Starting phenix.real_space_refine on Tue Feb 13 17:57:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kwy_0781/02_2024/6kwy_0781_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kwy_0781/02_2024/6kwy_0781.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kwy_0781/02_2024/6kwy_0781_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kwy_0781/02_2024/6kwy_0781_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kwy_0781/02_2024/6kwy_0781_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kwy_0781/02_2024/6kwy_0781.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kwy_0781/02_2024/6kwy_0781.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kwy_0781/02_2024/6kwy_0781_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kwy_0781/02_2024/6kwy_0781_trim_updated.pdb" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 47460 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: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 392 5.16 5 C 39646 2.51 5 N 10668 2.21 5 O 11779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 90": "NH1" <-> "NH2" Residue "A TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 137": "OD1" <-> "OD2" Residue "C PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 163": "NH1" <-> "NH2" Residue "D ARG 5": "NH1" <-> "NH2" Residue "D PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 225": "OE1" <-> "OE2" Residue "G ARG 88": "NH1" <-> "NH2" Residue "G TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 192": "OE1" <-> "OE2" Residue "H ARG 143": "NH1" <-> "NH2" Residue "I ARG 25": "NH1" <-> "NH2" Residue "I ARG 69": "NH1" <-> "NH2" Residue "I ARG 79": "NH1" <-> "NH2" Residue "J TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 86": "NH1" <-> "NH2" Residue "J PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 153": "NH1" <-> "NH2" Residue "K PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 186": "NH1" <-> "NH2" Residue "L ARG 99": "NH1" <-> "NH2" Residue "L ARG 173": "NH1" <-> "NH2" Residue "M PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 100": "NH1" <-> "NH2" Residue "M TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 226": "NH1" <-> "NH2" Residue "Q PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 109": "NH1" <-> "NH2" Residue "S ARG 18": "NH1" <-> "NH2" Residue "S ARG 101": "NH1" <-> "NH2" Residue "S TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 239": "NH1" <-> "NH2" Residue "T ARG 169": "NH1" <-> "NH2" Residue "U TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 198": "NH1" <-> "NH2" Residue "W ARG 79": "NH1" <-> "NH2" Residue "W PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 86": "NH1" <-> "NH2" Residue "X PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 153": "NH1" <-> "NH2" Residue "Y PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 71": "NH1" <-> "NH2" Residue "Z PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 29": "NH1" <-> "NH2" Residue "c TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 61": "NH1" <-> "NH2" Residue "c ARG 84": "NH1" <-> "NH2" Residue "c PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 121": "NH1" <-> "NH2" Residue "c ARG 135": "NH1" <-> "NH2" Residue "c PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 261": "NH1" <-> "NH2" Residue "c ARG 300": "NH1" <-> "NH2" Residue "c ARG 348": "NH1" <-> "NH2" Residue "c ARG 428": "NH1" <-> "NH2" Residue "c ARG 472": "NH1" <-> "NH2" Residue "c ARG 526": "NH1" <-> "NH2" Residue "c ARG 567": "NH1" <-> "NH2" Residue "c ARG 685": "NH1" <-> "NH2" Residue "c ARG 689": "NH1" <-> "NH2" Residue "c ARG 695": "NH1" <-> "NH2" Residue "c TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 807": "NH1" <-> "NH2" Residue "c PHE 891": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 914": "NH1" <-> "NH2" Residue "c ARG 943": "NH1" <-> "NH2" Residue "c ARG 951": "NH1" <-> "NH2" Residue "c ARG 969": "NH1" <-> "NH2" Residue "c ARG 973": "NH1" <-> "NH2" Residue "c ARG 1243": "NH1" <-> "NH2" Residue "c ARG 1297": "NH1" <-> "NH2" Residue "c ARG 1331": "NH1" <-> "NH2" Residue "c ARG 1340": "NH1" <-> "NH2" Residue "c ARG 1350": "NH1" <-> "NH2" Residue "c ARG 1377": "NH1" <-> "NH2" Residue "c ARG 1410": "NH1" <-> "NH2" Residue "c ARG 1435": "NH1" <-> "NH2" Residue "c ARG 1485": "NH1" <-> "NH2" Residue "c ARG 1536": "NH1" <-> "NH2" Residue "c ARG 1620": "NH1" <-> "NH2" Residue "c ARG 1658": "NH1" <-> "NH2" Residue "c TYR 1659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 1811": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 62499 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1671 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 205} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1645 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "C" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1641 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 206} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1741 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1881 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 229} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1909 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 239} 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: "G" Number of atoms: 1860 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 237, 1857 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 228} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 237, 1857 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 228} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 1887 Chain: "H" Number of atoms: 1672 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1659 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Conformer: "B" Number of residues, atoms: 220, 1659 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} bond proxies already assigned to first conformer: 1671 Chain: "I" Number of atoms: 1633 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 204, 1591 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Conformer: "B" Number of residues, atoms: 204, 1591 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} bond proxies already assigned to first conformer: 1574 Chain: "J" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1561 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 188} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "K" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1543 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 198} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "L" Number of atoms: 1656 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 213, 1650 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 213, 1650 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 1672 Chain: "M" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1687 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 208} Chain: "N" Number of atoms: 1515 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 202, 1510 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 202, 1510 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1530 Chain: "O" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1779 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 219} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 1919 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1911 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 241} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 247, 1911 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 241} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1931 Chain: "Q" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1817 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1768 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "S" Number of atoms: 1871 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 238, 1856 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 226} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 238, 1856 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 226} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 1871 Chain: "T" Number of atoms: 1867 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 240, 1864 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 240, 1864 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 1895 Chain: "U" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1885 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 235} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "V" Number of atoms: 1655 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1645 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 220, 1645 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1660 Chain: "W" Number of atoms: 1604 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 204, 1587 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 204, 1587 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 1597 Chain: "X" Number of atoms: 1574 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 196, 1571 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} Conformer: "B" Number of residues, atoms: 196, 1571 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} bond proxies already assigned to first conformer: 1599 Chain: "Y" Number of atoms: 1564 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 199, 1543 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 196} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 199, 1543 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 196} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1550 Chain: "Z" Number of atoms: 1644 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 213, 1641 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Conformer: "B" Number of residues, atoms: 213, 1641 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 1667 Chain: "a" Number of atoms: 1688 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 216, 1683 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 208} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 216, 1683 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 208} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1710 Chain: "b" Number of atoms: 1526 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 1521 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} Conformer: "B" Number of residues, atoms: 203, 1521 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} bond proxies already assigned to first conformer: 1542 Chain: "c" Number of atoms: 14723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1813, 14723 Unusual residues: {'IHP': 1, 'K0W': 1} Classifications: {'peptide': 1811, 'undetermined': 2} Link IDs: {'PCIS': 2, 'PTRANS': 93, 'TRANS': 1715, None: 2} Not linked: pdbres="ALA c1843 " pdbres="K0W c1901 " Not linked: pdbres="K0W c1901 " pdbres="IHP c1902 " Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N ALYS I 16 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS I 16 " occ=0.50 residue: pdb=" N AASN I 17 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN I 17 " occ=0.50 residue: pdb=" N AGLU I 77 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU I 77 " occ=0.50 residue: pdb=" N AGLY I 78 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY I 78 " occ=0.50 residue: pdb=" N ALYS W 16 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS W 16 " occ=0.50 Time building chain proxies: 30.73, per 1000 atoms: 0.49 Number of scatterers: 62499 At special positions: 0 Unit cell: (158.08, 161.2, 231.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 392 16.00 P 14 15.00 O 11779 8.00 N 10668 7.00 C 39646 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 16.58 Conformation dependent library (CDL) restraints added in 11.5 seconds 15870 Ramachandran restraints generated. 7935 Oldfield, 0 Emsley, 7935 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14876 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 247 helices and 69 sheets defined 39.5% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.55 Creating SS restraints... Processing helix chain 'A' and resid 19 through 29 Processing helix chain 'A' and resid 79 through 100 removed outlier: 3.522A pdb=" N VAL A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 99 " --> pdb=" O GLN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 122 removed outlier: 3.680A pdb=" N TYR A 120 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N THR A 121 " --> pdb=" O MET A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 Processing helix chain 'A' and resid 183 through 197 removed outlier: 3.695A pdb=" N THR A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 230 removed outlier: 3.735A pdb=" N ASP A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 101 removed outlier: 3.679A pdb=" N GLU B 89 " --> pdb=" O VAL B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 120 removed outlier: 3.685A pdb=" N ALA B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 178 removed outlier: 3.944A pdb=" N GLN B 177 " --> pdb=" O SER B 173 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP B 178 " --> pdb=" O MET B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 200 removed outlier: 3.741A pdb=" N LYS B 199 " --> pdb=" O LYS B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 248 Processing helix chain 'C' and resid 20 through 27 removed outlier: 3.555A pdb=" N VAL C 26 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS C 27 " --> pdb=" O GLN C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 97 removed outlier: 3.918A pdb=" N ILE C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN C 92 " --> pdb=" O ARG C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 165 through 175 removed outlier: 3.962A pdb=" N LYS C 174 " --> pdb=" O GLU C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 198 removed outlier: 3.878A pdb=" N ILE C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU C 197 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL C 198 " --> pdb=" O ALA C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 237 removed outlier: 3.526A pdb=" N GLU C 235 " --> pdb=" O GLU C 231 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS C 236 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 28 Processing helix chain 'D' and resid 61 through 63 No H-bonds generated for 'chain 'D' and resid 61 through 63' Processing helix chain 'D' and resid 82 through 103 removed outlier: 5.072A pdb=" N THR D 87 " --> pdb=" O ALA D 83 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU D 88 " --> pdb=" O ASP D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 119 Processing helix chain 'D' and resid 174 through 184 removed outlier: 3.661A pdb=" N SER D 180 " --> pdb=" O GLY D 176 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 206 Processing helix chain 'D' and resid 231 through 240 removed outlier: 3.541A pdb=" N GLU D 236 " --> pdb=" O GLU D 232 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASP D 240 " --> pdb=" O GLU D 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 28 removed outlier: 3.688A pdb=" N GLU E 27 " --> pdb=" O GLU E 23 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA E 28 " --> pdb=" O TYR E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 98 removed outlier: 3.526A pdb=" N LEU E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 116 Processing helix chain 'E' and resid 118 through 120 No H-bonds generated for 'chain 'E' and resid 118 through 120' Processing helix chain 'E' and resid 166 through 178 removed outlier: 3.561A pdb=" N ARG E 174 " --> pdb=" O THR E 170 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N SER E 177 " --> pdb=" O GLU E 173 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU E 178 " --> pdb=" O ARG E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 198 removed outlier: 3.767A pdb=" N THR E 198 " --> pdb=" O ALA E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 233 No H-bonds generated for 'chain 'E' and resid 230 through 233' Processing helix chain 'F' and resid 21 through 30 Processing helix chain 'F' and resid 81 through 102 Processing helix chain 'F' and resid 111 through 123 removed outlier: 3.823A pdb=" N TYR F 118 " --> pdb=" O ARG F 114 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 177 Processing helix chain 'F' and resid 186 through 199 removed outlier: 4.210A pdb=" N LYS F 191 " --> pdb=" O ARG F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 220 No H-bonds generated for 'chain 'F' and resid 218 through 220' Processing helix chain 'F' and resid 229 through 243 Processing helix chain 'G' and resid 23 through 35 removed outlier: 3.754A pdb=" N PHE G 29 " --> pdb=" O VAL G 25 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS G 30 " --> pdb=" O GLU G 26 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY G 35 " --> pdb=" O ALA G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 105 Processing helix chain 'G' and resid 111 through 127 removed outlier: 3.826A pdb=" N VAL G 124 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR G 125 " --> pdb=" O ILE G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 183 Processing helix chain 'G' and resid 191 through 206 removed outlier: 3.623A pdb=" N VAL G 195 " --> pdb=" O PHE G 191 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU G 202 " --> pdb=" O ALA G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 243 removed outlier: 3.819A pdb=" N ALA G 241 " --> pdb=" O ALA G 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 70 Processing helix chain 'H' and resid 76 through 89 Processing helix chain 'H' and resid 131 through 141 Processing helix chain 'H' and resid 148 through 165 Processing helix chain 'I' and resid 3 through 5 No H-bonds generated for 'chain 'I' and resid 3 through 5' Processing helix chain 'I' and resid 56 through 76 Processing helix chain 'I' and resid 83 through 97 removed outlier: 4.099A pdb=" N LYS I 97 " --> pdb=" O LEU I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 152 Processing helix chain 'I' and resid 159 through 176 removed outlier: 4.023A pdb=" N ARG I 176 " --> pdb=" O ASN I 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 71 Processing helix chain 'J' and resid 77 through 90 Processing helix chain 'J' and resid 136 through 146 removed outlier: 4.951A pdb=" N SER J 141 " --> pdb=" O PHE J 137 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ILE J 142 " --> pdb=" O LEU J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 170 Processing helix chain 'K' and resid 49 through 70 Processing helix chain 'K' and resid 76 through 90 removed outlier: 3.878A pdb=" N GLN K 89 " --> pdb=" O ASN K 85 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR K 90 " --> pdb=" O MET K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 132 through 142 removed outlier: 3.799A pdb=" N VAL K 138 " --> pdb=" O TYR K 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 166 Processing helix chain 'K' and resid 192 through 199 Processing helix chain 'L' and resid 58 through 79 Processing helix chain 'L' and resid 85 through 97 Processing helix chain 'L' and resid 142 through 152 Proline residue: L 147 - end of helix Processing helix chain 'L' and resid 168 through 185 removed outlier: 3.877A pdb=" N ARG L 185 " --> pdb=" O SER L 181 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 75 Processing helix chain 'M' and resid 85 through 101 Processing helix chain 'M' and resid 142 through 145 No H-bonds generated for 'chain 'M' and resid 142 through 145' Processing helix chain 'M' and resid 147 through 156 Processing helix chain 'M' and resid 162 through 179 Processing helix chain 'M' and resid 210 through 213 Processing helix chain 'N' and resid 49 through 70 Processing helix chain 'N' and resid 76 through 89 Processing helix chain 'N' and resid 132 through 134 No H-bonds generated for 'chain 'N' and resid 132 through 134' Processing helix chain 'N' and resid 136 through 142 Processing helix chain 'N' and resid 149 through 166 Processing helix chain 'N' and resid 191 through 193 No H-bonds generated for 'chain 'N' and resid 191 through 193' Processing helix chain 'O' and resid 19 through 29 Processing helix chain 'O' and resid 79 through 100 Processing helix chain 'O' and resid 106 through 121 removed outlier: 3.711A pdb=" N THR O 121 " --> pdb=" O MET O 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 166 through 176 Processing helix chain 'O' and resid 183 through 197 removed outlier: 3.953A pdb=" N SER O 197 " --> pdb=" O THR O 193 " (cutoff:3.500A) Processing helix chain 'O' and resid 222 through 228 Processing helix chain 'P' and resid 19 through 29 Processing helix chain 'P' and resid 80 through 101 Processing helix chain 'P' and resid 107 through 123 removed outlier: 3.747A pdb=" N ILE P 117 " --> pdb=" O ALA P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 168 through 178 Processing helix chain 'P' and resid 186 through 199 Processing helix chain 'P' and resid 230 through 247 removed outlier: 4.040A pdb=" N ALA P 247 " --> pdb=" O GLU P 243 " (cutoff:3.500A) Processing helix chain 'Q' and resid 17 through 26 Processing helix chain 'Q' and resid 77 through 98 Processing helix chain 'Q' and resid 104 through 119 Processing helix chain 'Q' and resid 165 through 174 Processing helix chain 'Q' and resid 184 through 197 removed outlier: 3.796A pdb=" N GLU Q 197 " --> pdb=" O LYS Q 193 " (cutoff:3.500A) Processing helix chain 'Q' and resid 222 through 238 removed outlier: 3.708A pdb=" N TYR Q 228 " --> pdb=" O GLU Q 224 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU Q 235 " --> pdb=" O GLU Q 231 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 31 Processing helix chain 'R' and resid 61 through 63 No H-bonds generated for 'chain 'R' and resid 61 through 63' Processing helix chain 'R' and resid 82 through 103 removed outlier: 4.161A pdb=" N THR R 87 " --> pdb=" O ASP R 84 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP R 90 " --> pdb=" O THR R 87 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR R 102 " --> pdb=" O HIS R 99 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR R 103 " --> pdb=" O TRP R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 119 removed outlier: 4.231A pdb=" N LEU R 119 " --> pdb=" O ALA R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 184 Processing helix chain 'R' and resid 191 through 205 Processing helix chain 'R' and resid 231 through 240 removed outlier: 4.361A pdb=" N ASP R 240 " --> pdb=" O GLU R 236 " (cutoff:3.500A) Processing helix chain 'S' and resid 20 through 30 removed outlier: 3.601A pdb=" N VAL S 29 " --> pdb=" O ALA S 25 " (cutoff:3.500A) Processing helix chain 'S' and resid 78 through 98 Processing helix chain 'S' and resid 