded: chain CD residue 160 VAL Chi-restraints excluded: chain CD residue 210 GLU Chi-restraints excluded: chain CD residue 242 THR Chi-restraints excluded: chain CD residue 261 MET Chi-restraints excluded: chain CD residue 308 MET Chi-restraints excluded: chain CD residue 342 LEU Chi-restraints excluded: chain CD residue 382 THR Chi-restraints excluded: chain yE residue 3 THR Chi-restraints excluded: chain yE residue 90 ASP Chi-restraints excluded: chain yE residue 92 VAL Chi-restraints excluded: chain yE residue 108 ILE Chi-restraints excluded: chain yE residue 146 ILE Chi-restraints excluded: chain yE residue 164 GLN Chi-restraints excluded: chain yE residue 167 VAL Chi-restraints excluded: chain yE residue 169 ASP Chi-restraints excluded: chain yE residue 209 ASP Chi-restraints excluded: chain UF residue 16 THR Chi-restraints excluded: chain UF residue 38 ILE Chi-restraints excluded: chain UF residue 43 VAL Chi-restraints excluded: chain UF residue 55 THR Chi-restraints excluded: chain UF residue 67 SER Chi-restraints excluded: chain UF residue 89 LEU Chi-restraints excluded: chain UF residue 96 VAL Chi-restraints excluded: chain dG residue 13 THR Chi-restraints excluded: chain dG residue 96 VAL Chi-restraints excluded: chain eH residue 31 ASN Chi-restraints excluded: chain eH residue 111 ARG Chi-restraints excluded: chain eH residue 113 LYS Chi-restraints excluded: chain xI residue 147 SER Chi-restraints excluded: chain xI residue 150 GLU Chi-restraints excluded: chain xI residue 154 LYS Chi-restraints excluded: chain qJ residue 29 GLN Chi-restraints excluded: chain qJ residue 50 ILE Chi-restraints excluded: chain qJ residue 53 VAL Chi-restraints excluded: chain qJ residue 110 LEU Chi-restraints excluded: chain LL residue 58 VAL Chi-restraints excluded: chain LL residue 121 SER Chi-restraints excluded: chain LL residue 124 ILE Chi-restraints excluded: chain LL residue 125 VAL Chi-restraints excluded: chain LL residue 159 VAL Chi-restraints excluded: chain KM residue 80 LEU Chi-restraints excluded: chain DO residue 6 VAL Chi-restraints excluded: chain DO residue 7 THR Chi-restraints excluded: chain DO residue 177 ASP Chi-restraints excluded: chain DO residue 227 THR Chi-restraints excluded: chain DO residue 230 VAL Chi-restraints excluded: chain DO residue 267 VAL Chi-restraints excluded: chain DO residue 307 GLN Chi-restraints excluded: chain DO residue 333 VAL Chi-restraints excluded: chain DO residue 354 VAL Chi-restraints excluded: chain DO residue 361 HIS Chi-restraints excluded: chain RP residue 14 VAL Chi-restraints excluded: chain RP residue 116 ASP Chi-restraints excluded: chain MQ residue 15 VAL Chi-restraints excluded: chain MQ residue 16 GLU Chi-restraints excluded: chain MQ residue 20 VAL Chi-restraints excluded: chain MQ residue 21 VAL Chi-restraints excluded: chain MQ residue 69 THR Chi-restraints excluded: chain MQ residue 90 VAL Chi-restraints excluded: chain MQ residue 130 THR Chi-restraints excluded: chain mS residue 34 SER Chi-restraints excluded: chain pT residue 87 ARG Chi-restraints excluded: chain pT residue 111 THR Chi-restraints excluded: chain pT residue 177 LEU Chi-restraints excluded: chain pT residue 200 CYS Chi-restraints excluded: chain pT residue 211 LEU Chi-restraints excluded: chain pT residue 267 VAL Chi-restraints excluded: chain pT residue 291 ASP Chi-restraints excluded: chain pT residue 327 GLU Chi-restraints excluded: chain pT residue 340 VAL Chi-restraints excluded: chain pT residue 387 VAL Chi-restraints excluded: chain pT residue 402 VAL Chi-restraints excluded: chain pT residue 412 LEU Chi-restraints excluded: chain pT residue 511 ASP Chi-restraints excluded: chain pT residue 514 VAL Chi-restraints excluded: chain pT residue 531 THR Chi-restraints excluded: chain YU residue 55 GLU Chi-restraints excluded: chain YU residue 74 TYR Chi-restraints excluded: chain YU residue 105 VAL Chi-restraints excluded: chain vV residue 155 TRP Chi-restraints excluded: chain vV residue 338 ILE Chi-restraints excluded: chain vV residue 374 ILE Chi-restraints excluded: chain nY residue 8 VAL Chi-restraints excluded: chain nY residue 26 VAL Chi-restraints excluded: chain nY residue 46 THR Chi-restraints excluded: chain nY residue 59 CYS Chi-restraints excluded: chain nY residue 63 THR Chi-restraints excluded: chain nY residue 72 SER Chi-restraints excluded: chain SZ residue 19 VAL Chi-restraints excluded: chain SZ residue 45 LEU Chi-restraints excluded: chain SZ residue 48 LEU Chi-restraints excluded: chain SZ residue 61 ILE Chi-restraints excluded: chain SZ residue 87 THR Chi-restraints excluded: chain SZ residue 96 ASP Chi-restraints excluded: chain SZ residue 128 GLU Chi-restraints excluded: chain SZ residue 160 THR Chi-restraints excluded: chain SZ residue 172 TYR Chi-restraints excluded: chain ia residue 11 LEU Chi-restraints excluded: chain ia residue 35 ASN Chi-restraints excluded: chain ia residue 64 SER Chi-restraints excluded: chain Ib residue 12 VAL Chi-restraints excluded: chain Ib residue 16 VAL Chi-restraints excluded: chain Ib residue 65 VAL Chi-restraints excluded: chain Ib residue 82 VAL Chi-restraints excluded: chain Ib residue 101 VAL Chi-restraints excluded: chain Ib residue 103 ILE Chi-restraints excluded: chain Ib residue 132 VAL Chi-restraints excluded: chain Ib residue 147 SER Chi-restraints excluded: chain Xc residue 25 VAL Chi-restraints excluded: chain Xc residue 69 GLU Chi-restraints excluded: chain Xc residue 70 THR Chi-restraints excluded: chain Xc residue 75 VAL Chi-restraints excluded: chain Xc residue 100 GLU Chi-restraints excluded: chain Xc residue 132 LEU Chi-restraints excluded: chain Xc residue 141 ILE Chi-restraints excluded: chain jh residue 5 THR Chi-restraints excluded: chain jh residue 25 ARG Chi-restraints excluded: chain jh residue 67 LEU Chi-restraints excluded: chain Hj residue 30 THR Chi-restraints excluded: chain Hj residue 98 ARG Chi-restraints excluded: chain Hj residue 132 VAL Chi-restraints excluded: chain Hj residue 164 VAL Chi-restraints excluded: chain Hj residue 203 VAL Chi-restraints excluded: chain Hj residue 217 THR Chi-restraints excluded: chain Qk residue 41 ASP Chi-restraints excluded: chain Qk residue 186 VAL Chi-restraints excluded: chain Tl residue 25 VAL Chi-restraints excluded: chain Tl residue 52 MET Chi-restraints excluded: chain Tl residue 72 VAL Chi-restraints excluded: chain Tl residue 89 LEU Chi-restraints excluded: chain Tl residue 104 GLU Chi-restraints excluded: chain Tl residue 110 LYS Chi-restraints excluded: chain Tl residue 128 LEU Chi-restraints excluded: chain sm residue 46 LYS Chi-restraints excluded: chain sm residue 97 THR Chi-restraints excluded: chain sm residue 102 LEU Chi-restraints excluded: chain No residue 18 VAL Chi-restraints excluded: chain No residue 196 THR Chi-restraints excluded: chain zp residue 38 LYS Chi-restraints excluded: chain zp residue 42 LEU Chi-restraints excluded: chain zp residue 101 THR Chi-restraints excluded: chain Zq residue 23 VAL Chi-restraints excluded: chain Zq residue 46 ILE Chi-restraints excluded: chain kr residue 14 LEU Chi-restraints excluded: chain kr residue 28 ASN Chi-restraints excluded: chain kr residue 41 THR Chi-restraints excluded: chain kr residue 65 LEU Chi-restraints excluded: chain Pv residue 24 VAL Chi-restraints excluded: chain Pv residue 94 LEU Chi-restraints excluded: chain ox residue 19 ASP Chi-restraints excluded: chain ox residue 54 CYS Chi-restraints excluded: chain ox residue 118 SER Chi-restraints excluded: chain Jy residue 18 VAL Chi-restraints excluded: chain Jy residue 34 SER Chi-restraints excluded: chain Jy residue 59 ILE Chi-restraints excluded: chain Jy residue 67 VAL Chi-restraints excluded: chain Jy residue 107 ASP Chi-restraints excluded: chain Jy residue 131 MET Chi-restraints excluded: chain Jy residue 141 ARG Chi-restraints excluded: chain Jy residue 148 VAL Chi-restraints excluded: chain Jy residue 161 SER Chi-restraints excluded: chain Ez residue 88 ILE Chi-restraints excluded: chain Ez residue 93 THR Chi-restraints excluded: chain Ez residue 159 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1406 random chunks: chunk 457 optimal weight: 6.9990 chunk 1223 optimal weight: 4.9990 chunk 268 optimal weight: 5.9990 chunk 797 optimal weight: 10.0000 chunk 335 optimal weight: 30.0000 chunk 1360 optimal weight: 0.4980 chunk 1129 optimal weight: 2.9990 chunk 629 optimal weight: 6.9990 chunk 113 optimal weight: 40.0000 chunk 449 optimal weight: 1.9990 chunk 714 optimal weight: 5.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B4 140 ASN tB 24 ASN ** tB 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** yE 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UF 25 ASN UF 109 GLN xI 201 ASN ** DO 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** RP 68 GLN MQ 27 GLN mS 27 GLN vV 176 GLN vV 292 GLN SZ 46 GLN Ib 49 ASN Ib 157 ASN Wg 54 GLN Hj 191 ASN Tl 103 GLN Tl 112 ASN No 11 GLN kr 76 ASN ** Gu 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** aw 25 HIS aw 120 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.169 162278 Z= 0.237 Angle : 0.583 12.381 237192 Z= 0.307 Chirality : 0.039 0.314 30051 Planarity : 0.004 0.060 17198 Dihedral : 22.388 179.955 66662 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.75 % Favored : 93.19 % Rotamer: Outliers : 4.89 % Allowed : 18.44 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.08), residues: 10628 helix: 1.30 (0.08), residues: 3974 sheet: -0.52 (0.14), residues: 1428 loop : -1.94 (0.08), residues: 5226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPDO 106 HIS 0.008 0.001 HISaw 25 PHE 0.029 0.002 PHEGu 229 TYR 0.020 0.001 TYRNo 4 ARG 0.008 0.000 ARGia 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21256 Ramachandran restraints generated. 10628 Oldfield, 0 Emsley, 10628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21256 Ramachandran restraints generated. 10628 Oldfield, 0 Emsley, 10628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1074 residues out of total 9273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 318 poor density : 756 time to evaluate : 8.958 Fit side-chains REVERT: b3 25 LYS cc_start: 0.7304 (OUTLIER) cc_final: 0.6343 (mttm) REVERT: B4 70 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7617 (ttm170) REVERT: O6 46 GLU cc_start: 0.6482 (OUTLIER) cc_final: 0.6276 (mp0) REVERT: O6 100 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7481 (mt-10) REVERT: F8 12 SER cc_start: 0.8902 (m) cc_final: 0.8392 (p) REVERT: F8 133 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.7110 (tt0) REVERT: v9 426 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.6693 (mm-30) REVERT: v9 431 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8392 (mm) REVERT: v9 434 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8422 (tttp) REVERT: rA 79 ARG cc_start: 0.7976 (ttp-110) cc_final: 0.7686 (ptp-170) REVERT: rA 269 LYS cc_start: 0.7211 (OUTLIER) cc_final: 0.6893 (ttpp) REVERT: rA 396 ARG cc_start: 0.6624 (ptp-170) cc_final: 0.6318 (ttp-170) REVERT: rA 464 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7023 (tt0) REVERT: tB 123 ASP cc_start: 0.8193 (m-30) cc_final: 0.7896 (m-30) REVERT: tB 124 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8426 (ptmm) REVERT: cC 40 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8184 (mppt) REVERT: cC 71 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7901 (mt0) REVERT: CD 102 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8397 (pt) REVERT: CD 244 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7685 (mtp180) REVERT: CD 342 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8823 (mp) REVERT: UF 89 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8352 (mt) REVERT: UF 102 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7251 (mm-30) REVERT: eH 111 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7828 (tpm170) REVERT: eH 113 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.7918 (tttp) REVERT: qJ 31 GLU cc_start: 0.7730 (tp30) cc_final: 0.7507 (tp30) REVERT: qJ 108 LYS cc_start: 0.7549 (tptp) cc_final: 0.7257 (tttm) REVERT: KM 80 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7236 (mp) REVERT: DO 6 VAL cc_start: 0.8714 (OUTLIER) cc_final: 0.8460 (t) REVERT: DO 307 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8189 (mt0) REVERT: DO 361 HIS cc_start: 0.5836 (OUTLIER) cc_final: 0.5410 (m90) REVERT: MQ 16 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.7866 (pm20) REVERT: mS 59 HIS cc_start: 0.7772 (OUTLIER) cc_final: 0.7400 (p90) REVERT: pT 87 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7548 (mtp180) REVERT: pT 134 ARG cc_start: 0.8134 (ptp90) cc_final: 0.7471 (ptp90) REVERT: pT 543 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8058 (mt) REVERT: YU 55 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6396 (mm-30) REVERT: vV 374 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7630 (mp) REVERT: SZ 61 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8774 (tp) REVERT: SZ 96 ASP cc_start: 