105 through 120 removed outlier: 4.012A pdb=" N ILE S 118 " --> pdb=" O SER S 114 " (cutoff:3.500A) Proline residue: S 119 - end of helix Processing helix chain 'S' and resid 165 through 181 removed outlier: 5.507A pdb=" N SER S 177 " --> pdb=" O GLU S 173 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLU S 178 " --> pdb=" O ARG S 174 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE S 179 " --> pdb=" O HIS S 175 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N MET S 180 " --> pdb=" O MET S 176 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLU S 181 " --> pdb=" O SER S 177 " (cutoff:3.500A) Processing helix chain 'S' and resid 184 through 198 removed outlier: 3.834A pdb=" N THR S 198 " --> pdb=" O ALA S 194 " (cutoff:3.500A) Processing helix chain 'S' and resid 228 through 233 Proline residue: S 231 - end of helix No H-bonds generated for 'chain 'S' and resid 228 through 233' Processing helix chain 'T' and resid 21 through 32 Processing helix chain 'T' and resid 81 through 102 Processing helix chain 'T' and resid 108 through 122 removed outlier: 3.892A pdb=" N TYR T 122 " --> pdb=" O TYR T 118 " (cutoff:3.500A) Processing helix chain 'T' and resid 169 through 176 Processing helix chain 'T' and resid 181 through 183 No H-bonds generated for 'chain 'T' and resid 181 through 183' Processing helix chain 'T' and resid 186 through 200 removed outlier: 4.448A pdb=" N LYS T 191 " --> pdb=" O ARG T 187 " (cutoff:3.500A) Processing helix chain 'T' and resid 218 through 220 No H-bonds generated for 'chain 'T' and resid 218 through 220' Processing helix chain 'T' and resid 229 through 243 Processing helix chain 'U' and resid 23 through 33 removed outlier: 3.819A pdb=" N ASN U 33 " --> pdb=" O PHE U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 84 through 105 Processing helix chain 'U' and resid 111 through 126 removed outlier: 3.903A pdb=" N VAL U 124 " --> pdb=" O ASP U 120 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR U 125 " --> pdb=" O ILE U 121 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR U 126 " --> pdb=" O SER U 122 " (cutoff:3.500A) Processing helix chain 'U' and resid 172 through 184 Processing helix chain 'U' and resid 191 through 205 Processing helix chain 'U' and resid 232 through 243 Processing helix chain 'V' and resid 49 through 70 Processing helix chain 'V' and resid 76 through 89 Processing helix chain 'V' and resid 131 through 141 Processing helix chain 'V' and resid 148 through 163 Processing helix chain 'W' and resid 56 through 77 Processing helix chain 'W' and resid 83 through 97 removed outlier: 4.172A pdb=" N LYS W 97 " --> pdb=" O LEU W 93 " (cutoff:3.500A) Processing helix chain 'W' and resid 142 through 152 Processing helix chain 'W' and resid 159 through 176 removed outlier: 4.237A pdb=" N ARG W 176 " --> pdb=" O ASN W 172 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 71 Processing helix chain 'X' and resid 77 through 93 removed outlier: 4.307A pdb=" N ARG X 93 " --> pdb=" O ALA X 89 " (cutoff:3.500A) Processing helix chain 'X' and resid 134 through 146 removed outlier: 4.642A pdb=" N LEU X 140 " --> pdb=" O PHE X 137 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER X 141 " --> pdb=" O LEU X 138 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR X 146 " --> pdb=" O LEU X 143 " (cutoff:3.500A) Processing helix chain 'X' and resid 153 through 170 Processing helix chain 'Y' and resid 49 through 70 Processing helix chain 'Y' and resid 76 through 90 removed outlier: 4.088A pdb=" N GLN Y 89 " --> pdb=" O ASN Y 85 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N TYR Y 90 " --> pdb=" O MET Y 86 " (cutoff:3.500A) Processing helix chain 'Y' and resid 132 through 142 removed outlier: 3.803A pdb=" N VAL Y 138 " --> pdb=" O TYR Y 134 " (cutoff:3.500A) Processing helix chain 'Y' and resid 149 through 166 Processing helix chain 'Y' and resid 192 through 198 Processing helix chain 'Z' and resid 58 through 79 Processing helix chain 'Z' and resid 85 through 98 Processing helix chain 'Z' and resid 142 through 152 Proline residue: Z 147 - end of helix Processing helix chain 'Z' and resid 168 through 185 removed outlier: 3.659A pdb=" N ARG Z 185 " --> pdb=" O SER Z 181 " (cutoff:3.500A) Processing helix chain 'a' and resid 57 through 75 Processing helix chain 'a' and resid 85 through 101 Processing helix chain 'a' and resid 142 through 145 No H-bonds generated for 'chain 'a' and resid 142 through 145' Processing helix chain 'a' and resid 147 through 156 Processing helix chain 'a' and resid 162 through 179 Processing helix chain 'a' and resid 210 through 213 Processing helix chain 'b' and resid 49 through 70 Processing helix chain 'b' and resid 76 through 89 Processing helix chain 'b' and resid 132 through 134 No H-bonds generated for 'chain 'b' and resid 132 through 134' Processing helix chain 'b' and resid 136 through 142 Processing helix chain 'b' and resid 149 through 166 Processing helix chain 'c' and resid 33 through 35 No H-bonds generated for 'chain 'c' and resid 33 through 35' Processing helix chain 'c' and resid 43 through 64 removed outlier: 3.753A pdb=" N LEU c 50 " --> pdb=" O ALA c 46 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA c 62 " --> pdb=" O ASN c 58 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 86 Processing helix chain 'c' and resid 92 through 104 removed outlier: 3.715A pdb=" N LEU c 97 " --> pdb=" O GLU c 93 " (cutoff:3.500A) Processing helix chain 'c' and resid 113 through 127 removed outlier: 4.521A pdb=" N GLY c 118 " --> pdb=" O SER c 114 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE c 119 " --> pdb=" O MET c 115 " (cutoff:3.500A) Processing helix chain 'c' and resid 130 through 132 No H-bonds generated for 'chain 'c' and resid 130 through 132' Processing helix chain 'c' and resid 143 through 150 Processing helix chain 'c' and resid 170 through 183 removed outlier: 3.780A pdb=" N THR c 175 " --> pdb=" O ASN c 171 " (cutoff:3.500A) Proline residue: c 182 - end of helix Processing helix chain 'c' and resid 186 through 192 removed outlier: 4.103A pdb=" N THR c 189 " --> pdb=" O ALA c 186 " (cutoff:3.500A) Processing helix chain 'c' and resid 197 through 199 No H-bonds generated for 'chain 'c' and resid 197 through 199' Processing helix chain 'c' and resid 206 through 217 Processing helix chain 'c' and resid 224 through 226 No H-bonds generated for 'chain 'c' and resid 224 through 226' Processing helix chain 'c' and resid 231 through 233 No H-bonds generated for 'chain 'c' and resid 231 through 233' Processing helix chain 'c' and resid 235 through 244 Processing helix chain 'c' and resid 250 through 265 removed outlier: 3.892A pdb=" N GLN c 254 " --> pdb=" O GLN c 250 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG c 261 " --> pdb=" O ASN c 257 " (cutoff:3.500A) Processing helix chain 'c' and resid 276 through 286 removed outlier: 4.080A pdb=" N THR c 281 " --> pdb=" O PRO c 277 " (cutoff:3.500A) Processing helix chain 'c' and resid 308 through 318 removed outlier: 3.670A pdb=" N ILE c 313 " --> pdb=" O GLY c 309 " (cutoff:3.500A) Processing helix chain 'c' and resid 326 through 336 Processing helix chain 'c' and resid 343 through 345 No H-bonds generated for 'chain 'c' and resid 343 through 345' Processing helix chain 'c' and resid 348 through 371 removed outlier: 3.939A pdb=" N ASN c 351 " --> pdb=" O ARG c 348 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET c 354 " --> pdb=" O ASN c 351 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU c 356 " --> pdb=" O LEU c 353 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG c 359 " --> pdb=" O LEU c 356 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU c 360 " --> pdb=" O LEU c 357 " (cutoff:3.500A) Proline residue: c 361 - end of helix Processing helix chain 'c' and resid 384 through 386 No H-bonds generated for 'chain 'c' and resid 384 through 386' Processing helix chain 'c' and resid 390 through 408 removed outlier: 3.657A pdb=" N PHE c 396 " --> pdb=" O ASP c 392 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N GLN c 402 " --> pdb=" O GLN c 398 " (cutoff:3.500A) Proline residue: c 403 - end of helix Processing helix chain 'c' and resid 415 through 427 removed outlier: 3.954A pdb=" N ALA c 420 " --> pdb=" O GLU c 416 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N MET c 427 " --> pdb=" O ASN c 423 " (cutoff:3.500A) Processing helix chain 'c' and resid 429 through 431 No H-bonds generated for 'chain 'c' and resid 429 through 431' Processing helix chain 'c' and resid 433 through 438 Processing helix chain 'c' and resid 440 through 443 No H-bonds generated for 'chain 'c' and resid 440 through 443' Processing helix chain 'c' and resid 451 through 461 removed outlier: 3.531A pdb=" N ALA c 455 " --> pdb=" O HIS c 451 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL c 460 " --> pdb=" O THR c 456 " (cutoff:3.500A) Processing helix chain 'c' and resid 464 through 467 No H-bonds generated for 'chain 'c' and resid 464 through 467' Processing helix chain 'c' and resid 477 through 487 removed outlier: 4.499A pdb=" N LEU c 482 " --> pdb=" O THR c 479 " (cutoff:3.500A) Proline residue: c 483 - end of helix removed outlier: 3.796A pdb=" N ARG c 487 " --> pdb=" O LEU c 484 " (cutoff:3.500A) Processing helix chain 'c' and resid 489 through 491 No H-bonds generated for 'chain 'c' and resid 489 through 491' Processing helix chain 'c' and resid 497 through 507 removed outlier: 3.606A pdb=" N ILE c 502 " --> pdb=" O SER c 498 " (cutoff:3.500A) Processing helix chain 'c' and resid 531 through 537 removed outlier: 3.528A pdb=" N GLU c 535 " --> pdb=" O GLU c 531 " (cutoff:3.500A) Processing helix chain 'c' and resid 540 through 547 removed outlier: 4.197A pdb=" N GLU c 544 " --> pdb=" O ALA c 541 " (cutoff:3.500A) Processing helix chain 'c' and resid 549 through 559 Processing helix chain 'c' and resid 577 through 581 Processing helix chain 'c' and resid 584 through 595 Processing helix chain 'c' and resid 599 through 614 removed outlier: 4.027A pdb=" N VAL c 604 " --> pdb=" O GLU c 600 " (cutoff:3.500A) Processing helix chain 'c' and resid 623 through 637 removed outlier: 3.547A pdb=" N ASP c 629 " --> pdb=" O ARG c 625 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA c 633 " --> pdb=" O ASP c 629 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA c 634 " --> pdb=" O MET c 630 " (cutoff:3.500A) Processing helix chain 'c' and resid 639 through 657 removed outlier: 4.102A pdb=" N LYS c 644 " --> pdb=" O GLU c 640 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU c 645 " --> pdb=" O GLU c 641 " (cutoff:3.500A) Proline residue: c 648 - end of helix Processing helix chain 'c' and resid 671 through 682 removed outlier: 3.810A pdb=" N TRP c 675 " --> pdb=" O LYS c 671 " (cutoff:3.500A) Processing helix chain 'c' and resid 689 through 691 No H-bonds generated for 'chain 'c' and resid 689 through 691' Processing helix chain 'c' and resid 693 through 699 removed outlier: 4.699A pdb=" N GLU c 696 " --> pdb=" O LEU c 693 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLN c 697 " --> pdb=" O TYR c 694 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL c 699 " --> pdb=" O GLU c 696 " (cutoff:3.500A) Processing helix chain 'c' and resid 702 through 705 No H-bonds generated for 'chain 'c' and resid 702 through 705' Processing helix chain 'c' and resid 715 through 726 removed outlier: 3.876A pdb=" N LEU c 720 " --> pdb=" O LEU c 716 " (cutoff:3.500A) Processing helix chain 'c' and resid 752 through 754 No H-bonds generated for 'chain 'c' and resid 752 through 754' Processing helix chain 'c' and resid 774 through 785 Processing helix chain 'c' and resid 789 through 799 Processing helix chain 'c' and resid 807 through 823 removed outlier: 3.504A pdb=" N GLN c 812 " --> pdb=" O ASP c 808 " (cutoff:3.500A) Processing helix chain 'c' and resid 864 through 882 removed outlier: 3.552A pdb=" N ILE c 868 " --> pdb=" O HIS c 864 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS c 874 " --> pdb=" O THR c 870 " (cutoff:3.500A) Processing helix chain 'c' and resid 889 through 900 Processing helix chain 'c' and resid 908 through 924 Processing helix chain 'c' and resid 937 through 953 removed outlier: 3.617A pdb=" N VAL c 944 " --> pdb=" O LEU c 940 " (cutoff:3.500A) Processing helix chain 'c' and resid 963 through 975 removed outlier: 3.525A pdb=" N LEU c 974 " --> pdb=" O ASP c 970 " (cutoff:3.500A) Processing helix chain 'c' and resid 980 through 994 removed outlier: 3.648A pdb=" N GLN c 988 " --> pdb=" O ASN c 984 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR c 989 " --> pdb=" O LYS c 985 " (cutoff:3.500A) Processing helix chain 'c' and resid 1005 through 1008 No H-bonds generated for 'chain 'c' and resid 1005 through 1008' Processing helix chain 'c' and resid 1021 through 1032 Processing helix chain 'c' and resid 1049 through 1060 Proline residue: c1054 - end of helix removed outlier: 5.211A pdb=" N GLY c1060 " --> pdb=" O ILE c1056 " (cutoff:3.500A) Processing helix chain 'c' and resid 1070 through 1086 removed outlier: 3.629A pdb=" N ARG c1074 " --> pdb=" O PRO c1070 " (cutoff:3.500A) Processing helix chain 'c' and resid 1100 through 1105 Processing helix chain 'c' and resid 1127 through 1154 removed outlier: 3.564A pdb=" N ASP c1138 " --> pdb=" O GLU c1134 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA c1139 " --> pdb=" O LYS c1135 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU c1140 " --> pdb=" O ASN c1136 " (cutoff:3.500A) Processing helix chain 'c' and resid 1161 through 1174 removed outlier: 4.092A pdb=" N LEU c1174 " --> pdb=" O LEU c1170 " (cutoff:3.500A) Processing helix chain 'c' and resid 1183 through 1191 Processing helix chain 'c' and resid 1198 through 1214 Processing helix chain 'c' and resid 1247 through 1249 No H-bonds generated for 'chain 'c' and resid 1247 through 1249' Processing helix chain 'c' and resid 1260 through 1264 Processing helix chain 'c' and resid 1306 through 1313 Processing helix chain 'c' and resid 1316 through 1326 Processing helix chain 'c' and resid 1339 through 1351 Processing helix chain 'c' and resid 1356 through 1368 Proline residue: c1362 - end of helix removed outlier: 3.593A pdb=" N VAL c1368 " --> pdb=" O LEU c1364 " (cutoff:3.500A) Processing helix chain 'c' and resid 1374 through 1392 removed outlier: 4.121A pdb=" N LYS c1391 " --> pdb=" O ILE c1387 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N HIS c1392 " --> pdb=" O ARG c1388 " (cutoff:3.500A) Processing helix chain 'c' and resid 1395 through 1414 Proline residue: c1407 - end of helix Processing helix chain 'c' and resid 1421 through 1431 removed outlier: 4.125A pdb=" N ALA c1426 " --> pdb=" O ASN c1422 " (cutoff:3.500A) Processing helix chain 'c' and resid 1442 through 1447 Processing helix chain 'c' and resid 1460 through 1474 removed outlier: 3.613A pdb=" N GLN c1469 " --> pdb=" O LEU c1465 " (cutoff:3.500A) Processing helix chain 'c' and resid 1480 through 1493 removed outlier: 5.882A pdb=" N ARG c1485 " --> pdb=" O GLU c1481 " (cutoff:3.500A) Proline residue: c1492 - end of helix Processing helix chain 'c' and resid 1499 through 1512 removed outlier: 3.769A pdb=" N GLU c1503 " --> pdb=" O LYS c1499 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG c1504 " --> pdb=" O ASN c1500 " (cutoff:3.500A) Processing helix chain 'c' and resid 1530 through 1540 removed outlier: 3.667A pdb=" N ARG c1536 " --> pdb=" O GLU c1532 " (cutoff:3.500A) Processing helix chain 'c' and resid 1542 through 1544 No H-bonds generated for 'chain 'c' and resid 1542 through 1544' Processing helix chain 'c' and resid 1568 through 1584 removed outlier: 3.504A pdb=" N ALA c1583 " --> pdb=" O LYS c1579 " (cutoff:3.500A) Processing helix chain 'c' and resid 1600 through 1604 Processing helix chain 'c' and resid 1619 through 1630 Processing helix chain 'c' and resid 1639 through 1649 removed outlier: 3.649A pdb=" N LEU c1643 " --> pdb=" O VAL c1639 " (cutoff:3.500A) Processing helix chain 'c' and resid 1655 through 1670 removed outlier: 3.687A pdb=" N LEU c1662 " --> pdb=" O ARG c1658 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE c1670 " --> pdb=" O GLN c1666 " (cutoff:3.500A) Processing helix chain 'c' and resid 1673 through 1677 Processing helix chain 'c' and resid 1680 through 1695 removed outlier: 3.711A pdb=" N LYS c1684 " --> pdb=" O GLU c1680 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU c1695 " --> pdb=" O ILE c1691 " (cutoff:3.500A) Processing helix chain 'c' and resid 1699 through 1714 Processing helix chain 'c' and resid 1722 through 1732 Processing helix chain 'c' and resid 1756 through 1771 Processing helix chain 'c' and resid 1781 through 1791 removed outlier: 3.580A pdb=" N ASN c1787 " --> pdb=" O GLN c1783 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU c1788 " --> pdb=" O LEU c1784 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA c1790 " --> pdb=" O MET c1786 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N HIS c1791 " --> pdb=" O ASN c1787 " (cutoff:3.500A) Processing helix chain 'c' and resid 1798 through 1810 Processing helix chain 'c' and resid 1817 through 1823 removed outlier: 4.850A pdb=" N GLN c1822 " --> pdb=" O GLN c1818 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLN c1823 " --> pdb=" O GLU c1819 " (cutoff:3.500A) Processing helix chain 'c' and resid 1826 through 1833 removed outlier: 4.111A pdb=" N VAL c1831 " --> pdb=" O ASP c1827 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 159 through 162 removed outlier: 3.559A pdb=" N SER A 34 " --> pdb=" O MET A 162 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 71 through 77 Processing sheet with id= C, first strand: chain 'B' and resid 161 through 165 removed outlier: 5.947A pdb=" N THR B 33 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE B 213 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 156 through 158 removed outlier: 4.081A pdb=" N MET B 72 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N CYS B 74 " --> pdb=" O LYS B 67 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LYS B 67 " --> pdb=" O CYS B 74 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 41 through 45 Processing sheet with id= F, first strand: chain 'C' and resid 62 through 64 Processing sheet with id= G, first strand: chain 'D' and resid 167 through 170 Processing sheet with id= H, first strand: chain 'D' and resid 162 through 164 removed outlier: 4.120A pdb=" N ALA D 140 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N CYS D 76 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N GLU D 69 " --> pdb=" O CYS D 76 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N MET D 78 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE D 67 " --> pdb=" O MET D 78 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 158 through 161 Processing sheet with id= J, first strand: chain 'E' and resid 63 through 65 removed outlier: 4.151A pdb=" N ILE E 144 " --> pdb=" O CYS E 156 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 162 through 165 Processing sheet with id= L, first strand: chain 'F' and resid 66 through 68 Processing sheet with id= M, first strand: chain 'G' and resid 165 through 169 removed outlier: 6.109A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN G 53 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 69 through 71 Processing sheet with id= O, first strand: chain 'H' and resid 124 through 128 Processing sheet with id= P, first strand: chain 'H' and resid 119 through 121 removed outlier: 5.688A pdb=" N CYS H 43 " --> pdb=" O PHE H 36 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N PHE H 36 " --> pdb=" O CYS H 43 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N GLY H 45 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE H 34 " --> pdb=" O GLY H 45 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 135 through 139 removed outlier: 5.769A pdb=" N ALA I 9 " --> pdb=" O ASP I 24 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 41 through 43 removed outlier: 4.012A pdb=" N ALA I 53 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE I 120 " --> pdb=" O THR I 132 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR I 132 " --> pdb=" O ILE I 120 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 27 through 29 removed outlier: 6.123A pdb=" N ILE I 29 " --> pdb=" O MET I 33 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N MET I 33 " --> pdb=" O ILE I 29 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 129 through 132 Processing sheet with id= U, first strand: chain 'J' and resid 124 through 126 removed outlier: 6.432A pdb=" N LEU J 44 " --> pdb=" O LYS J 37 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LYS J 37 " --> pdb=" O LEU J 44 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N CYS J 46 " --> pdb=" O MET J 35 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N MET J 35 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 21 through 23 removed outlier: 6.204A pdb=" N SER J 23 " --> pdb=" O GLN J 27 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N GLN J 27 " --> pdb=" O SER J 23 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'K' and resid 125 through 129 removed outlier: 3.535A pdb=" N GLY K 11 " --> pdb=" O PHE K 8 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N HIS K 178 " --> pdb=" O ARG K 186 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ARG K 186 " --> pdb=" O HIS K 178 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ARG K 180 " --> pdb=" O TRP K 184 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TRP K 184 " --> pdb=" O ARG K 180 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'K' and resid 98 through 105 Processing sheet with id= Y, first strand: chain 'K' and resid 20 through 22 removed outlier: 6.114A pdb=" N ALA K 22 " --> pdb=" O ILE K 26 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ILE K 26 " --> pdb=" O ALA K 22 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'K' and resid 34 through 38 removed outlier: 6.635A pdb=" N LEU K 41 " --> pdb=" O ILE K 37 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'L' and resid 135 through 139 removed outlier: 5.758A pdb=" N THR L 11 " --> pdb=" O ASP L 26 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'L' and resid 130 through 133 removed outlier: 3.693A pdb=" N GLN L 131 " --> pdb=" O SER L 123 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL L 121 " --> pdb=" O ASP L 133 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN L 108 " --> pdb=" O PHE L 124 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR L 50 " --> pdb=" O THR L 47 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE L 52 " --> pdb=" O LYS L 45 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LYS L 45 " --> pdb=" O ILE L 52 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N CYS L 54 " --> pdb=" O CYS L 43 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N CYS L 43 " --> pdb=" O CYS L 54 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'L' and resid 29 through 31 removed outlier: 3.515A pdb=" N THR L 37 " --> pdb=" O LEU L 29 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLU L 31 " --> pdb=" O ILE L 35 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ILE L 35 " --> pdb=" O GLU L 31 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'M' and resid 136 through 138 removed outlier: 3.731A pdb=" N ALA M 23 " --> pdb=" O LEU M 12 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'M' and resid 42 through 44 removed outlier: 3.517A pdb=" N THR M 109 " --> pdb=" O SER M 54 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'M' and resid 28 through 30 removed outlier: 6.798A pdb=" N TYR M 30 " --> pdb=" O ALA M 34 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ALA M 34 " --> pdb=" O TYR M 30 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'N' and resid 125 through 129 removed outlier: 3.566A pdb=" N GLY N 11 " --> pdb=" O PHE N 8 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'N' and resid 121 through 123 removed outlier: 3.948A pdb=" N VAL N 111 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE N 41 " --> pdb=" O HIS N 38 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N CYS N 43 " --> pdb=" O PRO N 36 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ARG N 45 " --> pdb=" O LEU N 34 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU N 34 " --> pdb=" O ARG N 45 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'N' and resid 20 through 22 removed outlier: 6.244A pdb=" N THR N 22 " --> pdb=" O ILE N 26 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ILE N 26 " --> pdb=" O THR N 22 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'O' and resid 159 through 162 Processing sheet with id= AK, first strand: chain 'O' and resid 71 through 77 removed outlier: 3.633A pdb=" N GLY O 72 " --> pdb=" O CYS O 136 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'P' and resid 161 through 164 removed outlier: 3.528A pdb=" N ILE P 37 " --> pdb=" O LEU P 44 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'P' and resid 65 through 67 Processing sheet with id= AN, first strand: chain 'Q' and resid 158 through 161 Processing sheet with id= AO, first strand: chain 'Q' and resid 62 through 64 Processing sheet with id= AP, first strand: chain 'R' and resid 167 through 170 Processing sheet with id= AQ, first strand: chain 'R' and resid 162 through 164 removed outlier: 6.501A pdb=" N CYS R 76 " --> pdb=" O GLU R 69 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N GLU R 69 " --> pdb=" O CYS R 76 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N MET R 78 " --> pdb=" O ILE R 67 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE R 67 " --> pdb=" O MET R 78 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'S' and resid 158 through 161 Processing sheet with id= AS, first strand: chain 'S' and resid 63 through 65 removed outlier: 3.508A pdb=" N ILE S 72 " --> pdb=" O LEU S 64 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU S 132 " --> pdb=" O THR S 147 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE S 144 " --> pdb=" O CYS S 156 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'T' and resid 162 through 165 Processing sheet with id= AU, first strand: chain 'T' and resid 66 through 68 Processing sheet with id= AV, first strand: chain 'U' and resid 165 through 169 removed outlier: 6.095A pdb=" N THR U 38 " --> pdb=" O GLN U 53 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR U 52 " --> pdb=" O GLU U 216 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU U 216 " --> pdb=" O THR U 52 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'U' and resid 69 through 71 removed outlier: 4.356A pdb=" N VAL U 151 " --> pdb=" O PHE U 163 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS U 161 " --> pdb=" O LYS U 153 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'V' and resid 124 through 128 Processing sheet with id= AY, first strand: chain 'V' and resid 119 through 121 removed outlier: 6.144A pdb=" N CYS V 43 " --> pdb=" O PHE V 36 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N PHE V 36 " --> pdb=" O CYS V 43 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLY V 45 " --> pdb=" O ILE V 34 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE V 34 " --> pdb=" O GLY V 45 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'W' and resid 135 through 139 removed outlier: 5.896A pdb=" N ALA W 9 " --> pdb=" O ASP W 24 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL W 184 " --> pdb=" O LEU W 199 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'W' and resid 41 through 43 removed outlier: 4.040A pdb=" N ALA W 53 " --> pdb=" O GLU W 105 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE W 120 " --> pdb=" O THR W 132 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR W 132 " --> pdb=" O ILE W 120 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'X' and resid 129 through 132 removed outlier: 3.562A pdb=" N LEU X 4 " --> pdb=" O HIS X 132 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'X' and resid 124 through 126 removed outlier: 3.562A pdb=" N SER X 39 " --> pdb=" O ILE X 42 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU X 44 " --> pdb=" O LYS X 37 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LYS X 37 " --> pdb=" O LEU X 44 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N CYS X 46 " --> pdb=" O MET X 35 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N MET X 35 " --> pdb=" O CYS X 46 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'X' and resid 21 through 23 removed outlier: 6.605A pdb=" N SER X 23 " --> pdb=" O GLN X 27 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLN X 27 " --> pdb=" O SER X 23 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'Y' and resid 125 through 129 removed outlier: 6.445A pdb=" N HIS Y 178 " --> pdb=" O ARG Y 186 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ARG Y 186 " --> pdb=" O HIS Y 178 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ARG Y 180 " --> pdb=" O TRP Y 184 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N TRP Y 184 " --> pdb=" O ARG Y 180 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'Y' and resid 34 through 36 Processing sheet with id= BG, first strand: chain 'Y' and resid 98 through 105 Processing sheet with id= BH, first strand: chain 'Y' and resid 20 through 22 removed outlier: 6.070A pdb=" N ALA Y 22 " --> pdb=" O ILE Y 26 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ILE Y 26 " --> pdb=" O ALA Y 22 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'Z' and resid 135 through 139 removed outlier: 5.907A pdb=" N THR Z 11 " --> pdb=" O ASP Z 26 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'Z' and resid 130 through 133 removed outlier: 3.564A pdb=" N GLN Z 131 " --> pdb=" O SER Z 123 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL Z 121 " --> pdb=" O ASP Z 133 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN Z 108 " --> pdb=" O PHE Z 124 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR Z 50 " --> pdb=" O THR Z 47 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR Z 47 " --> pdb=" O THR Z 50 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE Z 52 " --> pdb=" O LYS Z 45 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LYS Z 45 " --> pdb=" O ILE Z 52 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N CYS Z 54 " --> pdb=" O CYS Z 43 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N CYS Z 43 " --> pdb=" O CYS Z 54 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'Z' and resid 29 through 31 removed outlier: 3.535A pdb=" N THR Z 37 " --> pdb=" O LEU Z 29 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLU Z 31 " --> pdb=" O ILE Z 35 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE Z 35 " --> pdb=" O GLU Z 31 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'a' and resid 136 through 138 Processing sheet with id= BM, first strand: chain 'a' and resid 131 through 133 removed outlier: 3.513A pdb=" N THR a 49 " --> pdb=" O ASN a 46 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU a 51 " --> pdb=" O ARG a 44 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ARG a 44 " --> pdb=" O LEU a 51 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ALA a 53 " --> pdb=" O ILE a 42 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE a 42 " --> pdb=" O ALA a 53 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'a' and resid 28 through 30 removed outlier: 6.641A pdb=" N TYR a 30 " --> pdb=" O ALA a 34 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ALA a 34 " --> pdb=" O TYR a 30 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'b' and resid 125 through 128 removed outlier: 3.650A pdb=" N GLY b 11 " --> pdb=" O PHE b 8 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'b' and resid 121 through 123 removed outlier: 4.129A pdb=" N VAL b 111 " --> pdb=" O GLN b 123 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE b 41 " --> pdb=" O HIS b 38 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS b 43 " --> pdb=" O PRO b 36 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ARG b 45 " --> pdb=" O LEU b 34 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU b 34 " --> pdb=" O ARG b 45 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'b' and resid 20 through 22 removed outlier: 6.221A pdb=" N THR b 22 " --> pdb=" O ILE b 26 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ILE b 26 " --> pdb=" O THR b 22 " (cutoff:3.500A) 2959 hydrogen bonds defined for protein. 8462 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 24.04 Time building geometry restraints manager: 18.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 13142 1.32 - 1.45: 14291 1.45 - 1.57: 35634 1.57 - 1.69: 20 1.69 - 1.81: 629 Bond restraints: 63716 Sorted by residual: bond pdb=" C ILE I 41 " pdb=" N PHE I 42 " ideal model delta sigma weight residual 1.327 1.427 -0.100 1.71e-02 3.42e+03 3.43e+01 bond pdb=" C VAL c 276 " pdb=" N PRO c 277 " ideal model delta sigma weight residual 1.337 1.375 -0.039 9.80e-03 1.04e+04 1.56e+01 bond pdb=" C GLN c 789 " pdb=" N PRO c 790 " ideal model delta sigma weight residual 1.335 1.384 -0.049 1.36e-02 5.41e+03 1.28e+01 bond pdb=" C TRP c 164 " pdb=" N PHE c 165 " ideal model delta sigma weight residual 1.331 1.280 0.051 1.48e-02 4.57e+03 1.20e+01 bond pdb=" CA VAL F 227 " pdb=" CB VAL F 227 " ideal model delta sigma weight residual 1.537 1.580 -0.043 1.29e-02 6.01e+03 1.11e+01 ... (remaining 63711 not shown) Histogram of bond angle deviations from ideal: 93.23 - 102.27: 260 102.27 - 111.31: 25232 111.31 - 120.35: 36113 120.35 - 129.38: 24254 129.38 - 138.42: 410 Bond angle restraints: 86269 Sorted by residual: angle pdb=" N THR c 303 " pdb=" CA THR c 303 " pdb=" C THR c 303 " ideal model delta sigma weight residual 111.28 124.46 -13.18 1.09e+00 8.42e-01 1.46e+02 angle pdb=" N TRP U 189 " pdb=" CA TRP U 189 " pdb=" C TRP U 189 " ideal model delta sigma weight residual 109.24 128.34 -19.10 1.63e+00 3.76e-01 1.37e+02 angle pdb=" N GLU c1270 " pdb=" CA GLU c1270 " pdb=" C GLU c1270 " ideal model delta sigma weight residual 111.36 122.76 -11.40 1.09e+00 8.42e-01 1.09e+02 angle pdb=" C ASN c1112 " pdb=" N PRO c1113 " pdb=" CA PRO c1113 " ideal model delta sigma weight residual 119.84 131.66 -11.82 1.25e+00 6.40e-01 8.94e+01 angle pdb=" N ILE c1125 " pdb=" CA ILE c1125 " pdb=" C ILE c1125 " ideal model delta sigma weight residual 112.83 103.92 8.91 9.90e-01 1.02e+00 8.09e+01 ... (remaining 86264 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.76: 37507 24.76 - 49.52: 927 49.52 - 74.28: 64 74.28 - 99.03: 15 99.03 - 123.79: 6 Dihedral angle restraints: 38519 sinusoidal: 15316 harmonic: 23203 Sorted by residual: dihedral pdb=" CA LEU E 103 " pdb=" C LEU E 103 " pdb=" N PRO E 104 " pdb=" CA PRO E 104 " ideal model delta harmonic sigma weight residual 180.00 150.10 29.90 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA ASP c 670 " pdb=" C ASP c 670 " pdb=" N LYS c 671 " pdb=" CA LYS c 671 " ideal model delta harmonic sigma weight residual 180.00 -150.64 -29.36 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA TYR c 750 " pdb=" C TYR c 750 " pdb=" N PHE c 751 " pdb=" CA PHE c 751 " ideal model delta harmonic sigma weight residual -180.00 -150.72 -29.28 0 5.00e+00 4.00e-02 3.43e+01 ... (remaining 38516 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.005: 9752 1.005 - 2.010: 0 2.010 - 3.015: 0 3.015 - 4.020: 0 4.020 - 5.025: 2 Chirality restraints: 9754 Sorted by residual: chirality pdb=" C2 IHP c1902 " pdb=" C1 IHP c1902 " pdb=" C3 IHP c1902 " pdb=" O12 IHP c1902 " both_signs ideal model delta sigma weight residual False -2.52 2.51 -5.03 2.00e-01 2.50e+01 6.31e+02 chirality pdb=" C3 IHP c1902 " pdb=" C2 IHP c1902 " pdb=" C4 IHP c1902 " pdb=" O13 IHP c1902 " both_signs ideal model delta sigma weight residual False -2.34 2.53 -4.87 2.00e-01 2.50e+01 5.92e+02 chirality pdb=" CA TRP U 189 " pdb=" N TRP U 189 " pdb=" C TRP U 189 " pdb=" CB TRP U 189 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.20e+00 ... (remaining 9751 not shown) Planarity restraints: 11057 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY W 28 " 0.026 2.00e-02 2.50e+03 5.25e-02 2.76e+01 pdb=" C GLY W 28 " -0.091 2.00e-02 2.50e+03 pdb=" O GLY W 28 " 0.035 2.00e-02 2.50e+03 pdb=" N ILE W 29 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR c 373 " -0.025 2.00e-02 2.50e+03 5.20e-02 2.70e+01 pdb=" C TYR c 373 " 0.090 2.00e-02 2.50e+03 pdb=" O TYR c 373 " -0.034 2.00e-02 2.50e+03 pdb=" N LYS c 374 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP T 215 " -0.028 2.00e-02 2.50e+03 3.24e-02 2.62e+01 pdb=" CG TRP T 215 " 0.084 2.00e-02 2.50e+03 pdb=" CD1 TRP T 215 " -0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP T 215 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP T 215 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP T 215 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP T 215 " -0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP T 215 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP T 215 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP T 215 " -0.003 2.00e-02 2.50e+03 ... (remaining 11054 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 43 2.28 - 2.94: 25894 2.94 - 3.59: 91959 3.59 - 4.25: 159951 4.25 - 4.90: 266157 Nonbonded interactions: 544004 Sorted by model distance: nonbonded pdb=" O LYS c 324 " pdb=" N VAL c 326 " model vdw 1.627 2.520 nonbonded pdb=" OE1 GLU D 183 " pdb=" O ILE c1751 " model vdw 1.669 3.040 nonbonded pdb=" OG SER c 975 " pdb=" SG CYS c1030 " model vdw 1.747 2.800 nonbonded pdb=" O SER B 62 " pdb=" OE2 GLU B 212 " model vdw 1.772 3.040 nonbonded pdb=" O TRP G 189 " pdb=" CG2 THR G 190 " model vdw 1.857 3.460 ... (remaining 543999 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 'A' and (resid 18 through 50 or (resid 51 through 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 68 or (resid 69 and ( \ name N or name CA or name C or name O or name CB )) or resid 70 through 174 or ( \ resid 175 and (name N or name CA or name C or name O or name CB )) or resid 176 \ through 232)) selection = (chain 'O' and (resid 18 through 139 or (resid 140 and (name N or name CA or nam \ e C or name O or name CB )) or resid 141 through 198 or (resid 199 and (name N o \ r name CA or name C or name O or name CB )) or resid 200 through 232)) } ncs_group { reference = (chain 'B' and (resid 31 through 51 or (resid 52 and (name N or name CA or name \ C or name O or name CB )) or resid 53 through 198 or (resid 199 and (name N or n \ ame CA or name C or name O or name CB )) or resid 200 through 208 or (resid 209 \ through 210 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 1 through 228 or (resid 229 and (name N or name CA or name C or name O or name C \ B )) or resid 230 or (resid 231 and (name N or name CA or name C or name O or na \ me CB )) or resid 232 through 238 or (resid 239 and (name N or name CA or name C \ or name O or name CB )) or resid 240 through 248)) selection = (chain 'P' and (resid 31 through 53 or (resid 54 and (name N or name CA or name \ C or name O or name CB )) or resid 55 through 122 or resid 130 through 248)) } ncs_group { reference = (chain 'C' and (resid 19 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 46 or (resid 47 through 49 and (na \ me N or name CA or name C or name O or name CB )) or resid 50 through 173 or (re \ sid 174 and (name N or name CA or name C or name O or name CB )) or resid 175 th \ rough 181 or (resid 182 and (name N or name CA or name C or name O or name CB )) \ or resid 183 through 188 or (resid 189 and (name N or name CA or name C or name \ O or name CB )) or resid 190 through 192 or (resid 193 through 194 and (name N \ or name CA or name C or name O or name CB )) or resid 195 through 199 or resid 2 \ 05 through 217 or (resid 218 and (name N or name CA or name C or name O or name \ CB )) or resid 219 through 238)) selection = (chain 'Q' and (resid 19 through 117 or resid 126 through 169 or (resid 170 and \ (name N or name CA or name C or name O or name CB )) or resid 171 through 222 or \ (resid 223 through 224 and (name N or name CA or name C or name O or name CB )) \ or resid 225 through 231 or (resid 232 and (name N or name CA or name C or name \ O or name CB )) or resid 233 through 238)) } ncs_group { reference = (chain 'D' and (resid 9 through 207 or (resid 208 and (name N or name CA or name \ C or name O or name CB )) or resid 209 through 241)) selection = (chain 'R' and (resid 9 through 121 or resid 136 through 195 or (resid 196 and ( \ name N or name CA or name C or name O or name CB )) or resid 197 through 240 or \ (resid 241 and (name N or name CA or name C or name O or name CB or name CG1 or \ name CG2 or name CD1)))) } ncs_group { reference = (chain 'E' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 64 or resid 66 through 72 or resid 74 through 151 \ or resid 153 through 217 or (resid 218 and (name N or name CA or name C or name \ O or name CB )) or resid 219 through 237 or (resid 238 and (name N or name CA o \ r name C or name O or name CB )) or resid 239)) selection = (chain 'S' and (resid 2 through 53 or (resid 54 through 55 and (name N or name C \ A or name C or name O or name CB )) or resid 56 through 64 or resid 66 through 7 \ 2 or resid 74 through 151 or resid 153 through 207 or (resid 208 and (name N or \ name CA or name C or name O or name CB )) or resid 209 through 239)) } ncs_group { reference = (chain 'F' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 55 or (resid 56 and (name N or name CA or name C or name O \ or name CB )) or resid 57 through 132 or resid 134 through 187 or (resid 188 and \ (name N or name CA or name C or name O or name CB )) or resid 189 through 191 o \ r (resid 192 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 93 through 244)) selection = (chain 'T' and (resid 5 through 132 or resid 134 through 244)) } ncs_group { reference = (chain 'G' and (resid 9 through 54 or (resid 55 and (name N or name CA or name C \ or name O or name CB )) or resid 56 through 88 or resid 90 through 144 or (resi \ d 145 through 146 and (name N or name CA or name C or name O or name CB )) or re \ sid 147 through 245)) selection = (chain 'U' and (resid 9 through 88 or resid 90 through 180 or (resid 181 and (na \ me N or name CA or name C or name O or name CB )) or resid 182 through 245)) } ncs_group { reference = (chain 'H' and (resid 1 through 103 or resid 105 through 126 or resid 128 throug \ h 179 or (resid 180 and (name N or name CA or name C or name O or name CB )) or \ resid 181 through 186 or resid 188 through 193 or (resid 194 and (name N or name \ CA or name C or name O or name CB )) or resid 195 through 202 or (resid 203 and \ (name N or name CA or name C or name O or name CB )) or resid 204 through 220)) \ selection = (chain 'V' and (resid 1 through 103 or resid 105 through 126 or resid 128 throug \ h 186 or resid 188 through 220)) } ncs_group { reference = (chain 'I' and (resid 1 through 9 or resid 11 through 15 or resid 18 through 24 \ or resid 26 through 76 or resid 79 through 190 or (resid 191 and (name N or name \ CA or name C or name O or name CB )) or resid 192 through 204)) selection = (chain 'W' and (resid 1 through 9 or resid 11 through 15 or resid 18 through 24 \ or resid 26 through 76 or resid 79 through 204)) } ncs_group { reference = (chain 'J' and (resid 1 through 45 or resid 47 through 196)) selection = (chain 'X' and (resid 1 through 45 or resid 47 through 94 or (resid 95 and (name \ N or name CA or name C or name O or name CB )) or resid 96 through 108 or (resi \ d 109 and (name N or name CA or name C or name O or name CB )) or resid 110 thro \ ugh 196)) } ncs_group { reference = (chain 'K' and (resid 1 through 96 or resid 98 through 140 or resid 142 through \ 185 or resid 187 through 199)) selection = (chain 'Y' and (resid 1 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 88 or (resid 89 and (name N or name C \ A or name C or name O or name CB )) or resid 90 through 96 or resid 98 through 1 \ 40 or resid 142 through 185 or resid 187 through 199)) } ncs_group { reference = (chain 'L' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 or resid 4 through 42 or resid 44 through 161 or (resid 162 and (na \ me N or name CA or name C or name O or name CB )) or resid 163 through 168 or (r \ esid 169 and (name N or name CA or name C or name O or name CB )) or resid 170 t \ hrough 213)) selection = (chain 'Z' and (resid 1 through 2 or resid 4 through 42 or resid 44 through 199 \ or (resid 200 and (name N or name CA or name C or name O or name CB )) or resid \ 201 through 213)) } ncs_group { reference = (chain 'M' and (resid 1 through 166 or resid 168 through 205 or (resid 206 and ( \ name N or name CA or name C or name O or name CB )) or resid 207 through 216)) selection = (chain 'a' and (resid 1 through 166 or resid 168 through 216)) } ncs_group { reference = (chain 'N' and (resid 1 through 85 or resid 87 through 146 or resid 148 through \ 202)) selection = (chain 'b' and (resid 1 through 85 or resid 87 through 146 or resid 148 through \ 149 or (resid 150 and (name N or name CA or name C or name O or name CB )) or re \ sid 151 through 202)) } 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=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.470 Construct map_model_manager: 0.030 Extract box with map and model: 10.900 Check model and map are aligned: 0.650 Set scattering table: 0.420 Process input model: 134.040 Find NCS groups from input model: 4.090 Set up NCS constraints: 0.270 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: 0.010 Load rotamer database and sin/cos tables:8.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 160.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 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 : 0.011 0.128 63716 Z= 0.692 Angle : 1.229 19.186 86269 Z= 0.671 Chirality : 0.099 5.025 9754 Planarity : 0.008 0.100 11057 Dihedral : 11.137 123.792 23643 Min Nonbonded Distance : 1.627 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.46 % Favored : 94.42 % Rotamer: Outliers : 0.95 % Allowed : 4.10 % Favored : 94.94 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.08), residues: 7935 helix: -2.25 (0.07), residues: 3359 sheet: -1.13 (0.12), residues: 1541 loop : -2.14 (0.10), residues: 3035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.006 TRP T 215 HIS 0.028 0.004 HIS c 227 PHE 0.078 0.005 PHE L 124 TYR 0.081 0.006 TYR Y 112 ARG 0.019 0.002 ARG a 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15870 Ramachandran restraints generated. 7935 Oldfield, 0 Emsley, 7935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15870 Ramachandran restraints generated. 7935 Oldfield, 0 Emsley, 7935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1912 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 1862 time to evaluate : 5.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 80 THR cc_start: 0.8363 (m) cc_final: 0.7910 (p) REVERT: B 228 LEU cc_start: 0.8095 (tt) cc_final: 0.7884 (tp) REVERT: C 116 GLN cc_start: 0.7973 (tt0) cc_final: 0.7714 (tt0) REVERT: D 164 GLN cc_start: 0.8083 (tm130) cc_final: 0.7752 (tm130) REVERT: E 30 LYS cc_start: 0.8628 (mtmm) cc_final: 0.8324 (mtmm) REVERT: E 61 LYS cc_start: 0.8134 (mtmp) cc_final: 0.7854 (mmtm) REVERT: E 155 ASP cc_start: 0.8125 (t0) cc_final: 0.7855 (t0) REVERT: F 27 MET cc_start: 0.8131 (mtm) cc_final: 0.7885 (mtm) REVERT: F 170 GLN cc_start: 0.7596 (tp-100) cc_final: 0.7028 (pm20) REVERT: F 184 MET cc_start: 0.8546 (mtt) cc_final: 0.8293 (mtm) REVERT: H 135 MET cc_start: 0.9182 (tpp) cc_final: 0.8642 (tpp) REVERT: H 205 GLU cc_start: 0.6205 (mm-30) cc_final: 0.5949 (tp30) REVERT: I 11 MET cc_start: 0.8688 (ptp) cc_final: 0.8465 (ptp) REVERT: I 156 ASN cc_start: 0.8761 (m-40) cc_final: 0.8559 (m110) REVERT: K 36 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8259 (mt-10) REVERT: L 105 TYR cc_start: 0.7672 (t80) cc_final: 0.6830 (t80) REVERT: M 96 MET cc_start: 0.8364 (mmm) cc_final: 0.8123 (mmt) REVERT: N 154 GLN cc_start: 0.7684 (tp40) cc_final: 0.7444 (mm110) REVERT: O 94 GLN cc_start: 0.7638 (mm-40) cc_final: 0.7435 (mp10) REVERT: P 64 LYS cc_start: 0.8107 (mtpt) cc_final: 0.7790 (mtpt) REVERT: P 160 LYS cc_start: 0.8150 (mtmt) cc_final: 0.7834 (mttm) REVERT: R 209 LYS cc_start: 0.8241 (tttt) cc_final: 0.7798 (ttpt) REVERT: T 92 ARG cc_start: 0.8714 (mtt180) cc_final: 0.8486 (mtt180) REVERT: T 93 GLU cc_start: 0.7443 (tt0) cc_final: 0.7195 (pt0) REVERT: T 220 THR cc_start: 0.8027 (p) cc_final: 0.7592 (p) REVERT: U 194 THR cc_start: 0.7839 (m) cc_final: 0.7425 (p) REVERT: V 120 ASP cc_start: 0.7809 (m-30) cc_final: 0.7414 (m-30) REVERT: W 47 ARG cc_start: 0.7606 (mtt90) cc_final: 0.7302 (mtt180) REVERT: Y 18 SER cc_start: 0.8416 (p) cc_final: 0.8150 (p) REVERT: Z 184 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7607 (mm-30) REVERT: a 200 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7150 (mt-10) REVERT: b 149 LYS cc_start: 0.8518 (tttt) cc_final: 0.7947 (ttpt) REVERT: c 254 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7885 (mm-40) REVERT: c 498 SER cc_start: 0.8345 (t) cc_final: 0.8048 (m) REVERT: c 534 ARG cc_start: 0.7411 (ttp-110) cc_final: 0.6985 (ttm-80) REVERT: c 820 CYS cc_start: 0.6782 (t) cc_final: 0.6558 (t) REVERT: c 1247 HIS cc_start: 0.7832 (t-90) cc_final: 0.7458 (t-90) REVERT: c 1428 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8681 (mp) REVERT: c 1587 ARG cc_start: 0.7782 (mtt180) cc_final: 0.7555 (mtm-85) REVERT: c 1615 TYR cc_start: 0.5945 (m-10) cc_final: 0.5737 (m-10) outliers start: 50 outliers final: 14 residues processed: 1894 average time/residue: 1.5027 time to fit residues: 3580.9498 Evaluate side-chains 1064 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1049 time to evaluate : 5.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain F residue 215 TRP Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain c residue 172 ILE Chi-restraints excluded: chain c residue 427 MET Chi-restraints excluded: chain c residue 463 VAL Chi-restraints excluded: chain c residue 828 LEU Chi-restraints excluded: chain c residue 844 VAL Chi-restraints excluded: chain c residue 1020 THR Chi-restraints excluded: chain c residue 1224 ILE Chi-restraints excluded: chain c residue 1428 ILE Chi-restraints excluded: chain c residue 1443 LEU Chi-restraints excluded: chain c residue 1468 LEU Chi-restraints excluded: chain c residue 1747 VAL Chi-restraints excluded: chain c residue 1835 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 663 optimal weight: 0.9990 chunk 595 optimal weight: 0.9990 chunk 330 optimal weight: 0.8980 chunk 203 optimal weight: 2.9990 chunk 401 optimal weight: 0.8980 chunk 318 optimal weight: 6.9990 chunk 616 optimal weight: 0.0870 chunk 238 optimal weight: 8.9990 chunk 374 optimal weight: 4.9990 chunk 458 optimal weight: 0.9990 chunk 713 optimal weight: 0.7980 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 118 GLN B 84 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN C 175 ASN D 155 HIS ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN E 166 GLN E 185 ASN F 147 GLN ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 GLN G 150 GLN G 172 GLN H 153 ASN I 17 ASN B I 161 HIS J 8 GLN J 71 ASN J 101 ASN L 157 ASN M 81 HIS M 89 HIS M 188 GLN M 213 HIS N 62 GLN P 20 GLN P 51 ASN P 84 ASN P 100 GLN ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 149 GLN P 155 ASN Q 18 GLN Q 54 GLN Q 94 HIS ** Q 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 97 GLN ** R 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 16 GLN S 65 HIS B S 90 GLN T 101 ASN T 110 HIS T 143 ASN U 92 GLN U 147 GLN V 193 ASN W 156 ASN W 168 GLN W 172 ASN ** X 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 63 ASN X 71 ASN X 87 ASN X 174 ASN ** Y 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 70 ASN Y 119 ASN Y 162 GLN Z 79 ASN Z 151 ASN Z 157 ASN Z 160 ASN a 65 GLN a 213 HIS ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 110 GLN c 35 ASN c 58 ASN c 125 ASN c 159 HIS c 163 ASN c 208 GLN c 288 ASN c 310 HIS c 505 GLN c 527 ASN c 549 GLN c 596 GLN c 611 ASN c 697 GLN c 703 GLN c 712 GLN c 722 HIS c 796 GLN ** c 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 838 ASN c 863 ASN c 882 ASN c 907 HIS c 927 ASN c 947 GLN c1021 GLN c1044 HIS c1051 GLN c1109 GLN c1116 ASN c1132 GLN c1165 HIS ** c1351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c1363 HIS c1469 GLN c1613 ASN c1672 ASN c1679 ASN c1698 GLN c1714 GLN c1725 GLN c1760 HIS c1787 ASN c1813 HIS ** c1820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 63716 Z= 0.207 Angle : 0.671 13.551 86269 Z= 0.349 Chirality : 0.045 0.403 9754 Planarity : 0.005 0.058 11057 Dihedral : 6.465 89.766 8844 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.13 % Favored : 95.82 % Rotamer: Outliers : 3.84 % Allowed : 13.41 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.03 % Twisted Proline : 0.35 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.09), residues: 7935 helix: -0.46 (0.08), residues: 3382 sheet: -0.70 (0.12), residues: 1501 loop : -1.65 (0.10), residues: 3052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP T 215 HIS 0.010 0.001 HIS c 227 PHE 0.031 0.002 PHE A 198 TYR 0.030 0.002 TYR a 178 ARG 0.008 0.001 ARG c1377 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15870 Ramachandran restraints generated. 7935 Oldfield, 0 Emsley, 7935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15870 Ramachandran restraints generated. 7935 Oldfield, 0 Emsley, 7935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1523 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 1279 time to evaluate : 5.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 89 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7146 (tt0) REVERT: B 244 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7387 (mm-30) REVERT: C 38 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7160 (mmp80) REVERT: C 95 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7999 (mtt90) REVERT: C 116 GLN cc_start: 0.7500 (tt0) cc_final: 0.7272 (tt0) REVERT: D 114 GLN cc_start: 0.8617 (tt0) cc_final: 0.8349 (tt0) REVERT: D 164 GLN cc_start: 0.8199 (tm130) cc_final: 0.7800 (tm130) REVERT: E 8 ASN cc_start: 0.7151 (t0) cc_final: 0.6914 (OUTLIER) REVERT: E 26 MET cc_start: 0.7842 (mmm) cc_final: 0.7584 (mtm) REVERT: E 61 LYS cc_start: 0.8124 (mtmp) cc_final: 0.7827 (mmtm) REVERT: E 125 ARG cc_start: 0.6401 (mmm-85) cc_final: 0.6162 (mtp85) REVERT: F 150 MET cc_start: 0.8780 (tmm) cc_final: 0.8507 (tmm) REVERT: F 170 GLN cc_start: 0.7589 (tp-100) cc_final: 0.7124 (pm20) REVERT: F 184 MET cc_start: 0.8495 (mtt) cc_final: 0.8250 (mtm) REVERT: F 206 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7484 (p0) REVERT: G 10 ASP cc_start: 0.6306 (t0) cc_final: 0.6083 (t70) REVERT: G 21 ARG cc_start: 0.8643 (mtm-85) cc_final: 0.8263 (mtp180) REVERT: G 108 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6983 (tm-30) REVERT: H 135 MET cc_start: 0.9142 (tpp) cc_final: 0.8770 (tpp) REVERT: I 156 ASN cc_start: 0.8698 (m-40) cc_final: 0.8469 (m110) REVERT: J 38 MET cc_start: 0.8273 (mmp) cc_final: 0.7796 (mmp) REVERT: J 49 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7651 (tm-30) REVERT: K 36 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8453 (mt-10) REVERT: L 69 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7302 (mm-30) REVERT: L 105 TYR cc_start: 0.7527 (t80) cc_final: 0.6762 (t80) REVERT: M 56 ASP cc_start: 0.8443 (t70) cc_final: 0.8065 (t70) REVERT: M 59 ASP cc_start: 0.8691 (m-30) cc_final: 0.8279 (m-30) REVERT: M 96 MET cc_start: 0.8551 (mmm) cc_final: 0.8291 (mmt) REVERT: M 200 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: N 7 GLN cc_start: 0.8413 (tt0) cc_final: 0.7969 (tt0) REVERT: O 94 GLN cc_start: 0.7652 (mm-40) cc_final: 0.7396 (mp10) REVERT: P 187 LYS cc_start: 0.8217 (mtpp) cc_final: 0.7871 (mtmm) REVERT: P 213 ILE cc_start: 0.8408 (mt) cc_final: 0.8166 (mp) REVERT: Q 117 ARG cc_start: 0.8034 (ttm-80) cc_final: 0.7825 (ttm110) REVERT: R 209 LYS cc_start: 0.8152 (tttt) cc_final: 0.7810 (ttpt) REVERT: S 18 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7356 (mtp85) REVERT: S 189 LYS cc_start: 0.8221 (mttp) cc_final: 0.7850 (mmmt) REVERT: T 27 MET cc_start: 0.8199 (mtm) cc_final: 0.7901 (mtp) REVERT: T 31 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7952 (pm20) REVERT: U 11 ARG cc_start: 0.7660 (mtt-85) cc_final: 0.7442 (mmm-85) REVERT: V 120 ASP cc_start: 0.7742 (m-30) cc_final: 0.7387 (m-30) REVERT: V 215 LYS cc_start: 0.7113 (tppp) cc_final: 0.6532 (ttmt) REVERT: Y 18 SER cc_start: 0.8395 (p) cc_final: 0.8072 (p) REVERT: Y 67 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7804 (tt0) REVERT: Y 182 ASP cc_start: 0.8160 (p0) cc_final: 0.7783 (p0) REVERT: Z 69 GLU cc_start: 0.7311 (mt-10) cc_final: 0.7043 (mt-10) REVERT: Z 180 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8273 (mm) REVERT: Z 184 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7578 (mm-30) REVERT: Z 207 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8636 (m) REVERT: a 200 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7179 (mt-10) REVERT: b 86 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7856 (mtp) REVERT: b 93 ASP cc_start: 0.7522 (m-30) cc_final: 0.7296 (m-30) REVERT: c 54 GLN cc_start: 0.8337 (mm-40) cc_final: 0.8125 (mm110) REVERT: c 77 ARG cc_start: 0.7451 (ttt-90) cc_final: 0.7126 (ttm110) REVERT: c 379 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7786 (mm) REVERT: c 640 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6364 (mp0) REVERT: c 665 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7714 (m110) REVERT: c 809 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7841 (OUTLIER) REVERT: c 828 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8474 (mt) REVERT: c 1194 ASN cc_start: 0.8259 (OUTLIER) cc_final: 0.8053 (p0) REVERT: c 1247 HIS cc_start: 0.7427 (t-90) cc_final: 0.7211 (t70) REVERT: c 1417 THR cc_start: 0.8800 (m) cc_final: 0.8580 (p) REVERT: c 1587 ARG cc_start: 0.7858 (mtt180) cc_final: 0.7528 (mtm-85) REVERT: c 1720 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7411 (tmm) REVERT: c 1819 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7209 (pm20) REVERT: c 1832 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8421 (mp) outliers start: 244 outliers final: 55 residues processed: 1436 average time/residue: 1.4134 time to fit residues: 2591.0617 Evaluate side-chains 1121 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 1046 time to evaluate : 4.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 154 HIS Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 230 ASP Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain L residue 169 ASP Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain M residue 205 THR Chi-restraints excluded: chain O residue 131 VAL Chi-restraints excluded: chain P residue 207 SER Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain T residue 31 GLU Chi-restraints excluded: chain T residue 215 TRP Chi-restraints excluded: chain T residue 221 ASN Chi-restraints excluded: chain U residue 191 PHE Chi-restraints excluded: chain U residue 195 VAL Chi-restraints excluded: chain V residue 1 THR Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain Z residue 180 ILE Chi-restraints excluded: chain Z residue 207 THR Chi-restraints excluded: chain b residue 86 MET Chi-restraints excluded: chain c residue 102 LEU Chi-restraints excluded: chain c residue 111 LEU Chi-restraints excluded: chain c residue 172 ILE Chi-restraints excluded: chain c residue 247 ASN Chi-restraints excluded: chain c residue 379 LEU Chi-restraints excluded: chain c residue 486 MET Chi-restraints excluded: chain c residue 578 LEU Chi-restraints excluded: chain c residue 609 VAL Chi-restraints excluded: chain c residue 640 GLU Chi-restraints excluded: chain c residue 665 ASN Chi-restraints excluded: chain c residue 683 ILE Chi-restraints excluded: chain c residue 802 LYS Chi-restraints excluded: chain c residue 809 ASP Chi-restraints excluded: chain c residue 828 LEU Chi-restraints excluded: chain c residue 844 VAL Chi-restraints excluded: chain c residue 910 GLU Chi-restraints excluded: chain c residue 913 SER Chi-restraints excluded: chain c residue 1047 ASP Chi-restraints excluded: chain c residue 1164 GLU Chi-restraints excluded: chain c residue 1194 ASN Chi-restraints excluded: chain c residue 1255 THR Chi-restraints excluded: chain c residue 1272 THR Chi-restraints excluded: chain c residue 1285 VAL Chi-restraints excluded: chain c residue 1455 GLU Chi-restraints excluded: chain c residue 1465 LEU Chi-restraints excluded: chain c residue 1468 LEU Chi-restraints excluded: chain c residue 1602 LEU Chi-restraints excluded: chain c residue 1720 MET Chi-restraints excluded: chain c residue 1735 LYS Chi-restraints excluded: chain c residue 1747 VAL Chi-restraints excluded: chain c residue 1819 GLU Chi-restraints excluded: chain c residue 1832 LEU Chi-restraints excluded: chain c residue 1835 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 396 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 594 optimal weight: 4.9990 chunk 486 optimal weight: 3.9990 chunk 196 optimal weight: 8.9990 chunk 715 optimal weight: 4.9990 chunk 772 optimal weight: 0.7980 chunk 636 optimal weight: 2.9990 chunk 709 optimal weight: 6.9990 chunk 243 optimal weight: 2.9990 chunk 573 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN B 84 ASN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN D 41 GLN D 164 GLN E 21 GLN E 185 ASN ** F 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 GLN G 172 GLN K 162 GLN ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 106 GLN N 154 GLN O 101 GLN ** O 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 HIS P 84 ASN P 100 GLN P 109 GLN P 123 GLN Q 159 ASN ** R 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 16 GLN S 31 GLN S 60 GLN T 101 ASN U 92 GLN U 147 GLN U 150 GLN V 57 GLN V 193 ASN W 156 ASN W 161 HIS X 8 GLN X 61 GLN ** Y 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 160 ASN b 28 ASN b 62 GLN b 110 GLN c 329 HIS c 402 GLN c 796 GLN c 826 ASN c1086 GLN c1351 ASN c1644 GLN ** c1672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 63716 Z= 0.432 Angle : 0.748 13.061 86269 Z= 0.385 Chirality : 0.049 0.219 9754 Planarity : 0.006 0.067 11057 Dihedral : 6.428 94.162 8831 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.95 % Favored : 94.99 % Rotamer: Outliers : 4.73 % Allowed : 14.86 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.03 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.09), residues: 7935 helix: 0.10 (0.09), residues: 3408 sheet: -0.48 (0.13), residues: 1518 loop : -1.45 (0.11), residues: 3009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP T 215 HIS 0.010 0.002 HIS c1760 PHE 0.039 0.003 PHE L 101 TYR 0.033 0.003 TYR Y 153 ARG 0.008 0.001 ARG a 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15870 Ramachandran restraints generated. 7935 Oldfield, 0 Emsley, 7935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15870 Ramachandran restraints generated. 7935 Oldfield, 0 Emsley, 7935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1290 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 304 poor density : 986 time to evaluate : 5.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.6041 (mmt180) REVERT: B 89 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7180 (tt0) REVERT: B 244 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7417 (mm-30) REVERT: C 38 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7204 (mmp80) REVERT: C 207 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7730 (tp30) REVERT: D 81 LEU cc_start: 0.7947 (pp) cc_final: 0.7711 (pp) REVERT: E 8 ASN cc_start: 0.7492 (t0) cc_final: 0.7245 (OUTLIER) REVERT: E 61 LYS cc_start: 0.8121 (mtmp) cc_final: 0.7794 (mmtm) REVERT: E 125 ARG cc_start: 0.6840 (mmm-85) cc_final: 0.6016 (mtp85) REVERT: F 150 MET cc_start: 0.8812 (tmm) cc_final: 0.8589 (tmm) REVERT: F 169 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7551 (ptt90) REVERT: F 170 GLN cc_start: 0.7713 (tp-100) cc_final: 0.7169 (pm20) REVERT: F 179 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7608 (tp) REVERT: F 184 MET cc_start: 0.8566 (mtt) cc_final: 0.8311 (mtm) REVERT: F 206 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7582 (p0) REVERT: F 218 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7240 (mt-10) REVERT: F 242 SER cc_start: 0.8282 (OUTLIER) cc_final: 0.7761 (p) REVERT: G 108 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7022 (tm-30) REVERT: H 64 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7398 (tt0) REVERT: I 11 MET cc_start: 0.8860 (ptm) cc_final: 0.8520 (ptp) REVERT: I 156 ASN cc_start: 0.8825 (m-40) cc_final: 0.8565 (m110) REVERT: J 38 MET cc_start: 0.8355 (mmp) cc_final: 0.7979 (mmp) REVERT: J 49 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7786 (tm-30) REVERT: L 69 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7281 (mm-30) REVERT: L 105 TYR cc_start: 0.7865 (t80) cc_final: 0.6890 (t80) REVERT: L 172 MET cc_start: 0.8153 (mmm) cc_final: 0.7798 (mmm) REVERT: L 184 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8127 (mm-30) REVERT: M 110 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7748 (mtm) REVERT: N 147 MET cc_start: 0.9226 (mtp) cc_final: 0.8898 (mtm) REVERT: O 94 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7472 (mp10) REVERT: P 187 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7960 (mtpp) REVERT: Q 53 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7237 (mt) REVERT: Q 105 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7391 (tp30) REVERT: R 20 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.6767 (mmm-85) REVERT: R 209 LYS cc_start: 0.8110 (tttt) cc_final: 0.7767 (ttpt) REVERT: S 18 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7376 (mtp85) REVERT: S 203 GLN cc_start: 0.5982 (mm-40) cc_final: 0.5568 (tp40) REVERT: T 27 MET cc_start: 0.8368 (mtm) cc_final: 0.7987 (mtp) REVERT: U 53 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7836 (mm-40) REVERT: U 196 GLU cc_start: 0.5827 (OUTLIER) cc_final: 0.5049 (mp0) REVERT: V 120 ASP cc_start: 0.7758 (m-30) cc_final: 0.7356 (m-30) REVERT: W 2 ILE cc_start: 0.8316 (mp) cc_final: 0.7831 (mt) REVERT: W 76 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8286 (ttmm) REVERT: Y 38 ASN cc_start: 0.7926 (p0) cc_final: 0.7666 (p0) REVERT: Y 45 MET cc_start: 0.8432 (ttm) cc_final: 0.8151 (ttp) REVERT: Y 62 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7606 (mp10) REVERT: Y 67 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: Y 72 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7831 (pt0) REVERT: Y 182 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7765 (p0) REVERT: Z 69 GLU cc_start: 0.7359 (mt-10) cc_final: 0.7129 (mt-10) REVERT: Z 180 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8454 (mm) REVERT: Z 184 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7612 (mm-30) REVERT: Z 207 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8664 (m) REVERT: a 5 MET cc_start: 0.7874 (mmm) cc_final: 0.7530 (mmp) REVERT: b 86 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7915 (mtp) REVERT: c 54 GLN cc_start: 0.8336 (mm-40) cc_final: 0.8078 (mm110) REVERT: c 77 ARG cc_start: 0.7420 (ttt-90) cc_final: 0.7129 (ttm110) REVERT: c 481 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7105 (ttp) REVERT: c 640 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6464 (mp0) REVERT: c 804 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6699 (mm-30) REVERT: c 809 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7916 (OUTLIER) REVERT: c 985 LYS cc_start: 0.8118 (mtpp) cc_final: 0.7741 (ttpp) REVERT: c 1102 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7762 (mm-30) REVERT: c 1164 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7892 (tt0) REVERT: c 1194 ASN cc_start: 0.8427 (OUTLIER) cc_final: 0.8167 (p0) REVERT: c 1247 HIS cc_start: 0.7728 (t-90) cc_final: 0.7384 (t-90) REVERT: c 1334 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7317 (mtpt) REVERT: c 1468 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8345 (tp) REVERT: c 1499 LYS cc_start: 0.8601 (tmtt) cc_final: 0.8256 (tmtt) REVERT: c 1523 THR cc_start: 0.8596 (m) cc_final: 0.8272 (p) REVERT: c 1577 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8606 (mp) REVERT: c 1587 ARG cc_start: 0.7830 (mtt180) cc_final: 0.7505 (mtm-85) REVERT: c 1615 TYR cc_start: 0.7179 (m-10) cc_final: 0.6929 (m-80) REVERT: c 1687 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7984 (ttt90) REVERT: c 1720 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7682 (tmm) REVERT: c 1810 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7795 (ptt180) REVERT: c 1819 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7272 (pm20) REVERT: c 1832 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8556 (mp) outliers start: 304 outliers final: 113 residues processed: 1191 average time/residue: 1.4730 time to fit residues: 2246.5820 Evaluate side-chains 1056 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 903 time to evaluate : 5.