0.7250 (OUTLIER) cc_final: 0.6843 (m-30) REVERT: SZ 128 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7155 (tt0) REVERT: SZ 172 TYR cc_start: 0.9027 (OUTLIER) cc_final: 0.7641 (t80) REVERT: ia 11 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8232 (mt) REVERT: ia 91 ASN cc_start: 0.7897 (m-40) cc_final: 0.7635 (m110) REVERT: Xc 69 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: Xc 141 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.7799 (mp) REVERT: xd 23 ARG cc_start: 0.8005 (mtp85) cc_final: 0.7084 (mmp-170) REVERT: jh 25 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.7207 (tmm-80) REVERT: li 23 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8139 (mp) REVERT: Hj 67 ILE cc_start: 0.7844 (tp) cc_final: 0.7471 (mp) REVERT: Tl 89 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8544 (mt) REVERT: Tl 104 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7131 (mp0) REVERT: Tl 128 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7832 (mp) REVERT: sm 42 LYS cc_start: 0.5292 (ttmt) cc_final: 0.4802 (pttt) REVERT: sm 46 LYS cc_start: 0.5979 (OUTLIER) cc_final: 0.5446 (mttm) REVERT: sm 49 LEU cc_start: 0.7823 (tt) cc_final: 0.7332 (tp) REVERT: sm 62 LYS cc_start: 0.6973 (mtpt) cc_final: 0.6153 (mptt) REVERT: ox 124 LYS cc_start: 0.8563 (ttmt) cc_final: 0.8039 (tmtm) REVERT: Jy 19 LEU cc_start: 0.8162 (mp) cc_final: 0.7902 (mp) REVERT: Jy 65 ILE cc_start: 0.8879 (mm) cc_final: 0.8560 (mt) REVERT: Jy 84 LEU cc_start: 0.6473 (mt) cc_final: 0.6135 (mt) REVERT: Jy 141 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.6841 (ptm160) REVERT: Ez 35 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7367 (mtm-85) REVERT: Ez 88 ILE cc_start: 0.7477 (OUTLIER) cc_final: 0.6793 (tt) outliers start: 318 outliers final: 191 residues processed: 976 average time/residue: 2.0321 time to fit residues: 2966.4615 Evaluate side-chains 983 residues out of total 9273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 747 time to evaluate : 8.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h1 residue 60 GLU Chi-restraints excluded: chain g2 residue 71 THR Chi-restraints excluded: chain g2 residue 94 LEU Chi-restraints excluded: chain g2 residue 104 VAL Chi-restraints excluded: chain g2 residue 105 VAL Chi-restraints excluded: chain b3 residue 25 LYS Chi-restraints excluded: chain b3 residue 26 THR Chi-restraints excluded: chain B4 residue 31 THR Chi-restraints excluded: chain B4 residue 45 VAL Chi-restraints excluded: chain B4 residue 47 GLN Chi-restraints excluded: chain B4 residue 70 ARG Chi-restraints excluded: chain B4 residue 169 ILE Chi-restraints excluded: chain V5 residue 56 ASP Chi-restraints excluded: chain V5 residue 61 THR Chi-restraints excluded: chain V5 residue 74 MET Chi-restraints excluded: chain V5 residue 115 THR Chi-restraints excluded: chain O6 residue 3 VAL Chi-restraints excluded: chain O6 residue 41 LEU Chi-restraints excluded: chain O6 residue 46 GLU Chi-restraints excluded: chain O6 residue 100 GLU Chi-restraints excluded: chain F8 residue 15 VAL Chi-restraints excluded: chain F8 residue 71 VAL Chi-restraints excluded: chain F8 residue 84 VAL Chi-restraints excluded: chain F8 residue 91 VAL Chi-restraints excluded: chain F8 residue 133 GLU Chi-restraints excluded: chain v9 residue 404 LEU Chi-restraints excluded: chain v9 residue 409 VAL Chi-restraints excluded: chain v9 residue 412 LEU Chi-restraints excluded: chain v9 residue 426 GLU Chi-restraints excluded: chain v9 residue 428 ILE Chi-restraints excluded: chain v9 residue 430 ILE Chi-restraints excluded: chain v9 residue 431 LEU Chi-restraints excluded: chain v9 residue 434 LYS Chi-restraints excluded: chain rA residue 11 VAL Chi-restraints excluded: chain rA residue 73 ASP Chi-restraints excluded: chain rA residue 178 VAL Chi-restraints excluded: chain rA residue 201 THR Chi-restraints excluded: chain rA residue 221 THR Chi-restraints excluded: chain rA residue 233 ASN Chi-restraints excluded: chain rA residue 263 THR Chi-restraints excluded: chain rA residue 269 LYS Chi-restraints excluded: chain rA residue 327 ASN Chi-restraints excluded: chain rA residue 328 VAL Chi-restraints excluded: chain rA residue 374 ARG Chi-restraints excluded: chain rA residue 398 LEU Chi-restraints excluded: chain rA residue 464 GLU Chi-restraints excluded: chain rA residue 486 VAL Chi-restraints excluded: chain rA residue 595 ASP Chi-restraints excluded: chain tB residue 9 CYS Chi-restraints excluded: chain tB residue 32 CYS Chi-restraints excluded: chain tB residue 34 SER Chi-restraints excluded: chain tB residue 79 VAL Chi-restraints excluded: chain tB residue 124 LYS Chi-restraints excluded: chain tB residue 135 ARG Chi-restraints excluded: chain cC residue 40 LYS Chi-restraints excluded: chain cC residue 71 GLN Chi-restraints excluded: chain cC residue 75 ASN Chi-restraints excluded: chain CD residue 56 ILE Chi-restraints excluded: chain CD residue 85 VAL Chi-restraints excluded: chain CD residue 102 LEU Chi-restraints excluded: chain CD residue 114 VAL Chi-restraints excluded: chain CD residue 160 VAL Chi-restraints excluded: chain CD residue 210 GLU Chi-restraints excluded: chain CD residue 242 THR Chi-restraints excluded: chain CD residue 244 ARG Chi-restraints excluded: chain CD residue 261 MET Chi-restraints excluded: chain CD residue 308 MET Chi-restraints excluded: chain CD residue 342 LEU Chi-restraints excluded: chain CD residue 382 THR Chi-restraints excluded: chain yE residue 3 THR Chi-restraints excluded: chain yE residue 90 ASP Chi-restraints excluded: chain yE residue 92 VAL Chi-restraints excluded: chain yE residue 108 ILE Chi-restraints excluded: chain yE residue 146 ILE Chi-restraints excluded: chain yE residue 164 GLN Chi-restraints excluded: chain yE residue 167 VAL Chi-restraints excluded: chain yE residue 169 ASP Chi-restraints excluded: chain yE residue 209 ASP Chi-restraints excluded: chain UF residue 16 THR Chi-restraints excluded: chain UF residue 38 ILE Chi-restraints excluded: chain UF residue 43 VAL Chi-restraints excluded: chain UF residue 55 THR Chi-restraints excluded: chain UF residue 58 GLU Chi-restraints excluded: chain UF residue 67 SER Chi-restraints excluded: chain UF residue 89 LEU Chi-restraints excluded: chain UF residue 96 VAL Chi-restraints excluded: chain dG residue 13 THR Chi-restraints excluded: chain dG residue 96 VAL Chi-restraints excluded: chain eH residue 31 ASN Chi-restraints excluded: chain eH residue 111 ARG Chi-restraints excluded: chain eH residue 113 LYS Chi-restraints excluded: chain xI residue 147 SER Chi-restraints excluded: chain xI residue 150 GLU Chi-restraints excluded: chain xI residue 154 LYS Chi-restraints excluded: chain qJ residue 29 GLN Chi-restraints excluded: chain qJ residue 50 ILE Chi-restraints excluded: chain qJ residue 53 VAL Chi-restraints excluded: chain LL residue 58 VAL Chi-restraints excluded: chain LL residue 63 VAL Chi-restraints excluded: chain LL residue 121 SER Chi-restraints excluded: chain LL residue 124 ILE Chi-restraints excluded: chain LL residue 125 VAL Chi-restraints excluded: chain LL residue 159 VAL Chi-restraints excluded: chain KM residue 80 LEU Chi-restraints excluded: chain DO residue 6 VAL Chi-restraints excluded: chain DO residue 7 THR Chi-restraints excluded: chain DO residue 177 ASP Chi-restraints excluded: chain DO residue 227 THR Chi-restraints excluded: chain DO residue 230 VAL Chi-restraints excluded: chain DO residue 267 VAL Chi-restraints excluded: chain DO residue 307 GLN Chi-restraints excluded: chain DO residue 333 VAL Chi-restraints excluded: chain DO residue 354 VAL Chi-restraints excluded: chain DO residue 361 HIS Chi-restraints excluded: chain RP residue 14 VAL Chi-restraints excluded: chain RP residue 116 ASP Chi-restraints excluded: chain MQ residue 15 VAL Chi-restraints excluded: chain MQ residue 16 GLU Chi-restraints excluded: chain MQ residue 20 VAL Chi-restraints excluded: chain MQ residue 21 VAL Chi-restraints excluded: chain MQ residue 69 THR Chi-restraints excluded: chain MQ residue 90 VAL Chi-restraints excluded: chain MQ residue 130 THR Chi-restraints excluded: chain mS residue 34 SER Chi-restraints excluded: chain mS residue 59 HIS Chi-restraints excluded: chain pT residue 87 ARG Chi-restraints excluded: chain pT residue 111 THR Chi-restraints excluded: chain pT residue 177 LEU Chi-restraints excluded: chain pT residue 200 CYS Chi-restraints excluded: chain pT residue 211 LEU Chi-restraints excluded: chain pT residue 267 VAL Chi-restraints excluded: chain pT residue 291 ASP Chi-restraints excluded: chain pT residue 318 LEU Chi-restraints excluded: chain pT residue 327 GLU Chi-restraints excluded: chain pT residue 340 VAL Chi-restraints excluded: chain pT residue 387 VAL Chi-restraints excluded: chain pT residue 412 LEU Chi-restraints excluded: chain pT residue 511 ASP Chi-restraints excluded: chain pT residue 514 VAL Chi-restraints excluded: chain pT residue 531 THR Chi-restraints excluded: chain pT residue 543 LEU Chi-restraints excluded: chain YU residue 55 GLU Chi-restraints excluded: chain YU residue 74 TYR Chi-restraints excluded: chain YU residue 105 VAL Chi-restraints excluded: chain vV residue 155 TRP Chi-restraints excluded: chain vV residue 245 SER Chi-restraints excluded: chain vV residue 314 GLN Chi-restraints excluded: chain vV residue 338 ILE Chi-restraints excluded: chain vV residue 374 ILE Chi-restraints excluded: chain nY residue 8 VAL Chi-restraints excluded: chain nY residue 26 VAL Chi-restraints excluded: chain nY residue 46 THR Chi-restraints excluded: chain nY residue 59 CYS Chi-restraints excluded: chain nY residue 63 THR Chi-restraints excluded: chain nY residue 72 SER Chi-restraints excluded: chain SZ residue 19 VAL Chi-restraints excluded: chain SZ residue 45 LEU Chi-restraints excluded: chain SZ residue 61 ILE Chi-restraints excluded: chain SZ residue 87 THR Chi-restraints excluded: chain SZ residue 96 ASP Chi-restraints excluded: chain SZ residue 128 GLU Chi-restraints excluded: chain SZ residue 160 THR Chi-restraints excluded: chain SZ residue 172 TYR Chi-restraints excluded: chain ia residue 11 LEU Chi-restraints excluded: chain ia residue 35 ASN Chi-restraints excluded: chain ia residue 64 SER Chi-restraints excluded: chain Ib residue 12 VAL Chi-restraints excluded: chain Ib residue 16 VAL Chi-restraints excluded: chain Ib residue 22 SER Chi-restraints excluded: chain Ib residue 65 VAL Chi-restraints excluded: chain Ib residue 82 VAL Chi-restraints excluded: chain Ib residue 101 VAL Chi-restraints excluded: chain Ib residue 103 ILE Chi-restraints excluded: chain Ib residue 132 VAL Chi-restraints excluded: chain Ib residue 147 SER Chi-restraints excluded: chain Xc residue 25 VAL Chi-restraints excluded: chain Xc residue 69 GLU Chi-restraints excluded: chain Xc residue 70 THR Chi-restraints excluded: chain Xc residue 75 VAL Chi-restraints excluded: chain Xc residue 100 GLU Chi-restraints excluded: chain Xc residue 104 VAL Chi-restraints excluded: chain Xc residue 132 LEU Chi-restraints excluded: chain Xc residue 141 ILE Chi-restraints excluded: chain jh residue 5 THR Chi-restraints excluded: chain jh residue 25 ARG Chi-restraints excluded: chain jh residue 67 LEU Chi-restraints excluded: chain li residue 23 LEU Chi-restraints excluded: chain Hj residue 30 THR Chi-restraints excluded: chain Hj residue 132 VAL Chi-restraints excluded: chain Hj residue 164 VAL Chi-restraints excluded: chain Hj residue 190 VAL Chi-restraints excluded: chain Hj residue 203 VAL Chi-restraints excluded: chain Hj residue 217 THR Chi-restraints excluded: chain Hj residue 218 ILE Chi-restraints excluded: chain Qk residue 41 ASP Chi-restraints excluded: chain Qk residue 186 VAL Chi-restraints excluded: chain Tl residue 25 VAL Chi-restraints excluded: chain Tl residue 27 LEU Chi-restraints excluded: chain Tl residue 52 MET Chi-restraints excluded: chain Tl residue 72 VAL Chi-restraints excluded: chain Tl residue 89 LEU Chi-restraints excluded: chain Tl residue 104 GLU Chi-restraints excluded: chain Tl residue 110 LYS Chi-restraints excluded: chain Tl residue 128 LEU Chi-restraints excluded: chain sm residue 46 LYS Chi-restraints excluded: chain sm residue 97 THR Chi-restraints excluded: chain sm residue 102 LEU Chi-restraints excluded: chain No residue 18 VAL Chi-restraints excluded: chain No residue 196 THR Chi-restraints excluded: chain zp residue 38 LYS Chi-restraints excluded: chain zp residue 42 LEU Chi-restraints excluded: chain zp residue 101 THR Chi-restraints excluded: chain zp residue 103 PHE Chi-restraints excluded: chain Zq residue 23 VAL Chi-restraints excluded: chain Zq residue 46 ILE Chi-restraints excluded: chain kr residue 14 LEU Chi-restraints excluded: chain kr residue 28 ASN Chi-restraints excluded: chain kr residue 41 THR Chi-restraints excluded: chain kr residue 65 LEU Chi-restraints excluded: chain Pv residue 24 VAL Chi-restraints excluded: chain Pv residue 94 LEU Chi-restraints excluded: chain Pv residue 148 LEU Chi-restraints excluded: chain ox residue 19 