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 154 HIS Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 169 ARG Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 230 ASP Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 204 CYS Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain K residue 1 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain L residue 169 ASP Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain M residue 205 THR Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 131 VAL Chi-restraints excluded: chain O residue 164 LYS Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 221 THR Chi-restraints excluded: chain P residue 34 CYS Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 174 MET Chi-restraints excluded: chain P residue 187 LYS Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 105 GLU Chi-restraints excluded: chain Q residue 191 VAL Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain T residue 142 VAL Chi-restraints excluded: chain T residue 215 TRP Chi-restraints excluded: chain T residue 221 ASN Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 53 GLN Chi-restraints excluded: chain U residue 58 ASP Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 73 THR Chi-restraints excluded: chain U residue 196 GLU Chi-restraints excluded: chain V residue 1 THR Chi-restraints excluded: chain V residue 81 ARG Chi-restraints excluded: chain W residue 76 LYS Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain X residue 25 ILE Chi-restraints excluded: chain Y residue 62 GLN Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain Y residue 72 GLU Chi-restraints excluded: chain Y residue 182 ASP Chi-restraints excluded: chain Y residue 185 ILE Chi-restraints excluded: chain Z residue 118 LYS Chi-restraints excluded: chain Z residue 180 ILE Chi-restraints excluded: chain Z residue 207 THR Chi-restraints excluded: chain a residue 152 GLU Chi-restraints excluded: chain a residue 194 GLU Chi-restraints excluded: chain b residue 86 MET Chi-restraints excluded: chain c residue 57 CYS Chi-restraints excluded: chain c residue 111 LEU Chi-restraints excluded: chain c residue 167 ASN Chi-restraints excluded: chain c residue 172 ILE Chi-restraints excluded: chain c residue 225 GLU Chi-restraints excluded: chain c residue 241 LEU Chi-restraints excluded: chain c residue 247 ASN Chi-restraints excluded: chain c residue 281 THR Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 318 MET Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain c residue 463 VAL Chi-restraints excluded: chain c residue 481 MET Chi-restraints excluded: chain c residue 512 THR Chi-restraints excluded: chain c residue 516 LEU Chi-restraints excluded: chain c residue 562 THR Chi-restraints excluded: chain c residue 578 LEU Chi-restraints excluded: chain c residue 609 VAL Chi-restraints excluded: chain c residue 640 GLU Chi-restraints excluded: chain c residue 802 LYS Chi-restraints excluded: chain c residue 804 GLU Chi-restraints excluded: chain c residue 809 ASP Chi-restraints excluded: chain c residue 816 ILE Chi-restraints excluded: chain c residue 820 CYS Chi-restraints excluded: chain c residue 844 VAL Chi-restraints excluded: chain c residue 872 ILE Chi-restraints excluded: chain c residue 913 SER Chi-restraints excluded: chain c residue 1047 ASP Chi-restraints excluded: chain c residue 1101 VAL Chi-restraints excluded: chain c residue 1135 LYS Chi-restraints excluded: chain c residue 1164 GLU Chi-restraints excluded: chain c residue 1194 ASN Chi-restraints excluded: chain c residue 1220 LYS Chi-restraints excluded: chain c residue 1224 ILE Chi-restraints excluded: chain c residue 1239 ILE Chi-restraints excluded: chain c residue 1255 THR Chi-restraints excluded: chain c residue 1272 THR Chi-restraints excluded: chain c residue 1285 VAL Chi-restraints excluded: chain c residue 1289 VAL Chi-restraints excluded: chain c residue 1323 ILE Chi-restraints excluded: chain c residue 1334 LYS Chi-restraints excluded: chain c residue 1404 LEU Chi-restraints excluded: chain c residue 1455 GLU Chi-restraints excluded: chain c residue 1465 LEU Chi-restraints excluded: chain c residue 1468 LEU Chi-restraints excluded: chain c residue 1476 GLU Chi-restraints excluded: chain c residue 1577 ILE Chi-restraints excluded: chain c residue 1602 LEU Chi-restraints excluded: chain c residue 1621 ASP Chi-restraints excluded: chain c residue 1687 ARG Chi-restraints excluded: chain c residue 1720 MET Chi-restraints excluded: chain c residue 1735 LYS Chi-restraints excluded: chain c residue 1747 VAL Chi-restraints excluded: chain c residue 1810 ARG Chi-restraints excluded: chain c residue 1819 GLU Chi-restraints excluded: chain c residue 1827 ASP Chi-restraints excluded: chain c residue 1832 LEU Chi-restraints excluded: chain c residue 1835 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 706 optimal weight: 0.9990 chunk 537 optimal weight: 2.9990 chunk 371 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 341 optimal weight: 6.9990 chunk 480 optimal weight: 0.8980 chunk 717 optimal weight: 1.9990 chunk 759 optimal weight: 0.9980 chunk 374 optimal weight: 4.9990 chunk 680 optimal weight: 0.0270 chunk 204 optimal weight: 0.7980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN D 99 HIS E 4 ASN E 185 ASN G 12 HIS G 172 GLN J 27 GLN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 152 GLN N 66 HIS N 106 GLN N 154 GLN N 193 GLN O 101 GLN O 111 GLN P 84 ASN P 100 GLN P 198 ASN Q 122 ASN ** R 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 16 GLN S 60 GLN S 152 ASN B U 150 GLN V 153 ASN V 193 ASN W 156 ASN X 8 GLN ** Y 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 160 ASN b 7 GLN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 110 GLN c 707 HIS c 818 HIS c1644 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 63716 Z= 0.186 Angle : 0.601 13.000 86269 Z= 0.312 Chirality : 0.043 0.173 9754 Planarity : 0.004 0.057 11057 Dihedral : 5.859 93.782 8829 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.23 % Favored : 95.73 % Rotamer: Outliers : 3.67 % Allowed : 16.52 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.03 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.09), residues: 7935 helix: 0.66 (0.09), residues: 3398 sheet: -0.34 (0.13), residues: 1511 loop : -1.22 (0.11), residues: 3026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP T 215 HIS 0.007 0.001 HIS c 227 PHE 0.026 0.001 PHE A 198 TYR 0.021 0.001 TYR Y 153 ARG 0.011 0.000 ARG O 3 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15870 Ramachandran restraints generated. 7935 Oldfield, 0 Emsley, 7935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15870 Ramachandran restraints generated. 7935 Oldfield, 0 Emsley, 7935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1269 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 1038 time to evaluate : 5.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 89 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7177 (tt0) REVERT: B 244 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7373 (mm-30) REVERT: C 166 LYS cc_start: 0.8331 (tptp) cc_final: 0.8064 (tmtt) REVERT: D 81 LEU cc_start: 0.7737 (pp) cc_final: 0.7480 (pp) REVERT: E 1 MET cc_start: 0.6325 (tpt) cc_final: 0.5784 (tpt) REVERT: E 8 ASN cc_start: 0.7356 (t0) cc_final: 0.7109 (OUTLIER) REVERT: E 60 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.6995 (tp40) REVERT: E 61 LYS cc_start: 0.8059 (mtmp) cc_final: 0.7719 (mmtm) REVERT: E 125 ARG cc_start: 0.6689 (mmm-85) cc_final: 0.6173 (mtp85) REVERT: F 150 MET cc_start: 0.8801 (tmm) cc_final: 0.8514 (tmm) REVERT: F 170 GLN cc_start: 0.7676 (tp-100) cc_final: 0.7182 (pm20) REVERT: F 184 MET cc_start: 0.8580 (mtt) cc_final: 0.8332 (mtm) REVERT: F 242 SER cc_start: 0.8155 (OUTLIER) cc_final: 0.7861 (p) REVERT: G 108 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7067 (tm-30) REVERT: I 11 MET cc_start: 0.8765 (ptm) cc_final: 0.8460 (ptp) REVERT: I 65 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7097 (mtt180) REVERT: I 156 ASN cc_start: 0.8703 (m-40) cc_final: 0.8470 (m110) REVERT: J 38 MET cc_start: 0.8264 (mmp) cc_final: 0.7989 (mmp) REVERT: L 69 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7245 (mm-30) REVERT: L 105 TYR cc_start: 0.7778 (t80) cc_final: 0.6833 (t80) REVERT: L 172 MET cc_start: 0.8091 (mmm) cc_final: 0.7789 (mmm) REVERT: M 46 ASN cc_start: 0.8615 (p0) cc_final: 0.8413 (p0) REVERT: M 56 ASP cc_start: 0.8475 (t70) cc_final: 0.8088 (t70) REVERT: M 59 ASP cc_start: 0.8719 (m-30) cc_final: 0.8294 (m-30) REVERT: M 141 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.7501 (m-80) REVERT: N 93 ASP cc_start: 0.7800 (m-30) cc_final: 0.7530 (m-30) REVERT: N 116 MET cc_start: 0.8064 (mtt) cc_final: 0.7785 (mtt) REVERT: N 147 MET cc_start: 0.9160 (mtp) cc_final: 0.8909 (mtm) REVERT: O 94 GLN cc_start: 0.7797 (mm-40) cc_final: 0.7319 (mp10) REVERT: P 198 ASN cc_start: 0.7499 (t0) cc_final: 0.7085 (t0) REVERT: P 236 LEU cc_start: 0.6568 (mt) cc_final: 0.6264 (mt) REVERT: Q 53 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7131 (mt) REVERT: R 206 MET cc_start: 0.7410 (mtp) cc_final: 0.7066 (mtp) REVERT: R 209 LYS cc_start: 0.8132 (tttt) cc_final: 0.7847 (ttpt) REVERT: S 18 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7328 (mtp85) REVERT: S 203 GLN cc_start: 0.6023 (mm-40) cc_final: 0.5628 (tp40) REVERT: T 144 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.6813 (m-30) REVERT: U 194 THR cc_start: 0.7744 (m) cc_final: 0.7141 (p) REVERT: U 196 GLU cc_start: 0.5924 (OUTLIER) cc_final: 0.4911 (mp0) REVERT: V 120 ASP cc_start: 0.7725 (m-30) cc_final: 0.7374 (m-30) REVERT: W 2 ILE cc_start: 0.8291 (mp) cc_final: 0.7820 (mt) REVERT: W 77 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8282 (tp30) REVERT: Y 18 SER cc_start: 0.8407 (p) cc_final: 0.8154 (p) REVERT: Y 38 ASN cc_start: 0.7928 (p0) cc_final: 0.7667 (p0) REVERT: Y 67 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7804 (tt0) REVERT: Y 72 GLU cc_start: 0.8076 (pt0) cc_final: 0.7842 (pt0) REVERT: Y 182 ASP cc_start: 0.8093 (p0) cc_final: 0.7717 (p0) REVERT: Z 69 GLU cc_start: 0.7320 (mt-10) cc_final: 0.7078 (mt-10) REVERT: Z 180 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8319 (mm) REVERT: Z 184 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7525 (mm-30) REVERT: c 54 GLN cc_start: 0.8325 (mm-40) cc_final: 0.8032 (mm110) REVERT: c 66 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8185 (pt0) REVERT: c 77 ARG cc_start: 0.7401 (ttt-90) cc_final: 0.7163 (ttp-110) REVERT: c 379 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7866 (mm) REVERT: c 568 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7314 (mt-10) REVERT: c 579 GLU cc_start: 0.7443 (pt0) cc_final: 0.7208 (pt0) REVERT: c 640 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6400 (mp0) REVERT: c 660 ASN cc_start: 0.6708 (t0) cc_final: 0.6448 (t0) REVERT: c 804 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6682 (mm-30) REVERT: c 809 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7866 (m-30) REVERT: c 872 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8252 (mm) REVERT: c 985 LYS cc_start: 0.8083 (mtpp) cc_final: 0.7738 (ttpp) REVERT: c 1194 ASN cc_start: 0.8247 (OUTLIER) cc_final: 0.8045 (p0) REVERT: c 1247 HIS cc_start: 0.7295 (t-90) cc_final: 0.7031 (t70) REVERT: c 1567 ARG cc_start: 0.6964 (mmm160) cc_final: 0.6513 (ttt-90) REVERT: c 1587 ARG cc_start: 0.7795 (mtt180) cc_final: 0.7463 (mtm-85) REVERT: c 1615 TYR cc_start: 0.7068 (m-10) cc_final: 0.6814 (m-80) REVERT: c 1617 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.6362 (tt0) REVERT: c 1644 GLN cc_start: 0.7506 (tp40) cc_final: 0.7119 (mm110) REVERT: c 1720 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7708 (tmm) REVERT: c 1810 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7603 (ptt180) REVERT: c 1819 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7302 (pm20) REVERT: c 1827 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7120 (m-30) REVERT: c 1832 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8534 (mp) outliers start: 231 outliers final: 74 residues processed: 1197 average time/residue: 1.4435 time to fit residues: 2218.9011 Evaluate side-chains 1030 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 931 time to evaluate : 5.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 60 GLN Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 230 ASP Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 204 CYS Chi-restraints excluded: chain I residue 65 ARG Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain K residue 1 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain L residue 169 ASP Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 141 TYR Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain M residue 205 THR Chi-restraints excluded: chain O residue 131 VAL Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 221 THR Chi-restraints excluded: chain P residue 34 CYS Chi-restraints excluded: chain P residue 174 MET Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 191 VAL Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain T residue 144 ASP Chi-restraints excluded: chain T residue 215 TRP Chi-restraints excluded: chain U residue 73 THR Chi-restraints excluded: chain U residue 196 GLU Chi-restraints excluded: chain V residue 81 ARG Chi-restraints excluded: chain W residue 77 GLU Chi-restraints excluded: chain X residue 25 ILE Chi-restraints excluded: chain X residue 69 MET Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain Z residue 118 LYS Chi-restraints excluded: chain Z residue 180 ILE Chi-restraints excluded: chain a residue 152 GLU Chi-restraints excluded: chain a residue 194 GLU Chi-restraints excluded: chain c residue 66 GLN Chi-restraints excluded: chain c residue 172 ILE Chi-restraints excluded: chain c residue 281 THR Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 379 LEU Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain c residue 463 VAL Chi-restraints excluded: chain c residue 502 ILE Chi-restraints excluded: chain c residue 512 THR Chi-restraints excluded: chain c residue 537 CYS Chi-restraints excluded: chain c residue 562 THR Chi-restraints excluded: chain c residue 578 LEU Chi-restraints excluded: chain c residue 609 VAL Chi-restraints excluded: chain c residue 640 GLU Chi-restraints excluded: chain c residue 669 LEU Chi-restraints excluded: chain c residue 802 LYS Chi-restraints excluded: chain c residue 804 GLU Chi-restraints excluded: chain c residue 809 ASP Chi-restraints excluded: chain c residue 820 CYS Chi-restraints excluded: chain c residue 844 VAL Chi-restraints excluded: chain c residue 872 ILE Chi-restraints excluded: chain c residue 1012 LEU Chi-restraints excluded: chain c residue 1194 ASN Chi-restraints excluded: chain c residue 1220 LYS Chi-restraints excluded: chain c residue 1224 ILE Chi-restraints excluded: chain c residue 1255 THR Chi-restraints excluded: chain c residue 1272 THR Chi-restraints excluded: chain c residue 1285 VAL Chi-restraints excluded: chain c residue 1323 ILE Chi-restraints excluded: chain c residue 1455 GLU Chi-restraints excluded: chain c residue 1465 LEU Chi-restraints excluded: chain c residue 1617 GLU Chi-restraints excluded: chain c residue 1720 MET Chi-restraints excluded: chain c residue 1747 VAL Chi-restraints excluded: chain c residue 1810 ARG Chi-restraints excluded: chain c residue 1819 GLU Chi-restraints excluded: chain c residue 1827 ASP Chi-restraints excluded: chain c residue 1832 LEU Chi-restraints excluded: chain c residue 1835 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 632 optimal weight: 0.6980 chunk 431 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 565 optimal weight: 5.9990 chunk 313 optimal weight: 3.9990 chunk 648 optimal weight: 6.9990 chunk 525 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 387 optimal weight: 8.9990 chunk 681 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN D 41 GLN D 164 GLN E 4 ASN E 185 ASN ** F 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 GLN H 30 ASN ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 HIS N 106 GLN N 154 GLN ** O 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 111 GLN P 40 ASN P 84 ASN P 100 GLN R 186 HIS ** R 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 GLN T 63 ASN U 150 GLN V 193 ASN W 156 ASN X 8 GLN X 61 GLN ** Y 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 160 ASN b 28 ASN c 607 GLN c 611 ASN c 703 GLN c 707 HIS c 818 HIS c1307 GLN ** c1672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 63716 Z= 0.521 Angle : 0.771 13.890 86269 Z= 0.395 Chirality : 0.051 0.255 9754 Planarity : 0.006 0.080 11057 Dihedral : 6.241 96.973 8827 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.08 % Favored : 94.87 % Rotamer: Outliers : 4.60 % Allowed : 16.63 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.03 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.09), residues: 7935 helix: 0.46 (0.09), residues: 3411 sheet: -0.33 (0.12), residues: 1533 loop : -1.23 (0.11), residues: 2991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP T 215 HIS 0.012 0.002 HIS a 89 PHE 0.036 0.003 PHE S 99 TYR 0.031 0.003 TYR Y 153 ARG 0.008 0.001 ARG H 198 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15870 Ramachandran restraints generated. 7935 Oldfield, 0 Emsley, 7935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15870 Ramachandran restraints generated. 7935 Oldfield, 0 Emsley, 7935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1211 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 917 time to evaluate : 5.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.5805 (mmt90) REVERT: B 48 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6954 (tt0) REVERT: B 51 ASN cc_start: 0.8116 (OUTLIER) cc_final: 0.7682 (p0) REVERT: B 89 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7188 (tt0) REVERT: B 135 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8620 (mp) REVERT: C 38 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7289 (mmp80) REVERT: C 207 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7760 (tp30) REVERT: E 29 VAL cc_start: 0.8749 (OUTLIER) cc_final: 0.8548 (t) REVERT: E 46 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8793 (mt) REVERT: E 61 LYS cc_start: 0.8100 (mtmp) cc_final: 0.7767 (mmtm) REVERT: F 150 MET cc_start: 0.8786 (tmm) cc_final: 0.8563 (tmm) REVERT: F 169 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7544 (ptt90) REVERT: F 170 GLN cc_start: 0.7755 (tp-100) cc_final: 0.7139 (pm20) REVERT: F 184 MET cc_start: 0.8567 (mtt) cc_final: 0.8332 (mtm) REVERT: F 242 SER cc_start: 0.8155 (OUTLIER) cc_final: 0.7845 (p) REVERT: G 108 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7077 (tm-30) REVERT: I 11 MET cc_start: 0.8906 (ptm) cc_final: 0.8696 (ptp) REVERT: I 65 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7346 (mtt180) REVERT: I 156 ASN cc_start: 0.8834 (m-40) cc_final: 0.8576 (m110) REVERT: J 38 MET cc_start: 0.8400 (mmp) cc_final: 0.8052 (mmp) REVERT: J 41 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8809 (mtpt) REVERT: J 49 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7827 (tm-30) REVERT: L 69 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7285 (mm-30) REVERT: L 105 TYR cc_start: 0.7957 (t80) cc_final: 0.6850 (t80) REVERT: L 172 MET cc_start: 0.8215 (mmm) cc_final: 0.7860 (mmm) REVERT: M 141 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.7545 (m-80) REVERT: N 7 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8425 (pt0) REVERT: N 147 MET cc_start: 0.9258 (mtp) cc_final: 0.8935 (mtm) REVERT: O 94 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7639 (mp10) REVERT: P 187 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7999 (mtpp) REVERT: Q 53 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.7069 (mt) REVERT: Q 105 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7343 (tp30) REVERT: R 20 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.6915 (mmm-85) REVERT: R 53 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7396 (mtp85) REVERT: R 149 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8294 (ttmm) REVERT: R 209 LYS cc_start: 0.8120 (tttt) cc_final: 0.7833 (ttpt) REVERT: S 18 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7337 (mtp85) REVERT: S 203 GLN cc_start: 0.5971 (mm-40) cc_final: 0.5530 (tp40) REVERT: T 17 ASP cc_start: 0.7159 (OUTLIER) cc_final: 0.6900 (m-30) REVERT: T 150 MET cc_start: 0.8089 (tmm) cc_final: 0.7504 (ttt) REVERT: U 34 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.6730 (mp10) REVERT: U 194 THR cc_start: 0.7746 (m) cc_final: 0.7230 (p) REVERT: V 10 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.7037 (t0) REVERT: V 120 ASP cc_start: 0.7745 (m-30) cc_final: 0.7304 (m-30) REVERT: V 215 LYS cc_start: 0.7175 (tppp) cc_final: 0.6670 (tmmt) REVERT: W 69 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8425 (mtt-85) REVERT: W 76 LYS cc_start: 0.8641 (ttmt) cc_final: 0.8422 (ttmm) REVERT: W 77 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8544 (tp30) REVERT: X 40 GLU cc_start: 0.7865 (tt0) cc_final: 0.7192 (tt0) REVERT: X 41 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8289 (mtmm) REVERT: Y 38 ASN cc_start: 0.7985 (p0) cc_final: 0.7776 (p0) REVERT: Y 67 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: Y 182 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7716 (p0) REVERT: Z 180 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8472 (mm) REVERT: Z 184 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7662 (mm-30) REVERT: Z 207 THR cc_start: 0.8959 (OUTLIER) cc_final: 0.8686 (m) REVERT: c 66 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8335 (pt0) REVERT: c 77 ARG cc_start: 0.7485 (ttt-90) cc_final: 0.7186 (ttm110) REVERT: c 246 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8348 (pm20) REVERT: c 481 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7149 (ttp) REVERT: c 486 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7894 (tpp) REVERT: c 568 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7335 (mt-10) REVERT: c 588 SER cc_start: 0.8650 (t) cc_final: 0.8292 (m) REVERT: c 640 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6478 (mp0) REVERT: c 660 ASN cc_start: 0.7197 (t0) cc_final: 0.6882 (t0) REVERT: c 804 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6769 (mm-30) REVERT: c 809 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7922 (OUTLIER) REVERT: c 1009 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8123 (mp) REVERT: c 1194 ASN cc_start: 0.8373 (OUTLIER) cc_final: 0.8085 (p0) REVERT: c 1247 HIS cc_start: 0.7797 (t-90) cc_final: 0.7556 (t70) REVERT: c 1283 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7454 (ttt) REVERT: c 1340 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7169 (mpt-90) REVERT: c 1439 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.8085 (mttp) REVERT: c 1615 TYR cc_start: 0.7094 (m-10) cc_final: 0.6811 (m-80) REVERT: c 1644 GLN cc_start: 0.7615 (tp40) cc_final: 0.7174 (mm-40) REVERT: c 1720 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7966 (tmm) REVERT: c 1810 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7724 (ptt180) REVERT: c 1819 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7296 (pm20) REVERT: c 1832 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8611 (mp) outliers start: 294 outliers final: 135 residues processed: 1124 average time/residue: 1.4591 time to fit residues: 2093.1909 Evaluate side-chains 1060 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 876 time to evaluate : 5.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 154 HIS Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 169 ARG Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 230 ASP Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 204 CYS Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain I residue 65 ARG Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain L residue 169 ASP Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 141 TYR Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain M residue 205 THR Chi-restraints excluded: chain N residue 7 GLN Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 65 GLU Chi-restraints excluded: chain O residue 131 VAL Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 221 THR Chi-restraints excluded: chain P residue 34 CYS Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 174 MET Chi-restraints excluded: chain P residue 187 LYS Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 100 ASP Chi-restraints excluded: chain Q residue 105 GLU Chi-restraints excluded: chain Q residue 113 SER Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 191 VAL Chi-restraints excluded: chain Q residue 217 LEU Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 53 ARG Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 149 LYS Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 142 VAL Chi-restraints excluded: chain T residue 144 ASP Chi-restraints excluded: chain T residue 215 TRP Chi-restraints excluded: chain T residue 221 ASN Chi-restraints excluded: chain U residue 34 GLN Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 73 THR Chi-restraints excluded: chain U residue 154 CYS Chi-restraints excluded: chain U residue 196 GLU Chi-restraints excluded: chain U residue 219 VAL Chi-restraints excluded: chain V residue 1 THR Chi-restraints excluded: chain V residue 10 ASP Chi-restraints excluded: chain V residue 81 ARG Chi-restraints excluded: chain V residue 156 SER Chi-restraints excluded: chain W residue 69 ARG Chi-restraints excluded: chain W residue 77 GLU Chi-restraints excluded: chain X residue 25 ILE Chi-restraints excluded: chain X residue 39 SER Chi-restraints excluded: chain X residue 41 LYS Chi-restraints excluded: chain X residue 172 ILE Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain Y residue 182 ASP Chi-restraints excluded: chain Y residue 185 ILE Chi-restraints excluded: chain Z residue 55 SER Chi-restraints excluded: chain Z residue 118 LYS Chi-restraints excluded: chain Z residue 166 LEU Chi-restraints excluded: chain Z residue 180 ILE Chi-restraints excluded: chain Z residue 207 THR Chi-restraints excluded: chain a residue 194 GLU Chi-restraints excluded: chain c residue 57 CYS Chi-restraints excluded: chain c residue 66 GLN Chi-restraints excluded: chain c residue 111 LEU Chi-restraints excluded: chain c residue 167 ASN Chi-restraints excluded: chain c residue 172 ILE Chi-restraints excluded: chain c residue 246 GLN Chi-restraints excluded: chain c residue 247 ASN Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 336 SER Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain c residue 436 VAL Chi-restraints excluded: chain c residue 439 ARG Chi-restraints excluded: chain c residue 463 VAL Chi-restraints excluded: chain c residue 481 MET Chi-restraints excluded: chain c residue 486 MET Chi-restraints excluded: chain c residue 512 THR Chi-restraints excluded: chain c residue 578 LEU Chi-restraints excluded: chain c residue 582 VAL Chi-restraints excluded: chain c residue 606 LEU Chi-restraints excluded: chain c residue 609 VAL Chi-restraints excluded: chain c residue 617 ILE Chi-restraints excluded: chain c residue 640 GLU Chi-restraints excluded: chain c residue 685 ARG Chi-restraints excluded: chain c residue 804 GLU Chi-restraints excluded: chain c residue 809 ASP Chi-restraints excluded: chain c residue 820 CYS Chi-restraints excluded: chain c residue 844 VAL Chi-restraints excluded: chain c residue 872 ILE Chi-restraints excluded: chain c residue 910 GLU Chi-restraints excluded: chain c residue 950 LEU Chi-restraints excluded: chain c residue 1009 LEU Chi-restraints excluded: chain c residue 1012 LEU Chi-restraints excluded: chain c residue 1047 ASP Chi-restraints excluded: chain c residue 1100 CYS Chi-restraints excluded: chain c residue 1120 LEU Chi-restraints excluded: chain c residue 1135 LYS Chi-restraints excluded: chain c residue 1154 VAL Chi-restraints excluded: chain c residue 1194 ASN Chi-restraints excluded: chain c residue 1220 LYS Chi-restraints excluded: chain c residue 1239 ILE Chi-restraints excluded: chain c residue 1255 THR Chi-restraints excluded: chain c residue 1272 THR Chi-restraints excluded: chain c residue 1283 MET Chi-restraints excluded: chain c residue 1285 VAL Chi-restraints excluded: chain c residue 1289 VAL Chi-restraints excluded: chain c residue 1323 ILE Chi-restraints excluded: chain c residue 1340 ARG Chi-restraints excluded: chain c residue 1422 ASN Chi-restraints excluded: chain c residue 1433 GLU Chi-restraints excluded: chain c residue 1439 LYS Chi-restraints excluded: chain c residue 1455 GLU Chi-restraints excluded: chain c residue 1465 LEU Chi-restraints excluded: chain c residue 1476 GLU Chi-restraints excluded: chain c residue 1611 ASN Chi-restraints excluded: chain c residue 1720 MET Chi-restraints excluded: chain c residue 1747 VAL Chi-restraints excluded: chain c residue 1810 ARG Chi-restraints excluded: chain c residue 1819 GLU Chi-restraints excluded: chain c residue 1827 ASP Chi-restraints excluded: chain c residue 1832 LEU Chi-restraints excluded: chain c residue 1835 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 255 optimal weight: 0.5980 chunk 684 optimal weight: 0.9990 chunk 150 optimal weight: 0.9980 chunk 446 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 760 optimal weight: 5.9990 chunk 631 optimal weight: 5.9990 chunk 352 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 251 optimal weight: 0.8980 chunk 399 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN D 164 GLN E 185 ASN F 201 HIS G 172 GLN H 30 ASN J 27 GLN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 152 GLN N 106 GLN N 154 GLN N 193 GLN O 101 GLN O 111 GLN O 168 ASN P 40 ASN P 84 ASN P 100 GLN P 198 ASN Q 120 GLN ** R 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 186 HIS ** R 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 16 GLN S 60 GLN S 166 GLN U 92 GLN U 150 GLN V 193 ASN W 156 ASN X 8 GLN ** Y 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 160 ASN a 47 ASN c 254 GLN c 703 GLN c 707 HIS c 818 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 63716 Z= 0.208 Angle : 0.608 13.023 86269 Z= 0.315 Chirality : 0.044 0.265 9754 Planarity : 0.004 0.049 11057 Dihedral : 5.784 96.801 8827 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.15 % Favored : 95.82 % Rotamer: Outliers : 3.38 % Allowed : 18.10 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.03 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.09), residues: 7935 helix: 0.86 (0.09), residues: 3412 sheet: -0.26 (0.13), residues: 1535 loop : -1.07 (0.11), residues: 2988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP T 215 HIS 0.007 0.001 HIS T 224 PHE 0.034 0.001 PHE A 198 TYR 0.022 0.001 TYR C 21 ARG 0.010 0.000 ARG b 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15870 Ramachandran restraints generated. 7935 Oldfield, 0 Emsley, 7935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15870 Ramachandran restraints generated. 7935 Oldfield, 0 Emsley, 7935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1178 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 966 time to evaluate : 4.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.5695 (mmt90) REVERT: B 48 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6846 (mt-10) REVERT: B 235 GLN cc_start: 0.7978 (tm-30) cc_final: 0.7760 (tp-100) REVERT: B 244 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7398 (mm-30) REVERT: C 38 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7269 (mmp80) REVERT: C 166 LYS cc_start: 0.8324 (tptp) cc_final: 0.7978 (tmtt) REVERT: E 61 LYS cc_start: 0.7965 (mtmp) cc_final: 0.7711 (mmtm) REVERT: E 125 ARG cc_start: 0.6880 (mmm-85) cc_final: 0.6070 (mtp85) REVERT: F 170 GLN cc_start: 0.7757 (tp-100) cc_final: 0.7193 (pm20) REVERT: F 184 MET cc_start: 0.8599 (mtt) cc_final: 0.8350 (mtm) REVERT: F 242 SER cc_start: 0.8094 (OUTLIER) cc_final: 0.7873 (p) REVERT: G 108 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7118 (tm-30) REVERT: I 3 MET cc_start: 0.8561 (mmt) cc_final: 0.8260 (mmt) REVERT: I 11 MET cc_start: 0.8824 (ptm) cc_final: 0.8522 (ptp) REVERT: I 65 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7109 (mtt180) REVERT: I 156 ASN cc_start: 0.8700 (m-40) cc_final: 0.8456 (m110) REVERT: J 38 MET cc_start: 0.8306 (mmp) cc_final: 0.8058 (mmp) REVERT: J 49 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7741 (tm-30) REVERT: L 69 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7291 (mm-30) REVERT: L 105 TYR cc_start: 0.7953 (t80) cc_final: 0.6893 (t80) REVERT: L 172 MET cc_start: 0.8161 (mmm) cc_final: 0.7820 (mmm) REVERT: M 30 TYR cc_start: 0.8120 (t80) cc_final: 0.7777 (t80) REVERT: M 46 ASN cc_start: 0.8599 (p0) cc_final: 0.8396 (p0) REVERT: M 56 ASP cc_start: 0.8470 (t70) cc_final: 0.8077 (t70) REVERT: M 59 ASP cc_start: 0.8767 (m-30) cc_final: 0.8363 (m-30) REVERT: M 141 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.7506 (m-80) REVERT: N 7 GLN cc_start: 0.8499 (tt0) cc_final: 0.8290 (pt0) REVERT: N 93 ASP cc_start: 0.7810 (m-30) cc_final: 0.7529 (m-30) REVERT: N 147 MET cc_start: 0.9132 (mtp) cc_final: 0.8929 (mtm) REVERT: N 192 ASP cc_start: 0.7320 (m-30) cc_final: 0.7097 (m-30) REVERT: O 94 GLN cc_start: 0.7774 (mm-40) cc_final: 0.7489 (mp10) REVERT: Q 53 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.6978 (mt) REVERT: R 206 MET cc_start: 0.7484 (mtp) cc_final: 0.7238 (mtp) REVERT: R 209 LYS cc_start: 0.8084 (tttt) cc_final: 0.7818 (ttpt) REVERT: S 18 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7278 (mtp85) REVERT: S 189 LYS cc_start: 0.8289 (mttt) cc_final: 0.7843 (mmmt) REVERT: S 203 GLN cc_start: 0.5975 (mm-40) cc_final: 0.5554 (tp40) REVERT: T 17 ASP cc_start: 0.6895 (OUTLIER) cc_final: 0.6643 (m-30) REVERT: T 27 MET cc_start: 0.8187 (mtm) cc_final: 0.7746 (mtp) REVERT: T 31 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7853 (pm20) REVERT: U 34 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.6715 (mp10) REVERT: U 53 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7861 (mm-40) REVERT: U 194 THR cc_start: 0.7442 (m) cc_final: 0.7008 (p) REVERT: V 10 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.6965 (t0) REVERT: V 120 ASP cc_start: 0.7715 (m-30) cc_final: 0.7331 (m-30) REVERT: W 76 LYS cc_start: 0.8533 (ttmt) cc_final: 0.8322 (ttmm) REVERT: W 77 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8262 (tp30) REVERT: Y 18 SER cc_start: 0.8545 (p) cc_final: 0.8260 (p) REVERT: Y 38 ASN cc_start: 0.8085 (p0) cc_final: 0.7872 (p0) REVERT: Y 67 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7801 (tt0) REVERT: Y 182 ASP cc_start: 0.8052 (p0) cc_final: 0.7708 (p0) REVERT: Z 180 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8319 (mm) REVERT: Z 184 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7584 (mm-30) REVERT: a 102 LYS cc_start: 0.8680 (mtpm) cc_final: 0.8435 (mtpt) REVERT: b 116 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.8109 (mtt) REVERT: c 77 ARG cc_start: 0.7417 (ttt-90) cc_final: 0.7194 (ttp-110) REVERT: c 379 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8050 (mm) REVERT: c 481 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7080 (ttp) REVERT: c 568 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7378 (mt-10) REVERT: c 588 SER cc_start: 0.8599 (t) cc_final: 0.8301 (m) REVERT: c 640 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6456 (mp0) REVERT: c 660 ASN cc_start: 0.6704 (t0) cc_final: 0.6425 (t0) REVERT: c 804 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6723 (mm-30) REVERT: c 809 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7878 (m-30) REVERT: c 872 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8325 (mm) REVERT: c 1247 HIS cc_start: 0.7344 (t-90) cc_final: 0.7085 (t70) REVERT: c 1615 TYR cc_start: 0.6940 (m-10) cc_final: 0.6665 (m-80) REVERT: c 1617 GLU cc_start: 0.6734 (tm-30) cc_final: 0.6501 (tt0) REVERT: c 1644 GLN cc_start: 0.7559 (tp40) cc_final: 0.7115 (mm-40) REVERT: c 1720 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7955 (tmm) REVERT: c 1810 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7571 (ptt180) REVERT: c 1819 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7322 (pm20) REVERT: c 1827 ASP cc_start: 0.7649 (OUTLIER) cc_final: 0.7103 (m-30) REVERT: c 1832 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8570 (mp) outliers start: 212 outliers final: 97 residues processed: 1115 average time/residue: 1.4682 time to fit residues: 2104.9803 Evaluate side-chains 1025 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 899 time to evaluate : 5.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 230 ASP Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain H residue 204 CYS Chi-restraints excluded: chain I residue 65 ARG Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain K residue 1 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain L residue 169 ASP Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 141 TYR Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain M residue 205 THR Chi-restraints excluded: chain O residue 65 GLU Chi-restraints excluded: chain O residue 131 VAL Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 221 THR Chi-restraints excluded: chain P residue 34 CYS Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 174 MET Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 191 VAL Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 114 SER Chi-restraints excluded: chain T residue 17 ASP Chi-restraints excluded: chain T residue 31 GLU Chi-restraints excluded: chain T residue 144 ASP Chi-restraints excluded: chain T residue 202 ASP Chi-restraints excluded: chain T residue 215 TRP Chi-restraints excluded: chain U residue 34 GLN Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 53 GLN Chi-restraints excluded: chain U residue 73 THR Chi-restraints excluded: chain U residue 154 CYS Chi-restraints excluded: chain U residue 196 GLU Chi-restraints excluded: chain U residue 219 VAL Chi-restraints excluded: chain V residue 10 ASP Chi-restraints excluded: chain V residue 81 ARG Chi-restraints excluded: chain V residue 156 SER Chi-restraints excluded: chain V residue 193 ASN Chi-restraints excluded: chain W residue 77 GLU Chi-restraints excluded: chain X residue 69 MET Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain Z residue 55 SER Chi-restraints excluded: chain Z residue 118 LYS Chi-restraints excluded: chain Z residue 180 ILE Chi-restraints excluded: chain Z residue 207 THR Chi-restraints excluded: chain a residue 194 GLU Chi-restraints excluded: chain b residue 116 MET Chi-restraints excluded: chain c residue 172 ILE Chi-restraints excluded: chain c residue 225 GLU Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 308 ILE Chi-restraints excluded: chain c residue 379 LEU Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain c residue 436 VAL Chi-restraints excluded: chain c residue 463 VAL Chi-restraints excluded: chain c residue 481 MET Chi-restraints excluded: chain c residue 512 THR Chi-restraints excluded: chain c residue 609 VAL Chi-restraints excluded: chain c residue 640 GLU Chi-restraints excluded: chain c residue 804 GLU Chi-restraints excluded: chain c residue 809 ASP Chi-restraints excluded: chain c residue 820 CYS Chi-restraints excluded: chain c residue 844 VAL Chi-restraints excluded: chain c residue 872 ILE Chi-restraints excluded: chain c residue 920 LEU Chi-restraints excluded: chain c residue 1047 ASP Chi-restraints excluded: chain c residue 1063 GLN Chi-restraints excluded: chain c residue 1100 CYS Chi-restraints excluded: chain c residue 1120 LEU Chi-restraints excluded: chain c residue 1154 VAL Chi-restraints excluded: chain c residue 1220 LYS Chi-restraints excluded: chain c residue 1224 ILE Chi-restraints excluded: chain c residue 1255 THR Chi-restraints excluded: chain c residue 1272 THR Chi-restraints excluded: chain c residue 1285 VAL Chi-restraints excluded: chain c residue 1323 ILE Chi-restraints excluded: chain c residue 1422 ASN Chi-restraints excluded: chain c residue 1433 GLU Chi-restraints excluded: chain c residue 1455 GLU Chi-restraints excluded: chain c residue 1465 LEU Chi-restraints excluded: chain c residue 1508 VAL Chi-restraints excluded: chain c residue 1662 LEU Chi-restraints excluded: chain c residue 1720 MET Chi-restraints excluded: chain c residue 1747 VAL Chi-restraints excluded: chain c residue 1810 ARG Chi-restraints excluded: chain c residue 1819 GLU Chi-restraints excluded: chain c residue 1827 ASP Chi-restraints excluded: chain c residue 1832 LEU Chi-restraints excluded: chain c residue 1835 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 733 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 433 optimal weight: 4.9990 chunk 555 optimal weight: 0.9980 chunk 430 optimal weight: 7.9990 chunk 640 optimal weight: 2.9990 chunk 424 optimal weight: 0.9980 chunk 757 optimal weight: 0.9980 chunk 474 optimal weight: 0.8980 chunk 461 optimal weight: 0.2980 chunk 349 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 ASN E 185 ASN G 224 ASN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 106 GLN N 154 GLN N 193 GLN O 101 GLN O 111 GLN O 168 ASN P 40 ASN P 84 ASN P 100 GLN P 155 ASN P 198 ASN ** R 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 186 HIS S 16 GLN S 60 GLN S 166 GLN T 63 ASN U 33 ASN U 150 GLN V 193 ASN W 156 ASN X 8 GLN X 61 GLN ** Y 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 160 ASN a 47 ASN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 254 GLN c 707 HIS c 819 ASN c 826 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 63716 Z= 0.197 Angle : 0.597 12.820 86269 Z= 0.309 Chirality : 0.043 0.322 9754 Planarity : 0.004 0.046 11057 Dihedral : 5.587 96.576 8827 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.42 % Favored : 95.56 % Rotamer: Outliers : 3.18 % Allowed : 18.71 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.03 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.09), residues: 7935 helix: 1.08 (0.09), residues: 3407 sheet: -0.19 (0.13), residues: 1531 loop : -1.01 (0.11), residues: 2997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP T 215 HIS 0.006 0.001 HIS R 186 PHE 0.039 0.001 PHE A 198 TYR 0.018 0.001 TYR c 714 ARG 0.009 0.000 ARG V 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15870 Ramachandran restraints generated. 7935 Oldfield, 0 Emsley, 7935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15870 Ramachandran restraints generated. 7935 Oldfield, 0 Emsley, 7935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1140 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 941 time to evaluate : 5.