ASP Chi-restraints excluded: chain ox residue 54 CYS Chi-restraints excluded: chain ox residue 118 SER Chi-restraints excluded: chain Jy residue 18 VAL Chi-restraints excluded: chain Jy residue 67 VAL Chi-restraints excluded: chain Jy residue 107 ASP Chi-restraints excluded: chain Jy residue 141 ARG Chi-restraints excluded: chain Jy residue 148 VAL Chi-restraints excluded: chain Jy residue 161 SER Chi-restraints excluded: chain Ez residue 35 ARG Chi-restraints excluded: chain Ez residue 68 THR Chi-restraints excluded: chain Ez residue 88 ILE Chi-restraints excluded: chain Ez residue 93 THR Chi-restraints excluded: chain Ez residue 159 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1406 random chunks: chunk 1311 optimal weight: 0.8980 chunk 153 optimal weight: 20.0000 chunk 775 optimal weight: 10.0000 chunk 993 optimal weight: 10.0000 chunk 769 optimal weight: 20.0000 chunk 1145 optimal weight: 7.9990 chunk 759 optimal weight: 10.0000 chunk 1355 optimal weight: 0.0370 chunk 848 optimal weight: 10.0000 chunk 826 optimal weight: 8.9990 chunk 625 optimal weight: 20.0000 overall best weight: 5.5866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B4 140 ASN V5 98 ASN tB 24 ASN tB 130 ASN yE 50 HIS ** yE 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UF 25 ASN UF 109 GLN ** DO 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** RP 68 GLN MQ 27 GLN mS 22 GLN mS 27 GLN ** pT 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** vV 176 GLN vV 292 GLN Ib 157 ASN Wg 54 GLN Hj 191 ASN Tl 103 GLN Tl 112 ASN No 11 GLN kr 76 ASN ** Gu 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** aw 25 HIS aw 120 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.196 162278 Z= 0.375 Angle : 0.682 14.528 237192 Z= 0.355 Chirality : 0.044 0.318 30051 Planarity : 0.005 0.097 17198 Dihedral : 22.485 179.985 66662 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.62 % Favored : 92.29 % Rotamer: Outliers : 5.13 % Allowed : 18.70 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.08), residues: 10628 helix: 1.05 (0.08), residues: 3973 sheet: -0.59 (0.14), residues: 1432 loop : -2.01 (0.08), residues: 5223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPjh 49 HIS 0.010 0.001 HISDO 311 PHE 0.040 0.002 PHEtB 31 TYR 0.021 0.002 TYRNo 4 ARG 0.006 0.001 ARGtB 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21256 Ramachandran restraints generated. 10628 Oldfield, 0 Emsley, 10628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21256 Ramachandran restraints generated. 10628 Oldfield, 0 Emsley, 10628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1082 residues out of total 9273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 334 poor density : 748 time to evaluate : 12.330 Fit side-chains REVERT: b3 25 LYS cc_start: 0.7313 (OUTLIER) cc_final: 0.6320 (mttm) REVERT: B4 70 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7580 (ttm170) REVERT: O6 46 GLU cc_start: 0.6624 (OUTLIER) cc_final: 0.6411 (mp0) REVERT: O6 84 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8237 (mt) REVERT: F8 12 SER cc_start: 0.8918 (m) cc_final: 0.8398 (p) REVERT: F8 133 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7183 (tt0) REVERT: v9 426 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.6807 (mm-30) REVERT: v9 431 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8414 (mm) REVERT: v9 434 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8476 (tttp) REVERT: rA 79 ARG cc_start: 0.8017 (ttp-110) cc_final: 0.7710 (ptp-170) REVERT: rA 269 LYS cc_start: 0.7260 (OUTLIER) cc_final: 0.7027 (ttpp) REVERT: rA 358 LEU cc_start: 0.6779 (OUTLIER) cc_final: 0.6426 (tm) REVERT: rA 396 ARG cc_start: 0.6664 (ptp-170) cc_final: 0.6401 (ttp-170) REVERT: rA 464 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7009 (tt0) REVERT: rA 535 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8047 (mpt) REVERT: tB 63 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8294 (tp) REVERT: tB 123 ASP cc_start: 0.8228 (m-30) cc_final: 0.7947 (m-30) REVERT: cC 40 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8194 (mppt) REVERT: CD 102 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8435 (pt) REVERT: CD 335 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8784 (tp) REVERT: CD 342 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8850 (mp) REVERT: UF 89 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8439 (mt) REVERT: UF 102 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7328 (mm-30) REVERT: dG 47 ASP cc_start: 0.7526 (OUTLIER) cc_final: 0.7207 (m-30) REVERT: eH 19 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8269 (ttp-170) REVERT: eH 113 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.7991 (tttp) REVERT: xI 153 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7550 (tptm) REVERT: qJ 108 LYS cc_start: 0.7601 (tptp) cc_final: 0.7327 (tttm) REVERT: LL 20 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7112 (mt-10) REVERT: KM 80 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7242 (mp) REVERT: DO 6 VAL cc_start: 0.8752 (OUTLIER) cc_final: 0.8542 (t) REVERT: DO 194 TYR cc_start: 0.8310 (OUTLIER) cc_final: 0.7102 (m-10) REVERT: DO 307 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8236 (mt0) REVERT: DO 361 HIS cc_start: 0.5920 (OUTLIER) cc_final: 0.5461 (m90) REVERT: MQ 16 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.7942 (pm20) REVERT: mS 59 HIS cc_start: 0.7799 (OUTLIER) cc_final: 0.7447 (p90) REVERT: pT 87 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7634 (mtp180) REVERT: pT 134 ARG cc_start: 0.8180 (ptp90) cc_final: 0.7513 (ptp90) REVERT: YU 55 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6461 (mm-30) REVERT: vV 374 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7684 (mp) REVERT: SZ 61 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8808 (tp) REVERT: SZ 96 ASP cc_start: 0.7306 (OUTLIER) cc_final: 0.6887 (m-30) REVERT: SZ 128 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7165 (tt0) REVERT: SZ 172 TYR cc_start: 0.9044 (OUTLIER) cc_final: 0.7803 (t80) REVERT: ia 11 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8269 (mt) REVERT: ia 91 ASN cc_start: 0.7943 (m-40) cc_final: 0.7705 (m110) REVERT: Xc 141 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.7821 (mp) REVERT: xd 13 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.6872 (mm110) REVERT: xd 23 ARG cc_start: 0.8015 (mtp85) cc_final: 0.7123 (mmp-170) REVERT: jh 25 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.7706 (tmm-80) REVERT: li 23 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8164 (mp) REVERT: Hj 67 ILE cc_start: 0.7996 (tp) cc_final: 0.7621 (mp) REVERT: Tl 89 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8627 (mt) REVERT: Tl 104 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: Tl 128 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7896 (mp) REVERT: sm 42 LYS cc_start: 0.5291 (OUTLIER) cc_final: 0.4756 (pttt) REVERT: sm 46 LYS cc_start: 0.6098 (OUTLIER) cc_final: 0.5506 (mttm) REVERT: sm 49 LEU cc_start: 0.7766 (tt) cc_final: 0.7287 (tp) REVERT: sm 62 LYS cc_start: 0.6969 (mtpt) cc_final: 0.6161 (mptt) REVERT: Pv 13 LYS cc_start: 0.8399 (mtmm) cc_final: 0.8058 (mtpt) REVERT: ox 124 LYS cc_start: 0.8565 (ttmt) cc_final: 0.8061 (tmtm) REVERT: Jy 19 LEU cc_start: 0.8244 (mp) cc_final: 0.7840 (mp) REVERT: Jy 65 ILE cc_start: 0.8819 (mm) cc_final: 0.8578 (mt) REVERT: Jy 84 LEU cc_start: 0.6464 (mt) cc_final: 0.6158 (mt) REVERT: Jy 141 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.6909 (ptm160) REVERT: Ez 35 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7365 (mtm-85) outliers start: 334 outliers final: 206 residues processed: 980 average time/residue: 2.0050 time to fit residues: 2963.1925 Evaluate side-chains 995 residues out of total 9273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 740 time to evaluate : 8.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h1 residue 30 GLU Chi-restraints excluded: chain h1 residue 60 GLU Chi-restraints excluded: chain g2 residue 71 THR Chi-restraints excluded: chain g2 residue 94 LEU Chi-restraints excluded: chain g2 residue 104 VAL Chi-restraints excluded: chain g2 residue 105 VAL Chi-restraints excluded: chain b3 residue 25 LYS Chi-restraints excluded: chain b3 residue 26 THR Chi-restraints excluded: chain B4 residue 31 THR Chi-restraints excluded: chain B4 residue 45 VAL Chi-restraints excluded: chain B4 residue 47 GLN Chi-restraints excluded: chain B4 residue 70 ARG Chi-restraints excluded: chain B4 residue 169 ILE Chi-restraints excluded: chain V5 residue 56 ASP Chi-restraints excluded: chain V5 residue 61 THR Chi-restraints excluded: chain V5 residue 74 MET Chi-restraints excluded: chain V5 residue 115 THR Chi-restraints excluded: chain O6 residue 3 VAL Chi-restraints excluded: chain O6 residue 41 LEU Chi-restraints excluded: chain O6 residue 46 GLU Chi-restraints excluded: chain O6 residue 84 LEU Chi-restraints excluded: chain F8 residue 15 VAL Chi-restraints excluded: chain F8 residue 71 VAL Chi-restraints excluded: chain F8 residue 84 VAL Chi-restraints excluded: chain F8 residue 91 VAL Chi-restraints excluded: chain F8 residue 133 GLU Chi-restraints excluded: chain v9 residue 404 LEU Chi-restraints excluded: chain v9 residue 409 VAL Chi-restraints excluded: chain v9 residue 412 LEU Chi-restraints excluded: chain v9 residue 426 GLU Chi-restraints excluded: chain v9 residue 428 ILE Chi-restraints excluded: chain v9 residue 430 ILE Chi-restraints excluded: chain v9 residue 431 LEU Chi-restraints excluded: chain v9 residue 434 LYS Chi-restraints excluded: chain rA residue 11 VAL Chi-restraints excluded: chain rA residue 73 ASP Chi-restraints excluded: chain rA residue 74 VAL Chi-restraints excluded: chain rA residue 178 VAL Chi-restraints excluded: chain rA residue 201 THR Chi-restraints excluded: chain rA residue 221 THR Chi-restraints excluded: chain rA residue 233 ASN Chi-restraints excluded: chain rA residue 263 THR Chi-restraints excluded: chain rA residue 269 LYS Chi-restraints excluded: chain rA residue 327 ASN Chi-restraints excluded: chain rA residue 328 VAL Chi-restraints excluded: chain rA residue 358 LEU Chi-restraints excluded: chain rA residue 374 ARG Chi-restraints excluded: chain rA residue 398 LEU Chi-restraints excluded: chain rA residue 464 GLU Chi-restraints excluded: chain rA residue 486 VAL Chi-restraints excluded: chain rA residue 512 SER Chi-restraints excluded: chain rA residue 535 MET Chi-restraints excluded: chain rA residue 595 ASP Chi-restraints excluded: chain tB residue 9 CYS Chi-restraints excluded: chain tB residue 32 CYS Chi-restraints excluded: chain tB residue 34 SER Chi-restraints excluded: chain tB residue 63 LEU Chi-restraints excluded: chain tB residue 79 VAL Chi-restraints excluded: chain tB residue 135 ARG Chi-restraints excluded: chain cC residue 40 LYS Chi-restraints excluded: chain cC residue 75 ASN Chi-restraints excluded: chain CD residue 56 ILE Chi-restraints excluded: chain CD residue 85 VAL Chi-restraints excluded: chain CD residue 102 LEU Chi-restraints excluded: chain CD residue 114 VAL Chi-restraints excluded: chain CD residue 160 VAL Chi-restraints excluded: chain CD residue 210 GLU Chi-restraints excluded: chain CD residue 242 THR Chi-restraints excluded: chain CD residue 261 MET Chi-restraints excluded: chain CD residue 335 ILE Chi-restraints excluded: chain CD residue 342 LEU Chi-restraints excluded: chain CD residue 382 THR Chi-restraints excluded: chain yE residue 3 THR Chi-restraints excluded: chain yE residue 90 ASP Chi-restraints excluded: chain yE residue 92 VAL Chi-restraints excluded: chain yE residue 108 ILE Chi-restraints excluded: chain yE residue 146 ILE Chi-restraints excluded: chain yE residue 164 GLN Chi-restraints excluded: chain yE residue 167 VAL Chi-restraints excluded: chain yE residue 169 ASP Chi-restraints excluded: chain yE residue 209 ASP Chi-restraints excluded: chain UF residue 16 THR Chi-restraints excluded: chain UF residue 38 ILE Chi-restraints excluded: chain UF residue 43 VAL Chi-restraints excluded: chain UF residue 55 THR Chi-restraints excluded: chain UF residue 58 GLU Chi-restraints excluded: chain UF residue 67 SER Chi-restraints excluded: chain UF residue 89 LEU Chi-restraints excluded: chain UF residue 96 VAL Chi-restraints excluded: chain dG residue 13 THR Chi-restraints excluded: chain dG residue 47 ASP Chi-restraints excluded: chain dG residue 96 VAL Chi-restraints excluded: chain eH residue 19 ARG Chi-restraints excluded: chain eH residue 31 ASN Chi-restraints excluded: chain eH residue 111 ARG Chi-restraints excluded: chain eH residue 113 LYS Chi-restraints excluded: chain xI residue 120 THR Chi-restraints excluded: chain xI residue 147 SER Chi-restraints excluded: chain xI residue 150 GLU Chi-restraints excluded: chain xI residue 153 LYS Chi-restraints excluded: chain xI residue 154 LYS Chi-restraints excluded: chain qJ residue 50 ILE Chi-restraints excluded: chain qJ residue 53 VAL Chi-restraints excluded: chain LL residue 20 GLU Chi-restraints excluded: chain LL residue 58 VAL Chi-restraints excluded: chain LL residue 63 VAL Chi-restraints excluded: chain LL residue 121 SER Chi-restraints excluded: chain LL residue 123 ILE Chi-restraints excluded: chain LL residue 124 ILE Chi-restraints excluded: chain LL residue 125 VAL Chi-restraints excluded: chain LL residue 159 VAL Chi-restraints excluded: chain KM residue 80 LEU Chi-restraints excluded: chain DO residue 6 VAL Chi-restraints excluded: chain DO residue 7 THR Chi-restraints excluded: chain DO residue 177 ASP Chi-restraints excluded: chain DO residue 194 TYR Chi-restraints excluded: chain DO residue 227 THR Chi-restraints excluded: chain DO residue 230 VAL Chi-restraints excluded: chain DO residue 267 VAL Chi-restraints excluded: chain DO residue 292 SER Chi-restraints excluded: chain DO residue 307 GLN Chi-restraints excluded: chain DO residue 333 VAL Chi-restraints excluded: chain DO residue 354 VAL Chi-restraints excluded: chain DO residue 359 LEU Chi-restraints excluded: chain DO residue 361 HIS Chi-restraints excluded: chain RP residue 14 VAL Chi-restraints excluded: chain MQ residue 15 VAL Chi-restraints excluded: chain MQ residue 16 GLU Chi-restraints excluded: chain MQ residue 20 VAL Chi-restraints excluded: chain MQ residue 21 VAL Chi-restraints excluded: chain MQ residue 69 THR Chi-restraints excluded: chain MQ residue 90 VAL Chi-restraints excluded: chain MQ residue 130 THR Chi-restraints excluded: chain mS residue 34 SER Chi-restraints excluded: chain mS residue 59 HIS Chi-restraints excluded: chain pT residue 48 ASP Chi-restraints excluded: chain pT residue 87 ARG Chi-restraints excluded: chain pT residue 111 THR Chi-restraints excluded: chain pT residue 177 LEU Chi-restraints excluded: chain pT residue 200 CYS Chi-restraints excluded: chain pT residue 211 LEU Chi-restraints excluded: chain pT residue 267 VAL Chi-restraints excluded: chain pT residue 327 GLU Chi-restraints excluded: chain pT residue 340 VAL Chi-restraints excluded: chain pT residue 387 VAL Chi-restraints excluded: chain pT residue 412 LEU Chi-restraints excluded: chain pT residue 450 LYS Chi-restraints excluded: chain pT residue 511 ASP Chi-restraints excluded: chain pT residue 514 VAL Chi-restraints excluded: chain pT residue 531 THR Chi-restraints excluded: chain pT residue 543 LEU Chi-restraints excluded: chain YU residue 55 GLU Chi-restraints excluded: chain YU residue 74 TYR Chi-restraints excluded: chain YU residue 105 VAL Chi-restraints excluded: chain vV residue 155 TRP Chi-restraints excluded: chain vV residue 214 LEU Chi-restraints excluded: chain vV residue 245 SER Chi-restraints excluded: chain vV residue 314 GLN Chi-restraints excluded: chain vV residue 338 ILE Chi-restraints excluded: chain vV residue 374 ILE Chi-restraints excluded: chain nY residue 8 VAL Chi-restraints excluded: chain nY residue 26 VAL Chi-restraints excluded: chain nY residue 46 THR Chi-restraints excluded: chain nY residue 59 CYS Chi-restraints excluded: chain nY residue 63 THR Chi-restraints excluded: chain nY residue 72 SER Chi-restraints excluded: chain SZ residue 19 VAL Chi-restraints excluded: chain SZ residue 45 LEU Chi-restraints excluded: chain SZ residue 48 LEU Chi-restraints excluded: chain SZ residue 61 ILE Chi-restraints excluded: chain SZ residue 87 THR Chi-restraints excluded: chain SZ residue 96 ASP Chi-restraints excluded: chain SZ residue 128 GLU Chi-restraints excluded: chain SZ residue 157 GLN Chi-restraints excluded: chain SZ residue 160 THR Chi-restraints excluded: chain SZ residue 172 TYR Chi-restraints excluded: chain ia residue 11 LEU Chi-restraints excluded: chain ia residue 35 ASN Chi-restraints excluded: chain ia residue 64 SER Chi-restraints excluded: chain ia residue 72 VAL Chi-restraints excluded: chain Ib residue 12 VAL Chi-restraints excluded: chain Ib residue 16 VAL Chi-restraints excluded: chain Ib residue 22 SER Chi-restraints excluded: chain Ib residue 65 VAL Chi-restraints excluded: chain Ib residue 101 VAL Chi-restraints excluded: chain Ib residue 103 ILE Chi-restraints excluded: chain Ib residue 132 VAL Chi-restraints excluded: chain Ib residue 147 SER Chi-restraints excluded: chain Xc residue 25 VAL Chi-restraints excluded: chain Xc residue 70 THR Chi-restraints excluded: chain Xc residue 75 VAL Chi-restraints excluded: chain Xc residue 100 GLU Chi-restraints excluded: chain Xc residue 104 VAL Chi-restraints excluded: chain Xc residue 132 LEU Chi-restraints excluded: chain Xc residue 141 ILE Chi-restraints excluded: chain xd residue 13 GLN Chi-restraints excluded: chain jh residue 5 THR Chi-restraints excluded: chain jh residue 25 ARG Chi-restraints excluded: chain jh residue 29 VAL Chi-restraints excluded: chain jh residue 67 LEU Chi-restraints excluded: chain li residue 23 LEU Chi-restraints excluded: chain Hj residue 30 THR Chi-restraints excluded: chain Hj residue 132 VAL Chi-restraints excluded: chain Hj residue 164 VAL Chi-restraints excluded: chain Hj residue 190 VAL Chi-restraints excluded: chain Hj residue 203 VAL Chi-restraints excluded: chain Hj residue 217 THR Chi-restraints excluded: chain Hj residue 218 ILE Chi-restraints excluded: chain Qk residue 41 ASP Chi-restraints excluded: chain Qk residue 186 VAL Chi-restraints excluded: chain Tl residue 25 VAL Chi-restraints excluded: chain Tl residue 52 MET Chi-restraints excluded: chain Tl residue 72 VAL Chi-restraints excluded: chain Tl residue 89 LEU Chi-restraints excluded: chain Tl residue 104 GLU Chi-restraints excluded: chain Tl residue 110 LYS Chi-restraints excluded: chain Tl residue 128 LEU Chi-restraints excluded: chain sm residue 42 LYS Chi-restraints excluded: chain sm residue 46 LYS Chi-restraints excluded: chain sm residue 97 THR Chi-restraints excluded: chain sm residue 102 LEU Chi-restraints excluded: chain No residue 18 VAL Chi-restraints excluded: chain No residue 19 LEU Chi-restraints excluded: chain No residue 196 THR Chi-restraints excluded: chain zp residue 9 SER Chi-restraints excluded: chain zp residue 38 LYS Chi-restraints excluded: chain zp residue 42 LEU Chi-restraints excluded: chain zp residue 101 THR Chi-restraints excluded: chain Zq residue 23 VAL Chi-restraints excluded: chain Zq residue 46 ILE Chi-restraints excluded: chain Zq residue 60 LYS Chi-restraints excluded: chain kr residue 14 LEU Chi-restraints excluded: chain kr residue 28 ASN Chi-restraints excluded: chain kr residue 41 THR Chi-restraints excluded: chain kr residue 48 SER Chi-restraints excluded: chain kr residue 65 LEU Chi-restraints excluded: chain Pv residue 24 VAL Chi-restraints excluded: chain Pv residue 94 LEU Chi-restraints excluded: chain Pv residue 110 THR Chi-restraints excluded: chain Pv residue 148 LEU Chi-restraints excluded: chain Pv residue 154 GLU Chi-restraints excluded: chain ox residue 19 ASP Chi-restraints excluded: chain ox residue 54 CYS Chi-restraints excluded: chain ox residue 118 SER Chi-restraints excluded: chain Jy residue 18 VAL Chi-restraints excluded: chain Jy residue 34 SER Chi-restraints excluded: chain Jy residue 67 VAL Chi-restraints excluded: chain Jy residue 107 ASP Chi-restraints excluded: chain Jy residue 141 ARG Chi-restraints excluded: chain Jy residue 148 VAL Chi-restraints excluded: chain Jy residue 161 SER Chi-restraints excluded: chain Ez residue 35 ARG Chi-restraints excluded: chain Ez residue 68 THR Chi-restraints excluded: chain Ez residue 93 THR Chi-restraints excluded: chain Ez residue 159 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1406 random chunks: chunk 838 optimal weight: 10.0000 chunk 541 optimal weight: 4.9990 chunk 809 optimal weight: 8.9990 chunk 408 optimal weight: 9.9990 chunk 266 optimal weight: 0.8980 chunk 262 optimal weight: 4.9990 chunk 861 optimal weight: 10.0000 chunk 923 optimal weight: 5.9990 chunk 670 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 chunk 1065 optimal weight: 10.0000 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B4 140 ASN tB 24 ASN yE 50 HIS ** yE 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UF 25 ASN UF 109 GLN ** DO 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** RP 68 GLN MQ 27 GLN mS 22 GLN mS 27 GLN pT 26 ASN ** pT 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** vV 176 GLN vV 292 GLN Ib 49 ASN Ib 157 ASN Wg 54 GLN Hj 77 GLN Hj 191 ASN Tl 112 ASN No 11 GLN No 158 HIS ** Gu 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** aw 25 HIS aw 120 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.176 162278 Z= 0.254 Angle : 0.601 12.880 237192 Z= 0.316 Chirality : 0.040 0.326 30051 Planarity : 0.004 0.063 17198 Dihedral : 22.420 179.889 66662 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.76 % Favored : 93.18 % Rotamer: Outliers : 4.50 % Allowed : 19.64 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.08), residues: 10628 helix: 1.23 (0.08), residues: 3972 sheet: -0.51 (0.14), residues: 1428 loop : -1.94 (0.08), residues: 5228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPDO 106 HIS 0.008 0.001 HISrA 272 PHE 0.031 0.002 PHEtB 31 TYR 0.023 0.002 TYRNo 4 ARG 0.005 0.000 ARGJy 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21256 Ramachandran restraints generated. 10628 Oldfield, 0 Emsley, 10628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21256 Ramachandran restraints generated. 10628 Oldfield, 0 Emsley, 10628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1039 residues out of total 9273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 293 poor density : 746 time to evaluate : 8.648 Fit side-chains revert: symmetry clash REVERT: b3 25 LYS cc_start: 0.7305 (OUTLIER) cc_final: 0.6314 (mttm) REVERT: B4 70 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7621 (ttm170) REVERT: O6 46 GLU cc_start: 0.6530 (OUTLIER) cc_final: 0.6324 (mp0) REVERT: f7 31 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8180 (ttpt) REVERT: F8 12 SER cc_start: 0.8905 (m) cc_final: 0.8387 (p) REVERT: v9 426 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.6742 (mm-30) REVERT: v9 434 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8422 (tttp) REVERT: rA 79 ARG cc_start: 0.7978 (ttp-110) cc_final: 0.7469 (ptp-110) REVERT: rA 269 LYS cc_start: 0.7227 (OUTLIER) cc_final: 0.6928 (ttpp) REVERT: rA 358 LEU cc_start: 0.6702 (OUTLIER) cc_final: 0.6350 (tm) REVERT: rA 396 ARG cc_start: 0.6610 (ptp-170) cc_final: 0.6366 (ttp-170) REVERT: rA 464 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7006 (tt0) REVERT: rA 535 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8158 (mpt) REVERT: tB 123 ASP cc_start: 0.8204 (m-30) cc_final: 0.7899 (m-30) REVERT: tB 138 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7302 (tt0) REVERT: cC 40 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8174 (mppt) REVERT: CD 102 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8413 (pt) REVERT: CD 335 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8747 (tp) REVERT: CD 342 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8831 (mp) REVERT: UF 89 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8415 (mt) REVERT: UF 102 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7275 (mm-30) REVERT: eH 113 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.7944 (tttp) REVERT: xI 117 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8488 (mp) REVERT: xI 153 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7537 (tptm) REVERT: LL 180 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.6794 (ttm170) REVERT: KM 80 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7237 (mp) REVERT: DO 307 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8193 (mt0) REVERT: DO 361 HIS cc_start: 0.5873 (OUTLIER) cc_final: 0.5410 (m90) REVERT: MQ 16 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.7907 (pm20) REVERT: mS 59 HIS cc_start: 0.7794 (OUTLIER) cc_final: 0.7435 (p90) REVERT: pT 87 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7505 (mtp180) REVERT: pT 134 ARG cc_start: 0.8158 (ptp90) cc_final: 0.7760 (ptp90) REVERT: pT 543 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8085 (mt) REVERT: YU 55 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6399 (mm-30) REVERT: vV 374 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7660 (mp) REVERT: SZ 61 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8788 (tp) REVERT: SZ 96 ASP cc_start: 0.7237 (OUTLIER) cc_final: 0.6820 (m-30) REVERT: SZ 104 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7614 (tt0) REVERT: SZ 128 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7139 (tt0) REVERT: SZ 172 TYR cc_start: 0.9031 (OUTLIER) cc_final: 0.7644 (t80) REVERT: ia 11 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8251 (mt) REVERT: ia 91 ASN cc_start: 0.7895 (m-40) cc_final: 0.7654 (m110) REVERT: Xc 141 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.7931 (mp) REVERT: xd 13 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.6876 (mm110) REVERT: xd 23 ARG cc_start: 0.8014 (mtp85) cc_final: 0.7097 (mmp-170) REVERT: xd 37 GLU cc_start: 0.7942 (pp20) cc_final: 0.7664 (mm-30) REVERT: jh 25 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.7366 (tmm-80) REVERT: li 23 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8137 (mp) REVERT: Hj 67 ILE cc_start: 0.7860 (tp) cc_final: 0.7482 (mp) REVERT: Tl 89 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8578 (mt) REVERT: Tl 104 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: Tl 128 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7837 (mp) REVERT: sm 42 LYS cc_start: 0.5253 (ttmt) cc_final: 0.4735 (pttt) REVERT: sm 46 LYS cc_start: 0.6115 (OUTLIER) cc_final: 0.5571 (mttm) REVERT: sm 49 LEU cc_start: 0.7767 (tt) cc_final: 0.7285 (tp) REVERT: sm 62 LYS cc_start: 0.6934 (mtpt) cc_final: 0.6122 (mptt) REVERT: Pv 13 LYS cc_start: 0.8313 (mtmm) cc_final: 0.8029 (mtpt) REVERT: ox 28 LYS cc_start: 0.6386 (tptt) cc_final: 0.6163 (tptt) REVERT: Jy 19 LEU cc_start: 0.8171 (mp) cc_final: 0.7800 (mp) REVERT: Jy 65 ILE cc_start: 0.8811 (mm) cc_final: 0.8562 (mt) REVERT: Jy 84 LEU cc_start: 0.6457 (mt) cc_final: 0.6137 (mt) REVERT: Jy 141 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.6893 (ptm160) REVERT: Ez 35 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7406 (mtm-85) outliers start: 293 outliers final: 202 residues processed: 958 average time/residue: 2.0198 time to fit residues: 2887.6314 Evaluate side-chains 982 residues out of total 9273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 735 time to evaluate : 7.