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.5726 (mmt90) REVERT: B 48 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6757 (mt-10) REVERT: B 231 LYS cc_start: 0.8026 (ptpt) cc_final: 0.7767 (ptpp) REVERT: B 244 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7395 (mm-30) REVERT: C 38 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7267 (mmp80) REVERT: C 166 LYS cc_start: 0.8306 (tptp) cc_final: 0.7956 (tmtt) REVERT: E 61 LYS cc_start: 0.7957 (mtmp) cc_final: 0.7705 (mmtm) REVERT: E 125 ARG cc_start: 0.6833 (mmm-85) cc_final: 0.6025 (mtp85) REVERT: F 150 MET cc_start: 0.8684 (tmm) cc_final: 0.8461 (tmm) REVERT: F 170 GLN cc_start: 0.7760 (tp-100) cc_final: 0.7217 (pm20) REVERT: F 184 MET cc_start: 0.8612 (mtt) cc_final: 0.8355 (mtm) REVERT: F 242 SER cc_start: 0.8089 (OUTLIER) cc_final: 0.7872 (p) REVERT: G 108 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7141 (tm-30) REVERT: I 11 MET cc_start: 0.8814 (ptm) cc_final: 0.8522 (ptp) REVERT: I 65 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7161 (mtt180) REVERT: I 156 ASN cc_start: 0.8648 (m-40) cc_final: 0.8416 (m110) REVERT: J 38 MET cc_start: 0.8284 (mmp) cc_final: 0.8047 (mmp) REVERT: J 49 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7682 (tm-30) REVERT: K 56 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7757 (mt-10) REVERT: K 136 TYR cc_start: 0.8829 (OUTLIER) cc_final: 0.6269 (t80) REVERT: L 69 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7225 (mm-30) REVERT: L 105 TYR cc_start: 0.7940 (t80) cc_final: 0.6893 (t80) REVERT: L 172 MET cc_start: 0.8130 (mmm) cc_final: 0.7767 (mmm) REVERT: M 46 ASN cc_start: 0.8636 (p0) cc_final: 0.8412 (p0) REVERT: M 56 ASP cc_start: 0.8469 (t70) cc_final: 0.8076 (t70) REVERT: M 59 ASP cc_start: 0.8758 (m-30) cc_final: 0.8344 (m-30) REVERT: M 141 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.7499 (m-80) REVERT: N 93 ASP cc_start: 0.7822 (m-30) cc_final: 0.7513 (m-30) REVERT: N 147 MET cc_start: 0.9106 (mtp) cc_final: 0.8852 (mtm) REVERT: N 192 ASP cc_start: 0.7356 (m-30) cc_final: 0.7148 (m-30) REVERT: O 94 GLN cc_start: 0.7765 (mm-40) cc_final: 0.7403 (mp10) REVERT: P 211 VAL cc_start: 0.7916 (OUTLIER) cc_final: 0.7619 (t) REVERT: Q 166 LYS cc_start: 0.8271 (tppt) cc_final: 0.8033 (mttp) REVERT: Q 191 VAL cc_start: 0.8059 (OUTLIER) cc_final: 0.7810 (p) REVERT: R 209 LYS cc_start: 0.8073 (tttt) cc_final: 0.7831 (ttpt) REVERT: S 18 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7275 (mtp85) REVERT: S 189 LYS cc_start: 0.8378 (mttt) cc_final: 0.7932 (mmmt) REVERT: S 203 GLN cc_start: 0.5808 (mm-40) cc_final: 0.5402 (tp40) REVERT: T 31 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7862 (pm20) REVERT: T 169 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6489 (ptp-170) REVERT: U 53 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7866 (mm-40) REVERT: U 190 THR cc_start: 0.6818 (p) cc_final: 0.6505 (m) REVERT: U 194 THR cc_start: 0.7473 (m) cc_final: 0.7057 (p) REVERT: U 199 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8165 (mp) REVERT: V 57 GLN cc_start: 0.8394 (mt0) cc_final: 0.8000 (mt0) REVERT: V 120 ASP cc_start: 0.7709 (m-30) cc_final: 0.7333 (m-30) REVERT: W 11 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8617 (ptp) REVERT: W 77 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8257 (tp30) REVERT: X 61 GLN cc_start: 0.8491 (tt0) cc_final: 0.8258 (mt0) REVERT: X 70 ARG cc_start: 0.8039 (mtt-85) cc_final: 0.7809 (mtt-85) REVERT: Y 18 SER cc_start: 0.8536 (p) cc_final: 0.8251 (p) REVERT: Y 38 ASN cc_start: 0.8029 (p0) cc_final: 0.7818 (p0) REVERT: Y 67 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: Y 182 ASP cc_start: 0.8047 (p0) cc_final: 0.7708 (p0) REVERT: Z 180 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8302 (mm) REVERT: Z 184 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7625 (mm-30) REVERT: a 102 LYS cc_start: 0.8725 (mtpm) cc_final: 0.8431 (mtpt) REVERT: c 77 ARG cc_start: 0.7433 (ttt-90) cc_final: 0.7203 (ttp-110) REVERT: c 270 ILE cc_start: 0.5338 (tp) cc_final: 0.5090 (tp) REVERT: c 481 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7087 (ttp) REVERT: c 530 THR cc_start: 0.7566 (m) cc_final: 0.7163 (p) REVERT: c 542 GLU cc_start: 0.7337 (mm-30) cc_final: 0.6991 (mp0) REVERT: c 568 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7370 (mt-10) REVERT: c 588 SER cc_start: 0.8611 (t) cc_final: 0.8322 (m) REVERT: c 640 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6504 (mp0) REVERT: c 660 ASN cc_start: 0.6633 (t0) cc_final: 0.6372 (t0) REVERT: c 804 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6773 (mm-30) REVERT: c 809 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7880 (OUTLIER) REVERT: c 872 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8325 (mm) REVERT: c 1247 HIS cc_start: 0.7236 (t-90) cc_final: 0.6977 (t70) REVERT: c 1615 TYR cc_start: 0.6841 (m-10) cc_final: 0.6614 (m-80) REVERT: c 1617 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.6504 (tt0) REVERT: c 1644 GLN cc_start: 0.7573 (tp40) cc_final: 0.7110 (mm-40) REVERT: c 1720 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7987 (tmm) REVERT: c 1747 VAL cc_start: 0.2609 (OUTLIER) cc_final: 0.2278 (t) REVERT: c 1810 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7578 (ptt180) REVERT: c 1819 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7280 (pm20) REVERT: c 1827 ASP cc_start: 0.7623 (OUTLIER) cc_final: 0.7077 (m-30) REVERT: c 1832 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8580 (mp) outliers start: 199 outliers final: 99 residues processed: 1075 average time/residue: 1.4554 time to fit residues: 1991.0343 Evaluate side-chains 1046 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 916 time to evaluate : 5.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 230 ASP Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 128 ASN Chi-restraints excluded: chain G residue 224 ASN Chi-restraints excluded: chain H residue 204 CYS Chi-restraints excluded: chain I residue 65 ARG Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain K residue 1 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 136 TYR Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain L residue 169 ASP Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 141 TYR Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain M residue 205 THR Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 131 VAL Chi-restraints excluded: chain O residue 164 LYS Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 221 THR Chi-restraints excluded: chain P residue 34 CYS Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 174 MET Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 191 VAL Chi-restraints excluded: chain Q residue 196 LEU Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain T residue 31 GLU Chi-restraints excluded: chain T residue 169 ARG Chi-restraints excluded: chain T residue 202 ASP Chi-restraints excluded: chain T residue 215 TRP Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 53 GLN Chi-restraints excluded: chain U residue 73 THR Chi-restraints excluded: chain U residue 154 CYS Chi-restraints excluded: chain U residue 196 GLU Chi-restraints excluded: chain U residue 199 ILE Chi-restraints excluded: chain U residue 219 VAL Chi-restraints excluded: chain V residue 81 ARG Chi-restraints excluded: chain V residue 156 SER Chi-restraints excluded: chain W residue 11 MET Chi-restraints excluded: chain W residue 77 GLU Chi-restraints excluded: chain X residue 39 SER Chi-restraints excluded: chain X residue 69 MET Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain Z residue 55 SER Chi-restraints excluded: chain Z residue 118 LYS Chi-restraints excluded: chain Z residue 180 ILE Chi-restraints excluded: chain Z residue 201 GLU Chi-restraints excluded: chain Z residue 207 THR Chi-restraints excluded: chain a residue 152 GLU Chi-restraints excluded: chain a residue 194 GLU Chi-restraints excluded: chain c residue 172 ILE Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain c residue 436 VAL Chi-restraints excluded: chain c residue 439 ARG Chi-restraints excluded: chain c residue 463 VAL Chi-restraints excluded: chain c residue 481 MET Chi-restraints excluded: chain c residue 512 THR Chi-restraints excluded: chain c residue 606 LEU Chi-restraints excluded: chain c residue 609 VAL Chi-restraints excluded: chain c residue 640 GLU Chi-restraints excluded: chain c residue 804 GLU Chi-restraints excluded: chain c residue 809 ASP Chi-restraints excluded: chain c residue 820 CYS Chi-restraints excluded: chain c residue 844 VAL Chi-restraints excluded: chain c residue 872 ILE Chi-restraints excluded: chain c residue 1012 LEU Chi-restraints excluded: chain c residue 1047 ASP Chi-restraints excluded: chain c residue 1063 GLN Chi-restraints excluded: chain c residue 1120 LEU Chi-restraints excluded: chain c residue 1154 VAL Chi-restraints excluded: chain c residue 1220 LYS Chi-restraints excluded: chain c residue 1272 THR Chi-restraints excluded: chain c residue 1285 VAL Chi-restraints excluded: chain c residue 1323 ILE Chi-restraints excluded: chain c residue 1353 ASP Chi-restraints excluded: chain c residue 1422 ASN Chi-restraints excluded: chain c residue 1433 GLU Chi-restraints excluded: chain c residue 1455 GLU Chi-restraints excluded: chain c residue 1465 LEU Chi-restraints excluded: chain c residue 1508 VAL Chi-restraints excluded: chain c residue 1526 ILE Chi-restraints excluded: chain c residue 1617 GLU Chi-restraints excluded: chain c residue 1662 LEU Chi-restraints excluded: chain c residue 1720 MET Chi-restraints excluded: chain c residue 1747 VAL Chi-restraints excluded: chain c residue 1810 ARG Chi-restraints excluded: chain c residue 1819 GLU Chi-restraints excluded: chain c residue 1827 ASP Chi-restraints excluded: chain c residue 1832 LEU Chi-restraints excluded: chain c residue 1835 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 468 optimal weight: 0.9980 chunk 302 optimal weight: 4.9990 chunk 452 optimal weight: 0.7980 chunk 228 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 chunk 481 optimal weight: 5.9990 chunk 516 optimal weight: 3.9990 chunk 374 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 595 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 ASN E 166 GLN E 185 ASN E 203 GLN G 224 ASN H 30 ASN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 106 GLN N 154 GLN N 193 GLN O 101 GLN O 111 GLN O 168 ASN P 40 ASN P 84 ASN P 100 GLN P 198 ASN ** R 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 186 HIS S 16 GLN S 60 GLN S 166 GLN T 63 ASN U 150 GLN V 193 ASN W 156 ASN X 8 GLN ** Y 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 160 ASN a 47 ASN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 254 GLN c 707 HIS c 818 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 63716 Z= 0.200 Angle : 0.597 14.965 86269 Z= 0.308 Chirality : 0.043 0.332 9754 Planarity : 0.004 0.053 11057 Dihedral : 5.512 96.711 8827 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.29 % Favored : 95.68 % Rotamer: Outliers : 3.05 % Allowed : 18.98 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.03 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.09), residues: 7935 helix: 1.19 (0.09), residues: 3408 sheet: -0.15 (0.13), residues: 1536 loop : -0.97 (0.11), residues: 2991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP T 215 HIS 0.008 0.001 HIS T 201 PHE 0.044 0.001 PHE A 198 TYR 0.019 0.001 TYR c 714 ARG 0.012 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15870 Ramachandran restraints generated. 7935 Oldfield, 0 Emsley, 7935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15870 Ramachandran restraints generated. 7935 Oldfield, 0 Emsley, 7935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1144 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 954 time to evaluate : 5.235 Fit side-chains revert: symmetry clash REVERT: A 73 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8629 (pt) REVERT: A 112 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.5698 (mmt90) REVERT: B 48 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6695 (mt-10) REVERT: B 89 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7140 (tt0) REVERT: B 231 LYS cc_start: 0.8014 (ptpt) cc_final: 0.7776 (ptpp) REVERT: B 235 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7760 (tp40) REVERT: B 244 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7398 (mm-30) REVERT: C 38 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7280 (mmp80) REVERT: C 166 LYS cc_start: 0.8297 (tptp) cc_final: 0.7955 (tmtt) REVERT: E 60 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.6871 (tp40) REVERT: E 61 LYS cc_start: 0.7948 (mtmp) cc_final: 0.7653 (mmtm) REVERT: E 125 ARG cc_start: 0.6801 (mmm-85) cc_final: 0.6044 (mtp85) REVERT: F 150 MET cc_start: 0.8672 (tmm) cc_final: 0.8440 (tmm) REVERT: F 170 GLN cc_start: 0.7780 (tp-100) cc_final: 0.7242 (pm20) REVERT: F 184 MET cc_start: 0.8612 (mtt) cc_final: 0.8338 (mtm) REVERT: F 242 SER cc_start: 0.8084 (OUTLIER) cc_final: 0.7874 (p) REVERT: G 108 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7137 (tm-30) REVERT: I 11 MET cc_start: 0.8821 (ptm) cc_final: 0.8530 (ptp) REVERT: I 156 ASN cc_start: 0.8624 (m-40) cc_final: 0.8394 (m110) REVERT: J 38 MET cc_start: 0.8278 (mmp) cc_final: 0.8048 (mmp) REVERT: J 49 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7680 (tm-30) REVERT: K 56 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7803 (mt-10) REVERT: K 136 TYR cc_start: 0.8827 (OUTLIER) cc_final: 0.6303 (t80) REVERT: K 187 VAL cc_start: 0.8732 (OUTLIER) cc_final: 0.8492 (m) REVERT: L 69 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7238 (mm-30) REVERT: L 105 TYR cc_start: 0.7924 (t80) cc_final: 0.6883 (t80) REVERT: L 172 MET cc_start: 0.8116 (mmm) cc_final: 0.7758 (mmm) REVERT: M 46 ASN cc_start: 0.8612 (p0) cc_final: 0.8395 (p0) REVERT: M 56 ASP cc_start: 0.8471 (t70) cc_final: 0.8101 (t70) REVERT: M 59 ASP cc_start: 0.8757 (m-30) cc_final: 0.8378 (m-30) REVERT: M 141 TYR cc_start: 0.8491 (OUTLIER) cc_final: 0.7493 (m-80) REVERT: N 24 SER cc_start: 0.9021 (p) cc_final: 0.8765 (t) REVERT: N 93 ASP cc_start: 0.7856 (m-30) cc_final: 0.7614 (m-30) REVERT: N 147 MET cc_start: 0.9097 (mtp) cc_final: 0.8850 (mtm) REVERT: O 94 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7443 (mp10) REVERT: P 211 VAL cc_start: 0.7858 (OUTLIER) cc_final: 0.7578 (t) REVERT: Q 53 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6858 (mt) REVERT: Q 166 LYS cc_start: 0.8270 (tppt) cc_final: 0.8030 (mttp) REVERT: Q 191 VAL cc_start: 0.8070 (OUTLIER) cc_final: 0.7827 (p) REVERT: R 209 LYS cc_start: 0.8092 (tttt) cc_final: 0.7840 (ttpt) REVERT: S 18 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7254 (mtp85) REVERT: S 189 LYS cc_start: 0.8398 (mttt) cc_final: 0.7948 (mmmt) REVERT: S 203 GLN cc_start: 0.5764 (mm-40) cc_final: 0.5324 (tp40) REVERT: T 31 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7915 (pm20) REVERT: T 144 ASP cc_start: 0.7061 (OUTLIER) cc_final: 0.6794 (m-30) REVERT: T 169 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6483 (ptp-170) REVERT: U 34 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.6749 (mp10) REVERT: U 53 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7868 (mm-40) REVERT: U 194 THR cc_start: 0.7467 (m) cc_final: 0.7032 (p) REVERT: U 199 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8131 (mp) REVERT: V 57 GLN cc_start: 0.8385 (mt0) cc_final: 0.7961 (mt0) REVERT: V 120 ASP cc_start: 0.7706 (m-30) cc_final: 0.7330 (m-30) REVERT: W 77 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8259 (tp30) REVERT: X 70 ARG cc_start: 0.8040 (mtt-85) cc_final: 0.7823 (mtt-85) REVERT: Y 18 SER cc_start: 0.8531 (p) cc_final: 0.8242 (p) REVERT: Y 67 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7803 (tt0) REVERT: Y 182 ASP cc_start: 0.8032 (p0) cc_final: 0.7691 (p0) REVERT: Z 180 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8296 (mm) REVERT: Z 184 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7639 (mm-30) REVERT: a 102 LYS cc_start: 0.8737 (mtpm) cc_final: 0.8443 (mtpt) REVERT: c 77 ARG cc_start: 0.7448 (ttt-90) cc_final: 0.7214 (ttp-110) REVERT: c 270 ILE cc_start: 0.5029 (tp) cc_final: 0.4827 (tp) REVERT: c 379 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8076 (mm) REVERT: c 481 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7080 (ttp) REVERT: c 530 THR cc_start: 0.7558 (m) cc_final: 0.7164 (p) REVERT: c 542 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7041 (mp0) REVERT: c 568 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7417 (mt-10) REVERT: c 588 SER cc_start: 0.8607 (t) cc_final: 0.8318 (m) REVERT: c 640 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6498 (mp0) REVERT: c 660 ASN cc_start: 0.6600 (t0) cc_final: 0.6325 (t0) REVERT: c 804 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6769 (mm-30) REVERT: c 809 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7864 (OUTLIER) REVERT: c 872 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8390 (mm) REVERT: c 1617 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6597 (tt0) REVERT: c 1644 GLN cc_start: 0.7485 (tp40) cc_final: 0.7133 (mm110) REVERT: c 1720 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7986 (tmm) REVERT: c 1747 VAL cc_start: 0.2654 (OUTLIER) cc_final: 0.2381 (t) REVERT: c 1801 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8523 (m) REVERT: c 1810 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7562 (ptt180) REVERT: c 1819 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7257 (pm20) REVERT: c 1827 ASP cc_start: 0.7489 (OUTLIER) cc_final: 0.6932 (m-30) REVERT: c 1832 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8575 (mp) outliers start: 190 outliers final: 108 residues processed: 1084 average time/residue: 1.4833 time to fit residues: 2044.6116 Evaluate side-chains 1055 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 909 time to evaluate : 5.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 154 HIS Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 60 GLN Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 230 ASP Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 128 ASN Chi-restraints excluded: chain H residue 204 CYS Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain K residue 1 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 136 TYR Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain L residue 169 ASP Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 141 TYR Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain M residue 205 THR Chi-restraints excluded: chain N residue 116 MET Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 65 GLU Chi-restraints excluded: chain O residue 131 VAL Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 221 THR Chi-restraints excluded: chain P residue 34 CYS Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 174 MET Chi-restraints excluded: chain P residue 200 THR Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 191 VAL Chi-restraints excluded: chain Q residue 196 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 226 ASP Chi-restraints excluded: chain T residue 31 GLU Chi-restraints excluded: chain T residue 142 VAL Chi-restraints excluded: chain T residue 144 ASP Chi-restraints excluded: chain T residue 169 ARG Chi-restraints excluded: chain T residue 215 TRP Chi-restraints excluded: chain U residue 34 GLN Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 53 GLN Chi-restraints excluded: chain U residue 73 THR Chi-restraints excluded: chain U residue 154 CYS Chi-restraints excluded: chain U residue 196 GLU Chi-restraints excluded: chain U residue 199 ILE Chi-restraints excluded: chain U residue 219 VAL Chi-restraints excluded: chain V residue 1 THR Chi-restraints excluded: chain V residue 81 ARG Chi-restraints excluded: chain V residue 156 SER Chi-restraints excluded: chain W residue 77 GLU Chi-restraints excluded: chain X residue 39 SER Chi-restraints excluded: chain X residue 69 MET Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain Z residue 55 SER Chi-restraints excluded: chain Z residue 118 LYS Chi-restraints excluded: chain Z residue 180 ILE Chi-restraints excluded: chain Z residue 201 GLU Chi-restraints excluded: chain Z residue 207 THR Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain a residue 152 GLU Chi-restraints excluded: chain c residue 94 ASP Chi-restraints excluded: chain c residue 167 ASN Chi-restraints excluded: chain c residue 172 ILE Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 379 LEU Chi-restraints excluded: chain c residue 436 VAL Chi-restraints excluded: chain c residue 439 ARG Chi-restraints excluded: chain c residue 463 VAL Chi-restraints excluded: chain c residue 481 MET Chi-restraints excluded: chain c residue 482 LEU Chi-restraints excluded: chain c residue 512 THR Chi-restraints excluded: chain c residue 606 LEU Chi-restraints excluded: chain c residue 609 VAL Chi-restraints excluded: chain c residue 617 ILE Chi-restraints excluded: chain c residue 640 GLU Chi-restraints excluded: chain c residue 804 GLU Chi-restraints excluded: chain c residue 809 ASP Chi-restraints excluded: chain c residue 820 CYS Chi-restraints excluded: chain c residue 844 VAL Chi-restraints excluded: chain c residue 872 ILE Chi-restraints excluded: chain c residue 1012 LEU Chi-restraints excluded: chain c residue 1063 GLN Chi-restraints excluded: chain c residue 1154 VAL Chi-restraints excluded: chain c residue 1220 LYS Chi-restraints excluded: chain c residue 1272 THR Chi-restraints excluded: chain c residue 1285 VAL Chi-restraints excluded: chain c residue 1323 ILE Chi-restraints excluded: chain c residue 1422 ASN Chi-restraints excluded: chain c residue 1433 GLU Chi-restraints excluded: chain c residue 1455 GLU Chi-restraints excluded: chain c residue 1465 LEU Chi-restraints excluded: chain c residue 1508 VAL Chi-restraints excluded: chain c residue 1526 ILE Chi-restraints excluded: chain c residue 1617 GLU Chi-restraints excluded: chain c residue 1662 LEU Chi-restraints excluded: chain c residue 1720 MET Chi-restraints excluded: chain c residue 1747 VAL Chi-restraints excluded: chain c residue 1801 THR Chi-restraints excluded: chain c residue 1810 ARG Chi-restraints excluded: chain c residue 1819 GLU Chi-restraints excluded: chain c residue 1827 ASP Chi-restraints excluded: chain c residue 1832 LEU Chi-restraints excluded: chain c residue 1835 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 689 optimal weight: 4.9990 chunk 725 optimal weight: 0.7980 chunk 662 optimal weight: 1.9990 chunk 705 optimal weight: 4.9990 chunk 424 optimal weight: 0.5980 chunk 307 optimal weight: 1.9990 chunk 554 optimal weight: 0.0060 chunk 216 optimal weight: 2.9990 chunk 637 optimal weight: 0.9990 chunk 667 optimal weight: 0.6980 chunk 703 optimal weight: 6.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 ASN E 185 ASN E 203 GLN H 30 ASN I 172 ASN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 106 GLN N 154 GLN N 193 GLN ** O 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 111 GLN O 168 ASN P 40 ASN P 84 ASN P 100 GLN P 155 ASN P 198 ASN ** R 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 186 HIS S 16 GLN S 60 GLN S 166 GLN T 63 ASN U 150 GLN W 156 ASN X 8 GLN Z 160 ASN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 254 GLN c 707 HIS ** c1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 63716 Z= 0.175 Angle : 0.585 14.048 86269 Z= 0.302 Chirality : 0.043 0.329 9754 Planarity : 0.004 0.046 11057 Dihedral : 5.382 96.487 8827 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.41 % Favored : 95.57 % Rotamer: Outliers : 2.75 % Allowed : 19.48 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.03 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.09), residues: 7935 helix: 1.29 (0.09), residues: 3413 sheet: -0.11 (0.13), residues: 1528 loop : -0.94 (0.11), residues: 2994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP T 215 HIS 0.007 0.001 HIS R 186 PHE 0.044 0.001 PHE A 198 TYR 0.019 0.001 TYR U 159 ARG 0.009 0.000 ARG b 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15870 Ramachandran restraints generated. 7935 Oldfield, 0 Emsley, 7935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15870 Ramachandran restraints generated. 7935 Oldfield, 0 Emsley, 7935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1130 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 960 time to evaluate : 5.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.5546 (mmt90) REVERT: B 48 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6595 (tt0) REVERT: B 231 LYS cc_start: 0.7978 (ptpt) cc_final: 0.7758 (ptpp) REVERT: B 235 GLN cc_start: 0.8016 (tm-30) cc_final: 0.7753 (tp40) REVERT: C 38 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.7285 (mmp80) REVERT: C 166 LYS cc_start: 0.8275 (tptp) cc_final: 0.7994 (tmtt) REVERT: E 60 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.6901 (pp30) REVERT: E 61 LYS cc_start: 0.7937 (mtmp) cc_final: 0.7459 (mmtm) REVERT: E 125 ARG cc_start: 0.6687 (mmm-85) cc_final: 0.6071 (mtp85) REVERT: F 150 MET cc_start: 0.8685 (tmm) cc_final: 0.8469 (tmm) REVERT: F 170 GLN cc_start: 0.7717 (tp-100) cc_final: 0.7209 (pm20) REVERT: F 184 MET cc_start: 0.8611 (mtt) cc_final: 0.8347 (mtm) REVERT: G 108 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7213 (tm-30) REVERT: I 11 MET cc_start: 0.8787 (ptm) cc_final: 0.8549 (ptp) REVERT: I 105 GLU cc_start: 0.7789 (mp0) cc_final: 0.7393 (mp0) REVERT: I 156 ASN cc_start: 0.8589 (m-40) cc_final: 0.8380 (m110) REVERT: J 38 MET cc_start: 0.8259 (mmp) cc_final: 0.8011 (mmp) REVERT: K 136 TYR cc_start: 0.8777 (OUTLIER) cc_final: 0.6330 (t80) REVERT: K 187 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8440 (m) REVERT: L 69 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7228 (mm-30) REVERT: L 105 TYR cc_start: 0.7904 (t80) cc_final: 0.6849 (t80) REVERT: L 107 TYR cc_start: 0.7668 (m-80) cc_final: 0.7404 (m-80) REVERT: L 172 MET cc_start: 0.8092 (mmm) cc_final: 0.7766 (mmm) REVERT: M 46 ASN cc_start: 0.8595 (p0) cc_final: 0.8376 (p0) REVERT: M 56 ASP cc_start: 0.8475 (t70) cc_final: 0.8093 (t70) REVERT: M 59 ASP cc_start: 0.8728 (m-30) cc_final: 0.8350 (m-30) REVERT: M 141 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.7489 (m-80) REVERT: N 24 SER cc_start: 0.8980 (p) cc_final: 0.8757 (t) REVERT: N 93 ASP cc_start: 0.7810 (m-30) cc_final: 0.7501 (m-30) REVERT: N 147 MET cc_start: 0.9062 (mtp) cc_final: 0.8860 (mtm) REVERT: O 91 LYS cc_start: 0.8088 (mtmt) cc_final: 0.7656 (mmpt) REVERT: O 94 GLN cc_start: 0.7758 (mm-40) cc_final: 0.7435 (mp10) REVERT: P 211 VAL cc_start: 0.7846 (OUTLIER) cc_final: 0.7520 (t) REVERT: P 236 LEU cc_start: 0.6621 (mt) cc_final: 0.6398 (mt) REVERT: Q 166 LYS cc_start: 0.8272 (tppt) cc_final: 0.8048 (mttp) REVERT: Q 191 VAL cc_start: 0.8009 (OUTLIER) cc_final: 0.7762 (p) REVERT: R 209 LYS cc_start: 0.8082 (tttt) cc_final: 0.7841 (ttpt) REVERT: S 18 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7213 (mtp85) REVERT: S 189 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7924 (mmmt) REVERT: S 203 GLN cc_start: 0.5747 (mm-40) cc_final: 0.5460 (tp40) REVERT: T 31 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7919 (pm20) REVERT: U 34 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.6773 (mp10) REVERT: U 53 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7843 (mm-40) REVERT: U 194 THR cc_start: 0.7395 (m) cc_final: 0.7004 (p) REVERT: V 57 GLN cc_start: 0.8283 (mt0) cc_final: 0.7925 (mt0) REVERT: V 120 ASP cc_start: 0.7677 (m-30) cc_final: 0.7358 (m-30) REVERT: Y 18 SER cc_start: 0.8479 (p) cc_final: 0.8203 (p) REVERT: Y 67 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7799 (tt0) REVERT: Y 182 ASP cc_start: 0.8042 (p0) cc_final: 0.7689 (p0) REVERT: Z 180 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8266 (mm) REVERT: Z 184 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7628 (mm-30) REVERT: a 102 LYS cc_start: 0.8733 (mtpm) cc_final: 0.8440 (mtpt) REVERT: c 77 ARG cc_start: 0.7438 (ttt-90) cc_final: 0.7212 (mtm110) REVERT: c 84 ARG cc_start: 0.8140 (ttm-80) cc_final: 0.7928 (ttp-110) REVERT: c 379 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8080 (mm) REVERT: c 481 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7066 (ttp) REVERT: c 530 THR cc_start: 0.7662 (m) cc_final: 0.7363 (p) REVERT: c 542 GLU cc_start: 0.7369 (mm-30) cc_final: 0.7034 (mp0) REVERT: c 588 SER cc_start: 0.8593 (t) cc_final: 0.8317 (m) REVERT: c 640 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6413 (mp0) REVERT: c 660 ASN cc_start: 0.6362 (t0) cc_final: 0.6118 (t0) REVERT: c 804 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6778 (mm-30) REVERT: c 809 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7867 (OUTLIER) REVERT: c 872 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8408 (mm) REVERT: c 1092 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7293 (mp) REVERT: c 1331 ARG cc_start: 0.8123 (mtp-110) cc_final: 0.7836 (mtp-110) REVERT: c 1340 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7054 (mpt-90) REVERT: c 1644 GLN cc_start: 0.7472 (tp40) cc_final: 0.7113 (mm110) REVERT: c 1720 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7938 (tmm) REVERT: c 1747 VAL cc_start: 0.2472 (OUTLIER) cc_final: 0.2187 (t) REVERT: c 1810 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7411 (ptt180) REVERT: c 1819 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7250 (pm20) REVERT: c 1827 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.6961 (m-30) REVERT: c 1832 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8573 (mp) outliers start: 170 outliers final: 101 residues processed: 1083 average time/residue: 1.4471 time to fit residues: 2008.7654 Evaluate side-chains 1039 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 908 time to evaluate : 5.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 154 HIS Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 60 GLN Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 230 ASP Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 128 ASN Chi-restraints excluded: chain H residue 204 CYS Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain K residue 1 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 136 TYR Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain L residue 169 ASP Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 110 MET Chi-restraints excluded: chain M residue 141 TYR Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain M residue 205 THR Chi-restraints excluded: chain N residue 116 MET Chi-restraints excluded: chain N residue 185 GLU Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 65 GLU Chi-restraints excluded: chain O residue 131 VAL Chi-restraints excluded: chain O residue 164 LYS Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 221 THR Chi-restraints excluded: chain P residue 34 CYS Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 174 MET Chi-restraints excluded: chain P residue 200 THR Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 191 VAL Chi-restraints excluded: chain Q residue 196 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 189 LYS Chi-restraints excluded: chain T residue 31 GLU Chi-restraints excluded: chain T residue 215 TRP Chi-restraints excluded: chain U residue 34 GLN Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 53 GLN Chi-restraints excluded: chain U residue 73 THR Chi-restraints excluded: chain U residue 154 CYS Chi-restraints excluded: chain U residue 196 GLU Chi-restraints excluded: chain U residue 219 VAL Chi-restraints excluded: chain V residue 1 THR Chi-restraints excluded: chain V residue 81 ARG Chi-restraints excluded: chain X residue 39 SER Chi-restraints excluded: chain X residue 69 MET Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain Z residue 55 SER Chi-restraints excluded: chain Z residue 118 LYS Chi-restraints excluded: chain Z residue 180 ILE Chi-restraints excluded: chain Z residue 201 GLU Chi-restraints excluded: chain Z residue 207 THR Chi-restraints excluded: chain a residue 152 GLU Chi-restraints excluded: chain c residue 94 ASP Chi-restraints excluded: chain c residue 167 ASN Chi-restraints excluded: chain c residue 172 ILE Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 379 LEU Chi-restraints excluded: chain c residue 436 VAL Chi-restraints excluded: chain c residue 439 ARG Chi-restraints excluded: chain c residue 463 VAL Chi-restraints excluded: chain c residue 481 MET Chi-restraints excluded: chain c residue 512 THR Chi-restraints excluded: chain c residue 609 VAL Chi-restraints excluded: chain c residue 617 ILE Chi-restraints excluded: chain c residue 640 GLU Chi-restraints excluded: chain c residue 804 GLU Chi-restraints excluded: chain c residue 809 ASP Chi-restraints excluded: chain c residue 820 CYS Chi-restraints excluded: chain c residue 872 ILE Chi-restraints excluded: chain c residue 888 LYS Chi-restraints excluded: chain c residue 1012 LEU Chi-restraints excluded: chain c residue 1063 GLN Chi-restraints excluded: chain c residue 1092 LEU Chi-restraints excluded: chain c residue 1120 LEU Chi-restraints excluded: chain c residue 1220 LYS Chi-restraints excluded: chain c residue 1272 THR Chi-restraints excluded: chain c residue 1285 VAL Chi-restraints excluded: chain c residue 1323 ILE Chi-restraints excluded: chain c residue 1340 ARG Chi-restraints excluded: chain c residue 1422 ASN Chi-restraints excluded: chain c residue 1433 GLU Chi-restraints excluded: chain c residue 1455 GLU Chi-restraints excluded: chain c residue 1508 VAL Chi-restraints excluded: chain c residue 1526 ILE Chi-restraints excluded: chain c residue 1662 LEU Chi-restraints excluded: chain c residue 1720 MET Chi-restraints excluded: chain c residue 1747 VAL Chi-restraints excluded: chain c residue 1810 ARG Chi-restraints excluded: chain c residue 1819 GLU Chi-restraints excluded: chain c residue 1827 ASP Chi-restraints excluded: chain c residue 1832 LEU Chi-restraints excluded: chain c residue 1835 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 463 optimal weight: 0.3980 chunk 746 optimal weight: 0.0050 chunk 455 optimal weight: 2.9990 chunk 354 optimal weight: 5.9990 chunk 518 optimal weight: 6.9990 chunk 783 optimal weight: 1.9990 chunk 720 optimal weight: 0.0970 chunk 623 optimal weight: 0.9980 chunk 64 optimal weight: 0.2980 chunk 481 optimal weight: 2.9990 chunk 382 optimal weight: 8.9990 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 ASN E 203 GLN G 224 ASN H 30 ASN I 168 GLN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 106 GLN N 154 GLN N 193 GLN ** O 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 111 GLN O 168 ASN P 40 ASN P 84 ASN P 100 GLN P 177 GLN P 198 ASN ** R 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 186 HIS S 60 GLN S 166 GLN T 63 ASN U 150 GLN W 156 ASN X 8 GLN X 61 GLN Z 160 ASN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 254 GLN c 707 HIS c 712 GLN ** c1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 63716 Z= 0.156 Angle : 0.574 13.848 86269 Z= 0.297 Chirality : 0.042 0.324 9754 Planarity : 0.004 0.060 11057 Dihedral : 5.259 96.104 8826 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.13 % Favored : 95.85 % Rotamer: Outliers : 2.23 % Allowed : 19.97 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.03 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.10), residues: 7935 helix: 1.44 (0.09), residues: 3400 sheet: -0.06 (0.13), residues: 1527 loop : -0.90 (0.11), residues: 3008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP T 215 HIS 0.007 0.001 HIS R 186 PHE 0.043 0.001 PHE A 198 TYR 0.021 0.001 TYR U 159 ARG 0.017 0.000 ARG A 176 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15870 Ramachandran restraints generated. 7935 Oldfield, 0 Emsley, 7935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15870 Ramachandran restraints generated. 7935 Oldfield, 0 Emsley, 7935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1124 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 989 time to evaluate : 5.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 ARG cc_start: 0.8073 (ttm110) cc_final: 0.7728 (ttm170) REVERT: B 66 TYR cc_start: 0.8623 (m-80) cc_final: 0.8416 (m-80) REVERT: B 231 LYS cc_start: 0.7936 (ptpt) cc_final: 0.7735 (ptpp) REVERT: B 235 GLN cc_start: 0.8032 (tm-30) cc_final: 0.7774 (tp40) REVERT: C 38 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7265 (mmp80) REVERT: C 60 ARG cc_start: 0.6345 (ttm-80) cc_final: 0.6041 (ttm110) REVERT: E 60 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7026 (pp30) REVERT: E 61 LYS cc_start: 0.7973 (mtmp) cc_final: 0.7501 (mmtm) REVERT: E 125 ARG cc_start: 0.6668 (mmm-85) cc_final: 0.6125 (mtp85) REVERT: F 170 GLN cc_start: 0.7682 (tp-100) cc_final: 0.7201 (pm20) REVERT: F 184 MET cc_start: 0.8611 (mtt) cc_final: 0.8332 (mtm) REVERT: G 108 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7228 (tm-30) REVERT: I 3 MET cc_start: 0.8263 (mmt) cc_final: 0.7716 (tpp) REVERT: I 11 MET cc_start: 0.8727 (ptm) cc_final: 0.8444 (ptp) REVERT: I 105 GLU cc_start: 0.7746 (mp0) cc_final: 0.7373 (mp0) REVERT: I 156 ASN cc_start: 0.8533 (m-40) cc_final: 0.8330 (m110) REVERT: J 38 MET cc_start: 0.8227 (mmp) cc_final: 0.7988 (mmp) REVERT: K 136 TYR cc_start: 0.8795 (OUTLIER) cc_final: 0.6458 (t80) REVERT: K 187 VAL cc_start: 0.8585 (OUTLIER) cc_final: 0.8373 (m) REVERT: L 69 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7214 (mm-30) REVERT: L 105 TYR cc_start: 0.7848 (t80) cc_final: 0.6822 (t80) REVERT: L 107 TYR cc_start: 0.7627 (m-80) cc_final: 0.7417 (m-80) REVERT: L 172 MET cc_start: 0.8086 (mmm) cc_final: 0.7781 (mmm) REVERT: M 46 ASN cc_start: 0.8558 (p0) cc_final: 0.8339 (p0) REVERT: M 56 ASP cc_start: 0.8465 (t70) cc_final: 0.8081 (t70) REVERT: M 59 ASP cc_start: 0.8668 (m-30) cc_final: 0.8242 (m-30) REVERT: M 141 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.7498 (m-80) REVERT: N 93 ASP cc_start: 0.7740 (m-30) cc_final: 0.7438 (m-30) REVERT: O 91 LYS cc_start: 0.8049 (mtmt) cc_final: 0.7633 (mmpt) REVERT: O 94 GLN cc_start: 0.7721 (mm-40) cc_final: 0.7404 (mp10) REVERT: O 176 ARG cc_start: 0.7076 (mmt90) cc_final: 0.6772 (mmt180) REVERT: P 198 ASN cc_start: 0.7383 (t0) cc_final: 0.6890 (t0) REVERT: P 211 VAL cc_start: 0.7721 (OUTLIER) cc_final: 0.7380 (t) REVERT: Q 166 LYS cc_start: 0.8253 (tppt) cc_final: 0.8037 (mttp) REVERT: Q 191 VAL cc_start: 0.8004 (OUTLIER) cc_final: 0.7770 (p) REVERT: R 209 LYS cc_start: 0.8064 (tttt) cc_final: 0.7831 (ttpt) REVERT: S 18 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7153 (mtp85) REVERT: S 189 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8013 (mmmt) REVERT: S 203 GLN cc_start: 0.5732 (mm-40) cc_final: 0.5428 (tp40) REVERT: T 31 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7997 (pm20) REVERT: T 144 ASP cc_start: 0.7111 (m-30) cc_final: 0.6730 (m-30) REVERT: U 34 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.6899 (mp10) REVERT: U 53 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7805 (mm-40) REVERT: U 194 THR cc_start: 0.7537 (m) cc_final: 0.7099 (p) REVERT: V 57 GLN cc_start: 0.8264 (mt0) cc_final: 0.7819 (mt0) REVERT: V 120 ASP cc_start: 0.7641 (m-30) cc_final: 0.7308 (m-30) REVERT: W 76 LYS cc_start: 0.8408 (ttmm) cc_final: 0.8085 (ptmt) REVERT: Y 18 SER cc_start: 0.8434 (p) cc_final: 0.8179 (p) REVERT: Y 182 ASP cc_start: 0.8032 (p0) cc_final: 0.7692 (p0) REVERT: Z 180 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8231 (mm) REVERT: Z 184 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7614 (mm-30) REVERT: a 102 LYS cc_start: 0.8745 (mtpm) cc_final: 0.8481 (mtpt) REVERT: c 77 ARG cc_start: 0.7386 (ttt-90) cc_final: 0.7167 (mtm110) REVERT: c 84 ARG cc_start: 0.8156 (ttm-80) cc_final: 0.7921 (ttp-110) REVERT: c 379 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8047 (mm) REVERT: c 530 THR cc_start: 0.7621 (m) cc_final: 0.7358 (p) REVERT: c 542 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7059 (mp0) REVERT: c 588 SER cc_start: 0.8566 (t) cc_final: 0.8275 (m) REVERT: c 804 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6783 (mm-30) REVERT: c 809 ASP cc_start: 0.8115 (t70) cc_final: 0.7895 (OUTLIER) REVERT: c 872 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8337 (mm) REVERT: c 1092 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7219 (mp) REVERT: c 1340 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7059 (mpt-90) REVERT: c 1644 GLN cc_start: 0.7451 (tp40) cc_final: 0.7080 (mm110) REVERT: c 1720 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7892 (tmm) REVERT: c 1747 VAL cc_start: 0.2273 (OUTLIER) cc_final: 0.2052 (t) REVERT: c 1810 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7330 (ptt180) REVERT: c 1819 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7235 (pm20) REVERT: c 1832 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8524 (mp) outliers start: 135 outliers final: 81 residues processed: 1092 average time/residue: 1.4484 time to fit residues: 2025.5392 Evaluate side-chains 1026 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 922 time to evaluate : 5.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 154 HIS Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 60 GLN Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 230 ASP Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 128 ASN Chi-restraints excluded: chain G residue 224 ASN Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain K residue 1 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 136 TYR Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain L residue 169 ASP Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 141 TYR Chi-restraints excluded: chain M residue 200 GLU Chi-restraints excluded: chain M residue 205 THR Chi-restraints excluded: chain N residue 116 MET Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 131 VAL Chi-restraints excluded: chain O residue 164 LYS Chi-restraints excluded: chain O residue 167 VAL Chi-restraints excluded: chain O residue 221 THR Chi-restraints excluded: chain P residue 34 CYS Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 174 MET Chi-restraints excluded: chain P residue 211 VAL Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 191 VAL Chi-restraints excluded: chain Q residue 196 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 189 LYS Chi-restraints excluded: chain T residue 31 GLU Chi-restraints excluded: chain T residue 215 TRP Chi-restraints excluded: chain U residue 34 GLN Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 53 GLN Chi-restraints excluded: chain U residue 73 THR Chi-restraints excluded: chain U residue 154 CYS Chi-restraints excluded: chain U residue 196 GLU Chi-restraints excluded: chain U residue 219 VAL Chi-restraints excluded: chain V residue 81 ARG Chi-restraints excluded: chain X residue 39 SER Chi-restraints excluded: chain Z residue 118 LYS Chi-restraints excluded: chain Z residue 180 ILE Chi-restraints excluded: chain Z residue 201 GLU Chi-restraints excluded: chain Z residue 207 THR Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain c residue 94 ASP Chi-restraints excluded: chain c residue 172 ILE Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 379 LEU Chi-restraints excluded: chain c residue 463 VAL Chi-restraints excluded: chain c residue 512 THR Chi-restraints excluded: chain c residue 609 VAL Chi-restraints excluded: chain c residue 804 GLU Chi-restraints excluded: chain c residue 872 ILE Chi-restraints excluded: chain c residue 1012 LEU Chi-restraints excluded: chain c residue 1092 LEU Chi-restraints excluded: chain c residue 1220 LYS Chi-restraints excluded: chain c residue 1272 THR Chi-restraints excluded: chain c residue 1285 VAL Chi-restraints excluded: chain c residue 1323 ILE Chi-restraints excluded: chain c residue 1340 ARG Chi-restraints excluded: chain c residue 1433 GLU Chi-restraints excluded: chain c residue 1526 ILE Chi-restraints excluded: chain c residue 1662 LEU Chi-restraints excluded: chain c residue 1720 MET Chi-restraints excluded: chain c residue 1747 VAL Chi-restraints excluded: chain c residue 1810 ARG Chi-restraints excluded: chain c residue 1819 GLU Chi-restraints excluded: chain c residue 1832 LEU Chi-restraints excluded: chain c residue 1835 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 495 optimal weight: 4.9990 chunk 664 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 574 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 173 optimal weight: 7.9990 chunk 624 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 641 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 ASN E 185 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 ASN G 193 GLN ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 GLN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 108 ASN N 106 GLN N 154 GLN N 193 GLN ** O 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 168 ASN P 40 ASN P 84 ASN P 100 GLN P 177 GLN ** R 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 186 HIS S 60 GLN S 166 GLN T 63 ASN U 150 GLN W 156 ASN X 8 GLN Z 160 ASN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 254 GLN ** c 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 707 HIS c 712 GLN ** c1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c1787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.138496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.117091 restraints weight = 220110.232| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.72 r_work: 0.3293 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.237 63716 Z= 0.227 Angle : 0.642 59.175 86269 Z= 0.349 Chirality : 0.045 0.998 9754 Planarity : 0.004 0.056 11057 Dihedral : 5.259 96.188 8826 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.19 % Favored : 95.78 % Rotamer: Outliers : 2.08 % Allowed : 20.64 % Favored : 77.28 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.03 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.10), residues: 7935 helix: 1.44 (0.09), residues: 3400 sheet: -0.04 (0.13), residues: 1527 loop : -0.89 (0.11), residues: 3008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP T 215 HIS 0.007 0.001 HIS R 186 PHE 0.040 0.001 PHE A 198 TYR 0.017 0.001 TYR C 21 ARG 0.013 0.000 ARG A 176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28824.55 seconds wall clock time: 496 minutes 23.45 seconds (29783.45 seconds total)