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h1 residue 30 GLU Chi-restraints excluded: chain h1 residue 60 GLU Chi-restraints excluded: chain g2 residue 71 THR Chi-restraints excluded: chain g2 residue 94 LEU Chi-restraints excluded: chain g2 residue 104 VAL Chi-restraints excluded: chain g2 residue 105 VAL Chi-restraints excluded: chain b3 residue 25 LYS Chi-restraints excluded: chain b3 residue 26 THR Chi-restraints excluded: chain B4 residue 31 THR Chi-restraints excluded: chain B4 residue 45 VAL Chi-restraints excluded: chain B4 residue 47 GLN Chi-restraints excluded: chain B4 residue 70 ARG Chi-restraints excluded: chain B4 residue 169 ILE Chi-restraints excluded: chain V5 residue 56 ASP Chi-restraints excluded: chain V5 residue 61 THR Chi-restraints excluded: chain V5 residue 74 MET Chi-restraints excluded: chain V5 residue 115 THR Chi-restraints excluded: chain O6 residue 3 VAL Chi-restraints excluded: chain O6 residue 41 LEU Chi-restraints excluded: chain O6 residue 46 GLU Chi-restraints excluded: chain f7 residue 31 LYS Chi-restraints excluded: chain F8 residue 15 VAL Chi-restraints excluded: chain F8 residue 71 VAL Chi-restraints excluded: chain F8 residue 84 VAL Chi-restraints excluded: chain F8 residue 91 VAL Chi-restraints excluded: chain v9 residue 404 LEU Chi-restraints excluded: chain v9 residue 409 VAL Chi-restraints excluded: chain v9 residue 412 LEU Chi-restraints excluded: chain v9 residue 426 GLU Chi-restraints excluded: chain v9 residue 428 ILE Chi-restraints excluded: chain v9 residue 430 ILE Chi-restraints excluded: chain v9 residue 431 LEU Chi-restraints excluded: chain v9 residue 434 LYS Chi-restraints excluded: chain rA residue 11 VAL Chi-restraints excluded: chain rA residue 73 ASP Chi-restraints excluded: chain rA residue 74 VAL Chi-restraints excluded: chain rA residue 178 VAL Chi-restraints excluded: chain rA residue 201 THR Chi-restraints excluded: chain rA residue 221 THR Chi-restraints excluded: chain rA residue 233 ASN Chi-restraints excluded: chain rA residue 263 THR Chi-restraints excluded: chain rA residue 269 LYS Chi-restraints excluded: chain rA residue 327 ASN Chi-restraints excluded: chain rA residue 328 VAL Chi-restraints excluded: chain rA residue 358 LEU Chi-restraints excluded: chain rA residue 374 ARG Chi-restraints excluded: chain rA residue 398 LEU Chi-restraints excluded: chain rA residue 464 GLU Chi-restraints excluded: chain rA residue 486 VAL Chi-restraints excluded: chain rA residue 535 MET Chi-restraints excluded: chain rA residue 595 ASP Chi-restraints excluded: chain tB residue 9 CYS Chi-restraints excluded: chain tB residue 32 CYS Chi-restraints excluded: chain tB residue 34 SER Chi-restraints excluded: chain tB residue 79 VAL Chi-restraints excluded: chain tB residue 135 ARG Chi-restraints excluded: chain tB residue 138 GLU Chi-restraints excluded: chain cC residue 40 LYS Chi-restraints excluded: chain cC residue 75 ASN Chi-restraints excluded: chain CD residue 56 ILE Chi-restraints excluded: chain CD residue 85 VAL Chi-restraints excluded: chain CD residue 102 LEU Chi-restraints excluded: chain CD residue 114 VAL Chi-restraints excluded: chain CD residue 160 VAL Chi-restraints excluded: chain CD residue 210 GLU Chi-restraints excluded: chain CD residue 242 THR Chi-restraints excluded: chain CD residue 261 MET Chi-restraints excluded: chain CD residue 335 ILE Chi-restraints excluded: chain CD residue 342 LEU Chi-restraints excluded: chain CD residue 382 THR Chi-restraints excluded: chain yE residue 3 THR Chi-restraints excluded: chain yE residue 90 ASP Chi-restraints excluded: chain yE residue 92 VAL Chi-restraints excluded: chain yE residue 108 ILE Chi-restraints excluded: chain yE residue 146 ILE Chi-restraints excluded: chain yE residue 164 GLN Chi-restraints excluded: chain yE residue 167 VAL Chi-restraints excluded: chain yE residue 169 ASP Chi-restraints excluded: chain yE residue 209 ASP Chi-restraints excluded: chain UF residue 16 THR Chi-restraints excluded: chain UF residue 38 ILE Chi-restraints excluded: chain UF residue 43 VAL Chi-restraints excluded: chain UF residue 55 THR Chi-restraints excluded: chain UF residue 58 GLU Chi-restraints excluded: chain UF residue 67 SER Chi-restraints excluded: chain UF residue 89 LEU Chi-restraints excluded: chain UF residue 96 VAL Chi-restraints excluded: chain dG residue 13 THR Chi-restraints excluded: chain dG residue 96 VAL Chi-restraints excluded: chain eH residue 31 ASN Chi-restraints excluded: chain eH residue 111 ARG Chi-restraints excluded: chain eH residue 113 LYS Chi-restraints excluded: chain xI residue 117 LEU Chi-restraints excluded: chain xI residue 147 SER Chi-restraints excluded: chain xI residue 150 GLU Chi-restraints excluded: chain xI residue 153 LYS Chi-restraints excluded: chain xI residue 154 LYS Chi-restraints excluded: chain qJ residue 50 ILE Chi-restraints excluded: chain qJ residue 53 VAL Chi-restraints excluded: chain LL residue 58 VAL Chi-restraints excluded: chain LL residue 63 VAL Chi-restraints excluded: chain LL residue 121 SER Chi-restraints excluded: chain LL residue 124 ILE Chi-restraints excluded: chain LL residue 125 VAL Chi-restraints excluded: chain LL residue 159 VAL Chi-restraints excluded: chain LL residue 180 ARG Chi-restraints excluded: chain KM residue 80 LEU Chi-restraints excluded: chain DO residue 7 THR Chi-restraints excluded: chain DO residue 177 ASP Chi-restraints excluded: chain DO residue 227 THR Chi-restraints excluded: chain DO residue 230 VAL Chi-restraints excluded: chain DO residue 267 VAL Chi-restraints excluded: chain DO residue 307 GLN Chi-restraints excluded: chain DO residue 333 VAL Chi-restraints excluded: chain DO residue 354 VAL Chi-restraints excluded: chain DO residue 359 LEU Chi-restraints excluded: chain DO residue 361 HIS Chi-restraints excluded: chain RP residue 14 VAL Chi-restraints excluded: chain MQ residue 15 VAL Chi-restraints excluded: chain MQ residue 16 GLU Chi-restraints excluded: chain MQ residue 20 VAL Chi-restraints excluded: chain MQ residue 21 VAL Chi-restraints excluded: chain MQ residue 64 VAL Chi-restraints excluded: chain MQ residue 69 THR Chi-restraints excluded: chain MQ residue 90 VAL Chi-restraints excluded: chain MQ residue 130 THR Chi-restraints excluded: chain mS residue 34 SER Chi-restraints excluded: chain mS residue 59 HIS Chi-restraints excluded: chain pT residue 48 ASP Chi-restraints excluded: chain pT residue 87 ARG Chi-restraints excluded: chain pT residue 111 THR Chi-restraints excluded: chain pT residue 177 LEU Chi-restraints excluded: chain pT residue 200 CYS Chi-restraints excluded: chain pT residue 211 LEU Chi-restraints excluded: chain pT residue 267 VAL Chi-restraints excluded: chain pT residue 327 GLU Chi-restraints excluded: chain pT residue 340 VAL Chi-restraints excluded: chain pT residue 387 VAL Chi-restraints excluded: chain pT residue 412 LEU Chi-restraints excluded: chain pT residue 511 ASP Chi-restraints excluded: chain pT residue 531 THR Chi-restraints excluded: chain pT residue 543 LEU Chi-restraints excluded: chain YU residue 55 GLU Chi-restraints excluded: chain YU residue 74 TYR Chi-restraints excluded: chain YU residue 105 VAL Chi-restraints excluded: chain vV residue 155 TRP Chi-restraints excluded: chain vV residue 214 LEU Chi-restraints excluded: chain vV residue 245 SER Chi-restraints excluded: chain vV residue 299 SER Chi-restraints excluded: chain vV residue 314 GLN Chi-restraints excluded: chain vV residue 338 ILE Chi-restraints excluded: chain vV residue 374 ILE Chi-restraints excluded: chain nY residue 8 VAL Chi-restraints excluded: chain nY residue 26 VAL Chi-restraints excluded: chain nY residue 46 THR Chi-restraints excluded: chain nY residue 63 THR Chi-restraints excluded: chain nY residue 72 SER Chi-restraints excluded: chain SZ residue 19 VAL Chi-restraints excluded: chain SZ residue 45 LEU Chi-restraints excluded: chain SZ residue 61 ILE Chi-restraints excluded: chain SZ residue 87 THR Chi-restraints excluded: chain SZ residue 96 ASP Chi-restraints excluded: chain SZ residue 104 GLU Chi-restraints excluded: chain SZ residue 128 GLU Chi-restraints excluded: chain SZ residue 157 GLN Chi-restraints excluded: chain SZ residue 160 THR Chi-restraints excluded: chain SZ residue 172 TYR Chi-restraints excluded: chain ia residue 11 LEU Chi-restraints excluded: chain ia residue 35 ASN Chi-restraints excluded: chain ia residue 64 SER Chi-restraints excluded: chain ia residue 72 VAL Chi-restraints excluded: chain Ib residue 12 VAL Chi-restraints excluded: chain Ib residue 16 VAL Chi-restraints excluded: chain Ib residue 22 SER Chi-restraints excluded: chain Ib residue 65 VAL Chi-restraints excluded: chain Ib residue 82 VAL Chi-restraints excluded: chain Ib residue 101 VAL Chi-restraints excluded: chain Ib residue 103 ILE Chi-restraints excluded: chain Ib residue 132 VAL Chi-restraints excluded: chain Ib residue 147 SER Chi-restraints excluded: chain Xc residue 25 VAL Chi-restraints excluded: chain Xc residue 70 THR Chi-restraints excluded: chain Xc residue 75 VAL Chi-restraints excluded: chain Xc residue 100 GLU Chi-restraints excluded: chain Xc residue 104 VAL Chi-restraints excluded: chain Xc residue 132 LEU Chi-restraints excluded: chain Xc residue 141 ILE Chi-restraints excluded: chain xd residue 13 GLN Chi-restraints excluded: chain jh residue 5 THR Chi-restraints excluded: chain jh residue 25 ARG Chi-restraints excluded: chain jh residue 29 VAL Chi-restraints excluded: chain jh residue 67 LEU Chi-restraints excluded: chain li residue 23 LEU Chi-restraints excluded: chain Hj residue 30 THR Chi-restraints excluded: chain Hj residue 132 VAL Chi-restraints excluded: chain Hj residue 164 VAL Chi-restraints excluded: chain Hj residue 190 VAL Chi-restraints excluded: chain Hj residue 203 VAL Chi-restraints excluded: chain Hj residue 217 THR Chi-restraints excluded: chain Hj residue 218 ILE Chi-restraints excluded: chain Hj residue 227 ASP Chi-restraints excluded: chain Qk residue 41 ASP Chi-restraints excluded: chain Qk residue 186 VAL Chi-restraints excluded: chain Tl residue 25 VAL Chi-restraints excluded: chain Tl residue 52 MET Chi-restraints excluded: chain Tl residue 72 VAL Chi-restraints excluded: chain Tl residue 89 LEU Chi-restraints excluded: chain Tl residue 104 GLU Chi-restraints excluded: chain Tl residue 110 LYS Chi-restraints excluded: chain Tl residue 128 LEU Chi-restraints excluded: chain sm residue 46 LYS Chi-restraints excluded: chain sm residue 97 THR Chi-restraints excluded: chain sm residue 102 LEU Chi-restraints excluded: chain No residue 18 VAL Chi-restraints excluded: chain No residue 196 THR Chi-restraints excluded: chain zp residue 9 SER Chi-restraints excluded: chain zp residue 38 LYS Chi-restraints excluded: chain zp residue 42 LEU Chi-restraints excluded: chain zp residue 101 THR Chi-restraints excluded: chain zp residue 103 PHE Chi-restraints excluded: chain Zq residue 23 VAL Chi-restraints excluded: chain Zq residue 46 ILE Chi-restraints excluded: chain Zq residue 60 LYS Chi-restraints excluded: chain kr residue 14 LEU Chi-restraints excluded: chain kr residue 28 ASN Chi-restraints excluded: chain kr residue 41 THR Chi-restraints excluded: chain kr residue 65 LEU Chi-restraints excluded: chain Gu residue 179 LEU Chi-restraints excluded: chain Pv residue 24 VAL Chi-restraints excluded: chain Pv residue 94 LEU Chi-restraints excluded: chain Pv residue 110 THR Chi-restraints excluded: chain Pv residue 148 LEU Chi-restraints excluded: chain Pv residue 154 GLU Chi-restraints excluded: chain ox residue 19 ASP Chi-restraints excluded: chain ox residue 54 CYS Chi-restraints excluded: chain ox residue 118 SER Chi-restraints excluded: chain Jy residue 18 VAL Chi-restraints excluded: chain Jy residue 44 THR Chi-restraints excluded: chain Jy residue 67 VAL Chi-restraints excluded: chain Jy residue 107 ASP Chi-restraints excluded: chain Jy residue 141 ARG Chi-restraints excluded: chain Jy residue 148 VAL Chi-restraints excluded: chain Jy residue 161 SER Chi-restraints excluded: chain Ez residue 35 ARG Chi-restraints excluded: chain Ez residue 68 THR Chi-restraints excluded: chain Ez residue 93 THR Chi-restraints excluded: chain Ez residue 159 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1406 random chunks: chunk 1232 optimal weight: 1.9990 chunk 1298 optimal weight: 9.9990 chunk 1184 optimal weight: 8.9990 chunk 1262 optimal weight: 0.0000 chunk 1297 optimal weight: 4.9990 chunk 760 optimal weight: 10.0000 chunk 550 optimal weight: 0.7980 chunk 991 optimal weight: 10.0000 chunk 387 optimal weight: 9.9990 chunk 1141 optimal weight: 1.9990 chunk 1194 optimal weight: 7.9990 overall best weight: 1.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B4 140 ASN V5 132 ASN tB 24 ASN ** yE 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UF 25 ASN UF 109 GLN ** DO 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** RP 68 GLN MQ 27 GLN mS 22 GLN mS 27 GLN pT 26 ASN vV 176 GLN vV 292 GLN Ib 157 ASN Wg 54 GLN Hj 191 ASN Tl 103 GLN Tl 112 ASN No 11 GLN ** Gu 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** aw 25 HIS aw 120 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.171 162278 Z= 0.167 Angle : 0.572 12.651 237192 Z= 0.303 Chirality : 0.038 0.328 30051 Planarity : 0.004 0.060 17198 Dihedral : 22.416 179.930 66662 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.91 % Favored : 93.03 % Rotamer: Outliers : 4.24 % Allowed : 19.96 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.08), residues: 10628 helix: 1.36 (0.08), residues: 3973 sheet: -0.50 (0.14), residues: 1434 loop : -1.90 (0.08), residues: 5221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPDO 106 HIS 0.015 0.001 HISrA 272 PHE 0.026 0.001 PHEtB 31 TYR 0.025 0.001 TYRNo 4 ARG 0.007 0.000 ARGUF 104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21256 Ramachandran restraints generated. 10628 Oldfield, 0 Emsley, 10628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21256 Ramachandran restraints generated. 10628 Oldfield, 0 Emsley, 10628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1021 residues out of total 9273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 745 time to evaluate : 8.771 Fit side-chains revert: symmetry clash REVERT: B4 70 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7593 (ttm170) REVERT: f7 31 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8168 (ttpt) REVERT: F8 12 SER cc_start: 0.8901 (m) cc_final: 0.8361 (p) REVERT: v9 426 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.6723 (mm-30) REVERT: v9 434 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8406 (tttp) REVERT: rA 79 ARG cc_start: 0.7979 (ttp-110) cc_final: 0.7471 (ptp-110) REVERT: rA 358 LEU cc_start: 0.6679 (OUTLIER) cc_final: 0.6326 (tm) REVERT: rA 396 ARG cc_start: 0.6566 (ptp-170) cc_final: 0.6347 (ttp-170) REVERT: rA 464 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7017 (tt0) REVERT: rA 535 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8156 (mpt) REVERT: tB 123 ASP cc_start: 0.8189 (m-30) cc_final: 0.7887 (m-30) REVERT: tB 138 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7303 (tt0) REVERT: cC 40 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8171 (mppt) REVERT: CD 335 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8708 (tp) REVERT: CD 342 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8836 (mp) REVERT: UF 89 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8384 (mt) REVERT: UF 102 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7221 (mm-30) REVERT: dG 47 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.7194 (m-30) REVERT: eH 113 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.7924 (tttp) REVERT: xI 117 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8479 (mp) REVERT: qJ 108 LYS cc_start: 0.7504 (tptp) cc_final: 0.7197 (tttm) REVERT: KM 80 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7261 (mp) REVERT: DO 307 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.7980 (mt0) REVERT: DO 361 HIS cc_start: 0.5830 (OUTLIER) cc_final: 0.5371 (m90) REVERT: MQ 16 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7890 (pm20) REVERT: mS 59 HIS cc_start: 0.7783 (OUTLIER) cc_final: 0.7430 (p90) REVERT: pT 87 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7498 (mtp180) REVERT: pT 134 ARG cc_start: 0.8142 (ptp90) cc_final: 0.7749 (ptp90) REVERT: pT 543 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8084 (mt) REVERT: YU 55 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6397 (mm-30) REVERT: vV 374 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7637 (mp) REVERT: SZ 61 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8775 (tp) REVERT: SZ 96 ASP cc_start: 0.7216 (OUTLIER) cc_final: 0.6802 (m-30) REVERT: SZ 128 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7127 (tt0) REVERT: SZ 172 TYR cc_start: 0.9015 (OUTLIER) cc_final: 0.7612 (t80) REVERT: ia 11 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8236 (mt) REVERT: ia 91 ASN cc_start: 0.7874 (m-40) cc_final: 0.7634 (m110) REVERT: Xc 141 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.8014 (mp) REVERT: xd 23 ARG cc_start: 0.7999 (mtp85) cc_final: 0.7080 (mmp-170) REVERT: xd 37 GLU cc_start: 0.7921 (pp20) cc_final: 0.7652 (mm-30) REVERT: jh 25 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.7364 (tmm-80) REVERT: li 23 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8139 (mp) REVERT: Hj 67 ILE cc_start: 0.7844 (tp) cc_final: 0.7469 (mp) REVERT: Tl 89 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8548 (mt) REVERT: Tl 104 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7163 (mp0) REVERT: Tl 128 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7814 (mp) REVERT: sm 46 LYS cc_start: 0.6134 (OUTLIER) cc_final: 0.5573 (mttm) REVERT: sm 49 LEU cc_start: 0.7762 (tt) cc_final: 0.7279 (tp) REVERT: sm 62 LYS cc_start: 0.6961 (mtpt) cc_final: 0.6140 (mptt) REVERT: Gu 146 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.8121 (mt0) REVERT: Pv 13 LYS cc_start: 0.8284 (mtmm) cc_final: 0.8009 (mtpt) REVERT: ox 28 LYS cc_start: 0.6400 (tptt) cc_final: 0.6175 (tptt) REVERT: Jy 19 LEU cc_start: 0.8164 (mp) cc_final: 0.7808 (mp) REVERT: Jy 84 LEU cc_start: 0.6442 (mt) cc_final: 0.6124 (mt) REVERT: Jy 141 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.6864 (ptm160) REVERT: Ez 35 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7400 (mtm-85) REVERT: Ez 88 ILE cc_start: 0.7489 (OUTLIER) cc_final: 0.6748 (tt) outliers start: 276 outliers final: 190 residues processed: 948 average time/residue: 2.0525 time to fit residues: 2903.6520 Evaluate side-chains 965 residues out of total 9273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 735 time to evaluate : 8.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h1 residue 30 GLU Chi-restraints excluded: chain h1 residue 60 GLU Chi-restraints excluded: chain g2 residue 71 THR Chi-restraints excluded: chain g2 residue 94 LEU Chi-restraints excluded: chain g2 residue 104 VAL Chi-restraints excluded: chain g2 residue 105 VAL Chi-restraints excluded: chain b3 residue 26 THR Chi-restraints excluded: chain B4 residue 45 VAL Chi-restraints excluded: chain B4 residue 47 GLN Chi-restraints excluded: chain B4 residue 70 ARG Chi-restraints excluded: chain B4 residue 169 ILE Chi-restraints excluded: chain V5 residue 56 ASP Chi-restraints excluded: chain V5 residue 61 THR Chi-restraints excluded: chain V5 residue 74 MET Chi-restraints excluded: chain V5 residue 115 THR Chi-restraints excluded: chain O6 residue 3 VAL Chi-restraints excluded: chain O6 residue 41 LEU Chi-restraints excluded: chain f7 residue 31 LYS Chi-restraints excluded: chain F8 residue 15 VAL Chi-restraints excluded: chain F8 residue 71 VAL Chi-restraints excluded: chain F8 residue 84 VAL Chi-restraints excluded: chain F8 residue 91 VAL Chi-restraints excluded: chain v9 residue 404 LEU Chi-restraints excluded: chain v9 residue 409 VAL Chi-restraints excluded: chain v9 residue 412 LEU Chi-restraints excluded: chain v9 residue 426 GLU Chi-restraints excluded: chain v9 residue 428 ILE Chi-restraints excluded: chain v9 residue 430 ILE Chi-restraints excluded: chain v9 residue 431 LEU Chi-restraints excluded: chain v9 residue 434 LYS Chi-restraints excluded: chain rA residue 11 VAL Chi-restraints excluded: chain rA residue 73 ASP Chi-restraints excluded: chain rA residue 74 VAL Chi-restraints excluded: chain rA residue 178 VAL Chi-restraints excluded: chain rA residue 201 THR Chi-restraints excluded: chain rA residue 221 THR Chi-restraints excluded: chain rA residue 233 ASN Chi-restraints excluded: chain rA residue 263 THR Chi-restraints excluded: chain rA residue 327 ASN Chi-restraints excluded: chain rA residue 328 VAL Chi-restraints excluded: chain rA residue 358 LEU Chi-restraints excluded: chain rA residue 374 ARG Chi-restraints excluded: chain rA residue 398 LEU Chi-restraints excluded: chain rA residue 464 GLU Chi-restraints excluded: chain rA residue 486 VAL Chi-restraints excluded: chain rA residue 512 SER Chi-restraints excluded: chain rA residue 535 MET Chi-restraints excluded: chain rA residue 595 ASP Chi-restraints excluded: chain tB residue 9 CYS Chi-restraints excluded: chain tB residue 32 CYS Chi-restraints excluded: chain tB residue 34 SER Chi-restraints excluded: chain tB residue 79 VAL Chi-restraints excluded: chain tB residue 135 ARG Chi-restraints excluded: chain tB residue 138 GLU Chi-restraints excluded: chain cC residue 40 LYS Chi-restraints excluded: chain cC residue 75 ASN Chi-restraints excluded: chain CD residue 56 ILE Chi-restraints excluded: chain CD residue 85 VAL Chi-restraints excluded: chain CD residue 114 VAL Chi-restraints excluded: chain CD residue 160 VAL Chi-restraints excluded: chain CD residue 210 GLU Chi-restraints excluded: chain CD residue 242 THR Chi-restraints excluded: chain CD residue 261 MET Chi-restraints excluded: chain CD residue 335 ILE Chi-restraints excluded: chain CD residue 342 LEU Chi-restraints excluded: chain CD residue 382 THR Chi-restraints excluded: chain yE residue 3 THR Chi-restraints excluded: chain yE residue 90 ASP Chi-restraints excluded: chain yE residue 92 VAL Chi-restraints excluded: chain yE residue 108 ILE Chi-restraints excluded: chain yE residue 146 ILE Chi-restraints excluded: chain yE residue 164 GLN Chi-restraints excluded: chain yE residue 167 VAL Chi-restraints excluded: chain yE residue 169 ASP Chi-restraints excluded: chain UF residue 16 THR Chi-restraints excluded: chain UF residue 38 ILE Chi-restraints excluded: chain UF residue 55 THR Chi-restraints excluded: chain UF residue 58 GLU Chi-restraints excluded: chain UF residue 67 SER Chi-restraints excluded: chain UF residue 89 LEU Chi-restraints excluded: chain UF residue 96 VAL Chi-restraints excluded: chain dG residue 13 THR Chi-restraints excluded: chain dG residue 47 ASP Chi-restraints excluded: chain dG residue 96 VAL Chi-restraints excluded: chain eH residue 31 ASN Chi-restraints excluded: chain eH residue 111 ARG Chi-restraints excluded: chain eH residue 113 LYS Chi-restraints excluded: chain xI residue 117 LEU Chi-restraints excluded: chain xI residue 120 THR Chi-restraints excluded: chain xI residue 147 SER Chi-restraints excluded: chain xI residue 150 GLU Chi-restraints excluded: chain qJ residue 29 GLN Chi-restraints excluded: chain qJ residue 50 ILE Chi-restraints excluded: chain qJ residue 53 VAL Chi-restraints excluded: chain LL residue 58 VAL Chi-restraints excluded: chain LL residue 63 VAL Chi-restraints excluded: chain LL residue 121 SER Chi-restraints excluded: chain LL residue 124 ILE Chi-restraints excluded: chain LL residue 125 VAL Chi-restraints excluded: chain LL residue 159 VAL Chi-restraints excluded: chain KM residue 80 LEU Chi-restraints excluded: chain DO residue 7 THR Chi-restraints excluded: chain DO residue 177 ASP Chi-restraints excluded: chain DO residue 227 THR Chi-restraints excluded: chain DO residue 230 VAL Chi-restraints excluded: chain DO residue 267 VAL Chi-restraints excluded: chain DO residue 292 SER Chi-restraints excluded: chain DO residue 307 GLN Chi-restraints excluded: chain DO residue 333 VAL Chi-restraints excluded: chain DO residue 354 VAL Chi-restraints excluded: chain DO residue 361 HIS Chi-restraints excluded: chain RP residue 14 VAL Chi-restraints excluded: chain RP residue 116 ASP Chi-restraints excluded: chain MQ residue 15 VAL Chi-restraints excluded: chain MQ residue 16 GLU Chi-restraints excluded: chain MQ residue 20 VAL Chi-restraints excluded: chain MQ residue 69 THR Chi-restraints excluded: chain MQ residue 90 VAL Chi-restraints excluded: chain MQ residue 130 THR Chi-restraints excluded: chain mS residue 59 HIS Chi-restraints excluded: chain pT residue 48 ASP Chi-restraints excluded: chain pT residue 87 ARG Chi-restraints excluded: chain pT residue 111 THR Chi-restraints excluded: chain pT residue 177 LEU Chi-restraints excluded: chain pT residue 200 CYS Chi-restraints excluded: chain pT residue 267 VAL Chi-restraints excluded: chain pT residue 327 GLU Chi-restraints excluded: chain pT residue 340 VAL Chi-restraints excluded: chain pT residue 387 VAL Chi-restraints excluded: chain pT residue 412 LEU Chi-restraints excluded: chain pT residue 511 ASP Chi-restraints excluded: chain pT residue 531 THR Chi-restraints excluded: chain pT residue 543 LEU Chi-restraints excluded: chain YU residue 55 GLU Chi-restraints excluded: chain YU residue 74 TYR Chi-restraints excluded: chain YU residue 105 VAL Chi-restraints excluded: chain vV residue 155 TRP Chi-restraints excluded: chain vV residue 299 SER Chi-restraints excluded: chain vV residue 314 GLN Chi-restraints excluded: chain vV residue 338 ILE Chi-restraints excluded: chain vV residue 374 ILE Chi-restraints excluded: chain nY residue 8 VAL Chi-restraints excluded: chain nY residue 26 VAL Chi-restraints excluded: chain nY residue 46 THR Chi-restraints excluded: chain nY residue 63 THR Chi-restraints excluded: chain nY residue 72 SER Chi-restraints excluded: chain SZ residue 19 VAL Chi-restraints excluded: chain SZ residue 45 LEU Chi-restraints excluded: chain SZ residue 61 ILE Chi-restraints excluded: chain SZ residue 87 THR Chi-restraints excluded: chain SZ residue 96 ASP Chi-restraints excluded: chain SZ residue 128 GLU Chi-restraints excluded: chain SZ residue 157 GLN Chi-restraints excluded: chain SZ residue 160 THR Chi-restraints excluded: chain SZ residue 172 TYR Chi-restraints excluded: chain ia residue 11 LEU Chi-restraints excluded: chain ia residue 35 ASN Chi-restraints excluded: chain ia residue 64 SER Chi-restraints excluded: chain ia residue 72 VAL Chi-restraints excluded: chain Ib residue 12 VAL Chi-restraints excluded: chain Ib residue 16 VAL Chi-restraints excluded: chain Ib residue 65 VAL Chi-restraints excluded: chain Ib residue 82 VAL Chi-restraints excluded: chain Ib residue 101 VAL Chi-restraints excluded: chain Ib residue 103 ILE Chi-restraints excluded: chain Ib residue 132 VAL Chi-restraints excluded: chain Xc residue 25 VAL Chi-restraints excluded: chain Xc residue 70 THR Chi-restraints excluded: chain Xc residue 75 VAL Chi-restraints excluded: chain Xc residue 100 GLU Chi-restraints excluded: chain Xc residue 104 VAL Chi-restraints excluded: chain Xc residue 132 LEU Chi-restraints excluded: chain Xc residue 141 ILE Chi-restraints excluded: chain jh residue 5 THR Chi-restraints excluded: chain jh residue 25 ARG Chi-restraints excluded: chain jh residue 29 VAL Chi-restraints excluded: chain jh residue 67 LEU Chi-restraints excluded: chain li residue 23 LEU Chi-restraints excluded: chain Hj residue 30 THR Chi-restraints excluded: chain Hj residue 164 VAL Chi-restraints excluded: chain Hj residue 190 VAL Chi-restraints excluded: chain Hj residue 203 VAL Chi-restraints excluded: chain Hj residue 217 THR Chi-restraints excluded: chain Hj residue 218 ILE Chi-restraints excluded: chain Hj residue 227 ASP Chi-restraints excluded: chain Qk residue 186 VAL Chi-restraints excluded: chain Tl residue 52 MET Chi-restraints excluded: chain Tl residue 72 VAL Chi-restraints excluded: chain Tl residue 89 LEU Chi-restraints excluded: chain Tl residue 104 GLU Chi-restraints excluded: chain Tl residue 110 LYS Chi-restraints excluded: chain Tl residue 128 LEU Chi-restraints excluded: chain sm residue 46 LYS Chi-restraints excluded: chain sm residue 97 THR Chi-restraints excluded: chain sm residue 102 LEU Chi-restraints excluded: chain No residue 18 VAL Chi-restraints excluded: chain No residue 196 THR Chi-restraints excluded: chain zp residue 9 SER Chi-restraints excluded: chain zp residue 38 LYS Chi-restraints excluded: chain zp residue 42 LEU Chi-restraints excluded: chain zp residue 101 THR Chi-restraints excluded: chain zp residue 103 PHE Chi-restraints excluded: chain Zq residue 23 VAL Chi-restraints excluded: chain Zq residue 46 ILE Chi-restraints excluded: chain Zq residue 60 LYS Chi-restraints excluded: chain kr residue 14 LEU Chi-restraints excluded: chain kr residue 28 ASN Chi-restraints excluded: chain kr residue 41 THR Chi-restraints excluded: chain kr residue 48 SER Chi-restraints excluded: chain kr residue 65 LEU Chi-restraints excluded: chain Gu residue 146 GLN Chi-restraints excluded: chain Gu residue 179 LEU Chi-restraints excluded: chain Pv residue 24 VAL Chi-restraints excluded: chain Pv residue 94 LEU Chi-restraints excluded: chain Pv residue 110 THR Chi-restraints excluded: chain Pv residue 148 LEU Chi-restraints excluded: chain ox residue 19 ASP Chi-restraints excluded: chain ox residue 54 CYS Chi-restraints excluded: chain ox residue 118 SER Chi-restraints excluded: chain Jy residue 18 VAL Chi-restraints excluded: chain Jy residue 44 THR Chi-restraints excluded: chain Jy residue 67 VAL Chi-restraints excluded: chain Jy residue 107 ASP Chi-restraints excluded: chain Jy residue 141 ARG Chi-restraints excluded: chain Jy residue 148 VAL Chi-restraints excluded: chain Ez residue 35 ARG Chi-restraints excluded: chain Ez residue 68 THR Chi-restraints excluded: chain Ez residue 88 ILE Chi-restraints excluded: chain Ez residue 93 THR Chi-restraints excluded: chain Ez residue 159 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1406 random chunks: chunk 1258 optimal weight: 20.0000 chunk 829 optimal weight: 10.0000 chunk 1335 optimal weight: 7.9990 chunk 815 optimal weight: 10.0000 chunk 633 optimal weight: 9.9990 chunk 928 optimal weight: 10.0000 chunk 1400 optimal weight: 9.9990 chunk 1289 optimal weight: 8.9990 chunk 1115 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 861 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B4 140 ASN tB 24 ASN yE 50 HIS ** yE 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UF 25 ASN UF 109 GLN ** DO 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** RP 68 GLN MQ 27 GLN mS 22 GLN mS 27 GLN vV 176 GLN vV 292 GLN Ib 49 ASN Ib 157 ASN Wg 54 GLN Hj 191 ASN Tl 103 GLN Tl 112 ASN No 11 GLN ** Gu 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** aw 25 HIS aw 120 ASN Ez 151 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.211 162278 Z= 0.500 Angle : 0.771 15.749 237192 Z= 0.396 Chirality : 0.048 0.425 30051 Planarity : 0.006 0.125 17198 Dihedral : 22.552 179.968 66660 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.00 % Favored : 91.91 % Rotamer: Outliers : 4.21 % Allowed : 20.16 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.04 (0.08), residues: 10628 helix: 0.88 (0.08), residues: 3964 sheet: -0.53 (0.14), residues: 1403 loop : -2.05 (0.08), residues: 5261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPjh 49 HIS 0.013 0.002 HISDO 311 PHE 0.052 0.003 PHEtB 31 TYR 0.027 0.002 TYRNo 4 ARG 0.007 0.001 ARGF8 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21256 Ramachandran restraints generated. 10628 Oldfield, 0 Emsley, 10628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21256 Ramachandran restraints generated. 10628 Oldfield, 0 Emsley, 10628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1015 residues out of total 9273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 741 time to evaluate : 8.810 Fit side-chains REVERT: b3 25 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.6259 (mttm) REVERT: B4 70 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7539 (ttm170) REVERT: O6 84 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8272 (mt) REVERT: f7 31 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8202 (ttpt) REVERT: F8 12 SER cc_start: 0.8918 (m) cc_final: 0.8387 (p) REVERT: v9 426 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.6762 (mm-30) REVERT: v9 434 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8489 (tttp) REVERT: rA 79 ARG cc_start: 0.8014 (ttp-110) cc_final: 0.7716 (ptp-170) REVERT: rA 358 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6359 (tm) REVERT: rA 396 ARG cc_start: 0.6665 (ptp-170) cc_final: 0.6435 (ttp-170) REVERT: rA 464 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.6997 (tt0) REVERT: rA 535 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8140 (mpt) REVERT: tB 63 LEU cc_start: 0.8650 (pp) cc_final: 0.8328 (tp) REVERT: tB 123 ASP cc_start: 0.8209 (m-30) cc_final: 0.7926 (m-30) REVERT: tB 138 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7585 (tt0) REVERT: tB 150 GLU cc_start: 0.5891 (OUTLIER) cc_final: 0.5443 (mt-10) REVERT: cC 40 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8192 (mppt) REVERT: CD 102 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8412 (pt) REVERT: CD 335 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8824 (tp) REVERT: CD 342 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8847 (mp) REVERT: UF 89 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8463 (mt) REVERT: UF 102 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7394 (mm-30) REVERT: dG 47 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7222 (m-30) REVERT: eH 113 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8009 (tttp) REVERT: xI 117 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8547 (mp) REVERT: xI 153 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7558 (tptm) REVERT: qJ 108 LYS cc_start: 0.7664 (tptp) cc_final: 0.7420 (tttm) REVERT: LL 180 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6818 (ttm170) REVERT: KM 80 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7168 (mp) REVERT: DO 307 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8256 (mt0) REVERT: DO 361 HIS cc_start: 0.5966 (OUTLIER) cc_final: 0.5471 (m90) REVERT: MQ 16 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.7989 (pm20) REVERT: mS 59 HIS cc_start: 0.7798 (OUTLIER) cc_final: 0.7434 (p90) REVERT: pT 87 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7670 (mtp180) REVERT: pT 134 ARG cc_start: 0.8192 (ptp90) cc_final: 0.7468 (ptp90) REVERT: YU 55 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6460 (mm-30) REVERT: vV 374 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7711 (mp) REVERT: SZ 61 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8811 (tp) REVERT: SZ 96 ASP cc_start: 0.7321 (OUTLIER) cc_final: 0.6894 (m-30) REVERT: SZ 104 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7668 (tt0) REVERT: SZ 128 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7157 (tt0) REVERT: SZ 172 TYR cc_start: 0.9057 (OUTLIER) cc_final: 0.7823 (t80) REVERT: ia 11 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8277 (mt) REVERT: ia 91 ASN cc_start: 0.7938 (m-40) cc_final: 0.7714 (m110) REVERT: Xc 141 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.7964 (mp) REVERT: xd 13 GLN cc_start: 0.7386 (OUTLIER) cc_final: 0.6880 (mm110) REVERT: xd 23 ARG cc_start: 0.8026 (mtp85) cc_final: 0.7149 (mmp-170) REVERT: jh 25 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.7824 (tmm-80) REVERT: li 23 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8188 (mp) REVERT: Hj 67 ILE cc_start: 0.8070 (tp) cc_final: 0.7659 (mp) REVERT: Tl 89 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8647 (mt) REVERT: Tl 104 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: Tl 128 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7952 (mp) REVERT: sm 46 LYS cc_start: 0.6190 (OUTLIER) cc_final: 0.5500 (mttm) REVERT: sm 49 LEU cc_start: 0.7740 (tt) cc_final: 0.7257 (tp) REVERT: sm 62 LYS cc_start: 0.6932 (mtpt) cc_final: 0.6117 (mptt) REVERT: zp 38 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.7824 (mtmt) REVERT: Gu 146 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8182 (mt0) REVERT: Pv 53 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7640 (t0) REVERT: Jy 19 LEU cc_start: 0.8266 (mp) cc_final: 0.7917 (mp) REVERT: Jy 65 ILE cc_start: 0.8758 (mm) cc_final: 0.8531 (mt) REVERT: Jy 84 LEU cc_start: 0.6484 (mt) cc_final: 0.6191 (mt) REVERT: Jy 141 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.6940 (ptm160) REVERT: Ez 35 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7398 (mtm-85) outliers start: 274 outliers final: 190 residues processed: 938 average time/residue: 2.0638 time to fit residues: 2897.0700 Evaluate side-chains 974 residues out of total 9273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 736 time to evaluate : 8.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h1 residue 30 GLU Chi-restraints excluded: chain h1 residue 60 GLU Chi-restraints excluded: chain g2 residue 71 THR Chi-restraints excluded: chain g2 residue 94 LEU Chi-restraints excluded: chain g2 residue 104 VAL Chi-restraints excluded: chain g2 residue 105 VAL Chi-restraints excluded: chain b3 residue 25 LYS Chi-restraints excluded: chain b3 residue 26 THR Chi-restraints excluded: chain B4 residue 31 THR Chi-restraints excluded: chain B4 residue 45 VAL Chi-restraints excluded: chain B4 residue 47 GLN Chi-restraints excluded: chain B4 residue 70 ARG Chi-restraints excluded: chain B4 residue 169 ILE Chi-restraints excluded: chain V5 residue 56 ASP Chi-restraints excluded: chain V5 residue 61 THR Chi-restraints excluded: chain V5 residue 74 MET Chi-restraints excluded: chain V5 residue 115 THR Chi-restraints excluded: chain O6 residue 3 VAL Chi-restraints excluded: chain O6 residue 41 LEU Chi-restraints excluded: chain O6 residue 84 LEU Chi-restraints excluded: chain f7 residue 31 LYS Chi-restraints excluded: chain F8 residue 15 VAL Chi-restraints excluded: chain F8 residue 71 VAL Chi-restraints excluded: chain F8 residue 84 VAL Chi-restraints excluded: chain F8 residue 91 VAL Chi-restraints excluded: chain v9 residue 404 LEU Chi-restraints excluded: chain v9 residue 407 CYS Chi-restraints excluded: chain v9 residue 409 VAL Chi-restraints excluded: chain v9 residue 412 LEU Chi-restraints excluded: chain v9 residue 426 GLU Chi-restraints excluded: chain v9 residue 428 ILE Chi-restraints excluded: chain v9 residue 430 ILE Chi-restraints excluded: chain v9 residue 434 LYS Chi-restraints excluded: chain rA residue 11 VAL Chi-restraints excluded: chain rA residue 73 ASP Chi-restraints excluded: chain rA residue 74 VAL Chi-restraints excluded: chain rA residue 178 VAL Chi-restraints excluded: chain rA residue 201 THR Chi-restraints excluded: chain rA residue 233 ASN Chi-restraints excluded: chain rA residue 263 THR Chi-restraints excluded: chain rA residue 327 ASN Chi-restraints excluded: chain rA residue 328 VAL Chi-restraints excluded: chain rA residue 358 LEU Chi-restraints excluded: chain rA residue 374 ARG Chi-restraints excluded: chain rA residue 398 LEU Chi-restraints excluded: chain rA residue 464 GLU Chi-restraints excluded: chain rA residue 486 VAL Chi-restraints excluded: chain rA residue 512 SER Chi-restraints excluded: chain rA residue 535 MET Chi-restraints excluded: chain tB residue 9 CYS Chi-restraints excluded: chain tB residue 32 CYS Chi-restraints excluded: chain tB residue 34 SER Chi-restraints excluded: chain tB residue 79 VAL Chi-restraints excluded: chain tB residue 135 ARG Chi-restraints excluded: chain tB residue 138 GLU Chi-restraints excluded: chain tB residue 150 GLU Chi-restraints excluded: chain cC residue 40 LYS Chi-restraints excluded: chain cC residue 75 ASN Chi-restraints excluded: chain CD residue 56 ILE Chi-restraints excluded: chain CD residue 85 VAL Chi-restraints excluded: chain CD residue 102 LEU Chi-restraints excluded: chain CD residue 114 VAL Chi-restraints excluded: chain CD residue 160 VAL Chi-restraints excluded: chain CD residue 210 GLU Chi-restraints excluded: chain CD residue 242 THR Chi-restraints excluded: chain CD residue 335 ILE Chi-restraints excluded: chain CD residue 342 LEU Chi-restraints excluded: chain CD residue 382 THR Chi-restraints excluded: chain yE residue 3 THR Chi-restraints excluded: chain yE residue 90 ASP Chi-restraints excluded: chain yE residue 92 VAL Chi-restraints excluded: chain yE residue 108 ILE Chi-restraints excluded: chain yE residue 146 ILE Chi-restraints excluded: chain yE residue 164 GLN Chi-restraints excluded: chain yE residue 167 VAL Chi-restraints excluded: chain yE residue 169 ASP Chi-restraints excluded: chain yE residue 181 LEU Chi-restraints excluded: chain yE residue 209 ASP Chi-restraints excluded: chain UF residue 16 THR Chi-restraints excluded: chain UF residue 38 ILE Chi-restraints excluded: chain UF residue 55 THR Chi-restraints excluded: chain UF residue 58 GLU Chi-restraints excluded: chain UF residue 67 SER Chi-restraints excluded: chain UF residue 89 LEU Chi-restraints excluded: chain UF residue 96 VAL Chi-restraints excluded: chain dG residue 13 THR Chi-restraints excluded: chain dG residue 47 ASP Chi-restraints excluded: chain dG residue 96 VAL Chi-restraints excluded: chain eH residue 31 ASN Chi-restraints excluded: chain eH residue 111 ARG Chi-restraints excluded: chain eH residue 113 LYS Chi-restraints excluded: chain xI residue 117 LEU Chi-restraints excluded: chain xI residue 120 THR Chi-restraints excluded: chain xI residue 147 SER Chi-restraints excluded: chain xI residue 150 GLU Chi-restraints excluded: chain xI residue 153 LYS Chi-restraints excluded: chain qJ residue 50 ILE Chi-restraints excluded: chain qJ residue 53 VAL Chi-restraints excluded: chain LL residue 58 VAL Chi-restraints excluded: chain LL residue 121 SER Chi-restraints excluded: chain LL residue 124 ILE Chi-restraints excluded: chain LL residue 125 VAL Chi-restraints excluded: chain LL residue 159 VAL Chi-restraints excluded: chain LL residue 180 ARG Chi-restraints excluded: chain KM residue 80 LEU Chi-restraints excluded: chain DO residue 7 THR Chi-restraints excluded: chain DO residue 177 ASP Chi-restraints excluded: chain DO residue 227 THR Chi-restraints excluded: chain DO residue 230 VAL Chi-restraints excluded: chain DO residue 267 VAL Chi-restraints excluded: chain DO residue 292 SER Chi-restraints excluded: chain DO residue 307 GLN Chi-restraints excluded: chain DO residue 333 VAL Chi-restraints excluded: chain DO residue 354 VAL Chi-restraints excluded: chain DO residue 359 LEU Chi-restraints excluded: chain DO residue 361 HIS Chi-restraints excluded: chain RP residue 14 VAL Chi-restraints excluded: chain MQ residue 15 VAL Chi-restraints excluded: chain MQ residue 16 GLU Chi-restraints excluded: chain MQ residue 20 VAL Chi-restraints excluded: chain MQ residue 64 VAL Chi-restraints excluded: chain MQ residue 69 THR Chi-restraints excluded: chain MQ residue 90 VAL Chi-restraints excluded: chain MQ residue 130 THR Chi-restraints excluded: chain mS residue 59 HIS Chi-restraints excluded: chain pT residue 48 ASP Chi-restraints excluded: chain pT residue 87 ARG Chi-restraints excluded: chain pT residue 111 THR Chi-restraints excluded: chain pT residue 177 LEU Chi-restraints excluded: chain pT residue 200 CYS Chi-restraints excluded: chain pT residue 267 VAL Chi-restraints excluded: chain pT residue 327 GLU Chi-restraints excluded: chain pT residue 340 VAL Chi-restraints excluded: chain pT residue 387 VAL Chi-restraints excluded: chain pT residue 412 LEU Chi-restraints excluded: chain pT residue 511 ASP Chi-restraints excluded: chain pT residue 514 VAL Chi-restraints excluded: chain pT residue 531 THR Chi-restraints excluded: chain pT residue 543 LEU Chi-restraints excluded: chain YU residue 55 GLU Chi-restraints excluded: chain YU residue 105 VAL Chi-restraints excluded: chain vV residue 155 TRP Chi-restraints excluded: chain vV residue 299 SER Chi-restraints excluded: chain vV residue 314 GLN Chi-restraints excluded: chain vV residue 338 ILE Chi-restraints excluded: chain vV residue 374 ILE Chi-restraints excluded: chain nY residue 8 VAL Chi-restraints excluded: chain nY residue 26 VAL Chi-restraints excluded: chain nY residue 46 THR Chi-restraints excluded: chain nY residue 63 THR Chi-restraints excluded: chain nY residue 72 SER Chi-restraints excluded: chain SZ residue 19 VAL Chi-restraints excluded: chain SZ residue 45 LEU Chi-restraints excluded: chain SZ residue 61 ILE Chi-restraints excluded: chain SZ residue 87 THR Chi-restraints excluded: chain SZ residue 96 ASP Chi-restraints excluded: chain SZ residue 104 GLU Chi-restraints excluded: chain SZ residue 128 GLU Chi-restraints excluded: chain SZ residue 157 GLN Chi-restraints excluded: chain SZ residue 160 THR Chi-restraints excluded: chain SZ residue 172 TYR Chi-restraints excluded: chain ia residue 11 LEU Chi-restraints excluded: chain ia residue 35 ASN Chi-restraints excluded: chain ia residue 64 SER Chi-restraints excluded: chain ia residue 72 VAL Chi-restraints excluded: chain Ib residue 12 VAL Chi-restraints excluded: chain Ib residue 16 VAL Chi-restraints excluded: chain Ib residue 65 VAL Chi-restraints excluded: chain Ib residue 101 VAL Chi-restraints excluded: chain Ib residue 103 ILE Chi-restraints excluded: chain Ib residue 132 VAL Chi-restraints excluded: chain Xc residue 25 VAL Chi-restraints excluded: chain Xc residue 70 THR Chi-restraints excluded: chain Xc residue 75 VAL Chi-restraints excluded: chain Xc residue 100 GLU Chi-restraints excluded: chain Xc residue 104 VAL Chi-restraints excluded: chain Xc residue 141 ILE Chi-restraints excluded: chain xd residue 13 GLN Chi-restraints excluded: chain jh residue 5 THR Chi-restraints excluded: chain jh residue 25 ARG Chi-restraints excluded: chain jh residue 29 VAL Chi-restraints excluded: chain jh residue 67 LEU Chi-restraints excluded: chain li residue 23 LEU Chi-restraints excluded: chain Hj residue 30 THR Chi-restraints excluded: chain Hj residue 132 VAL Chi-restraints excluded: chain Hj residue 164 VAL Chi-restraints excluded: chain Hj residue 190 VAL Chi-restraints excluded: chain Hj residue 203 VAL Chi-restraints excluded: chain Hj residue 217 THR Chi-restraints excluded: chain Hj residue 218 ILE Chi-restraints excluded: chain Qk residue 165 ILE Chi-restraints excluded: chain Qk residue 186 VAL Chi-restraints excluded: chain Tl residue 25 VAL Chi-restraints excluded: chain Tl residue 52 MET Chi-restraints excluded: chain Tl residue 72 VAL Chi-restraints excluded: chain Tl residue 89 LEU Chi-restraints excluded: chain Tl residue 104 GLU Chi-restraints excluded: chain Tl residue 110 LYS Chi-restraints excluded: chain Tl residue 128 LEU Chi-restraints excluded: chain sm residue 46 LYS Chi-restraints excluded: chain sm residue 97 THR Chi-restraints excluded: chain sm residue 102 LEU Chi-restraints excluded: chain No residue 18 VAL Chi-restraints excluded: chain No residue 19 LEU Chi-restraints excluded: chain No residue 196 THR Chi-restraints excluded: chain zp residue 9 SER Chi-restraints excluded: chain zp residue 38 LYS Chi-restraints excluded: chain zp residue 42 LEU Chi-restraints excluded: chain zp residue 101 THR Chi-restraints excluded: chain Zq residue 23 VAL Chi-restraints excluded: chain Zq residue 46 ILE Chi-restraints excluded: chain Zq residue 60 LYS Chi-restraints excluded: chain kr residue 14 LEU Chi-restraints excluded: chain kr residue 41 THR Chi-restraints excluded: chain kr residue 48 SER Chi-restraints excluded: chain kr residue 65 LEU Chi-restraints excluded: chain Gu residue 146 GLN Chi-restraints excluded: chain Gu residue 179 LEU Chi-restraints excluded: chain Pv residue 24 VAL Chi-restraints excluded: chain Pv residue 53 ASP Chi-restraints excluded: chain Pv residue 94 LEU Chi-restraints excluded: chain Pv residue 110 THR Chi-restraints excluded: chain Pv residue 148 LEU Chi-restraints excluded: chain ox residue 19 ASP Chi-restraints excluded: chain ox residue 54 CYS Chi-restraints excluded: chain ox residue 80 LEU Chi-restraints excluded: chain ox residue 118 SER Chi-restraints excluded: chain Jy residue 18 VAL Chi-restraints excluded: chain Jy residue 44 THR Chi-restraints excluded: chain Jy residue 67 VAL Chi-restraints excluded: chain Jy residue 107 ASP Chi-restraints excluded: chain Jy residue 141 ARG Chi-restraints excluded: chain Jy residue 148 VAL Chi-restraints excluded: chain Ez residue 35 ARG Chi-restraints excluded: chain Ez residue 68 THR Chi-restraints excluded: chain Ez residue 93 THR Chi-restraints excluded: chain Ez residue 153 THR Chi-restraints excluded: chain Ez residue 159 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1406 random chunks: chunk 683 optimal weight: 8.9990 chunk 885 optimal weight: 3.9990 chunk 1188 optimal weight: 9.9990 chunk 341 optimal weight: 1.9990 chunk 1028 optimal weight: 8.9990 chunk 164 optimal weight: 1.9990 chunk 309 optimal weight: 9.9990 chunk 1117 optimal weight: 0.8980 chunk 467 optimal weight: 6.9990 chunk 1147 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B4 140 ASN tB 24 ASN ** yE 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UF 25 ASN UF 109 GLN ** DO 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** RP 68 GLN MQ 27 GLN mS 22 GLN mS 27 GLN pT 26 ASN vV 176 GLN vV 292 GLN Ib 49 ASN Ib 157 ASN Wg 54 GLN Hj 191 ASN Tl 103 GLN Tl 112 ASN No 11 GLN ** Gu 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** aw 25 HIS aw 120 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.123419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.090551 restraints weight = 270489.840| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.17 r_work: 0.3186 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.162 162278 Z= 0.188 Angle : 0.565 13.495 237192 Z= 0.299 Chirality : 0.038 0.365 30051 Planarity : 0.004 0.059 17198 Dihedral : 22.394 179.814 66660 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.15 % Favored : 93.78 % Rotamer: Outliers : 3.58 % Allowed : 20.81 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.08), residues: 10628 helix: 1.34 (0.08), residues: 3966 sheet: -0.48 (0.14), residues: 1433 loop : -1.89 (0.08), residues: 5229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPMQ 85 HIS 0.012 0.001 HISrA 272 PHE 0.028 0.001 PHEzp 103 TYR 0.024 0.001 TYRNo 4 ARG 0.006 0.000 ARGUF 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 52205.88 seconds wall clock time: 904 minutes 57.52 seconds (54297.52 seconds total)