Starting phenix.real_space_refine on Fri Dec 8 07:27:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kwy_0781/12_2023/6kwy_0781_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kwy_0781/12_2023/6kwy_0781.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kwy_0781/12_2023/6kwy_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_0781/12_2023/6kwy_0781_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kwy_0781/12_2023/6kwy_0781_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kwy_0781/12_2023/6kwy_0781.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kwy_0781/12_2023/6kwy_0781.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kwy_0781/12_2023/6kwy_0781_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kwy_0781/12_2023/6kwy_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-1.21rc1-5172/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: 30.96, per 1000 atoms: 0.50 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: 16.54 Conformation dependent library (CDL) restraints added in 11.8 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: 9.98 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: 27.01 Time building geometry restraints manager: 18.42 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: 1.690 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: 0.040 Extract box with map and model: 10.930 Check model and map are aligned: 0.660 Set scattering table: 0.400 Process input model: 138.480 Find NCS groups from input model: 4.130 Set up NCS constraints: 0.280 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:8.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 165.530 ------------------------------------------------------------------------------- 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 : 5.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 14 residues processed: 1894 average time/residue: 1.5208 time to fit residues: 3630.4866 Evaluate side-chains 1059 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1045 time to evaluate : 5.264 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 3 average time/residue: 0.7096 time to fit residues: 10.2740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 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 116 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 91 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 N 154 GLN ** O 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 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 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: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 63716 Z= 0.204 Angle : 0.672 13.519 86269 Z= 0.349 Chirality : 0.045 0.422 9754 Planarity : 0.005 0.058 11057 Dihedral : 6.261 89.775 8819 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.18 % Favored : 95.77 % Rotamer: Outliers : 3.85 % Allowed : 13.62 % Favored : 82.53 % 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: -1.51 (0.09), residues: 7935 helix: -0.45 (0.08), residues: 3380 sheet: -0.70 (0.12), residues: 1501 loop : -1.65 (0.10), residues: 3054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP T 215 HIS 0.010 0.001 HIS c 227 PHE 0.030 0.002 PHE A 198 TYR 0.029 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 1512 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 1267 time to evaluate : 5.232 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 245 outliers final: 54 residues processed: 1426 average time/residue: 1.4433 time to fit residues: 2642.5660 Evaluate side-chains 1076 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 1022 time to evaluate : 5.074 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 40 residues processed: 16 average time/residue: 0.6266 time to fit residues: 23.6353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 594 optimal weight: 7.9990 chunk 486 optimal weight: 1.9990 chunk 196 optimal weight: 7.9990 chunk 715 optimal weight: 8.9990 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: 2.5588 ------------------------------------------------------------------------------- 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 E 21 GLN E 185 ASN ** F 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 GLN G 172 GLN I 156 ASN 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 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 T 101 ASN U 92 GLN U 147 GLN U 150 GLN V 57 GLN V 193 ASN W 156 ASN X 8 GLN X 61 GLN Y 38 ASN Z 160 ASN b 7 GLN b 28 ASN b 62 GLN b 110 GLN c 329 HIS c 402 GLN c 826 ASN c1086 GLN c1351 ASN c1441 HIS c1644 GLN ** c1672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 63716 Z= 0.415 Angle : 0.734 13.306 86269 Z= 0.378 Chirality : 0.048 0.214 9754 Planarity : 0.005 0.066 11057 Dihedral : 6.214 93.767 8819 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.97 % Favored : 94.96 % Rotamer: Outliers : 4.58 % Allowed : 15.21 % Favored : 80.21 % 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: -0.94 (0.09), residues: 7935 helix: 0.12 (0.09), residues: 3407 sheet: -0.48 (0.13), residues: 1516 loop : -1.44 (0.11), residues: 3012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP T 215 HIS 0.010 0.002 HIS c1760 PHE 0.037 0.003 PHE L 101 TYR 0.034 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 1269 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 975 time to evaluate : 5.255 Fit side-chains revert: symmetry clash outliers start: 294 outliers final: 114 residues processed: 1178 average time/residue: 1.4598 time to fit residues: 2215.0653 Evaluate side-chains 1011 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 897 time to evaluate : 5.241 Switching outliers to nearest non-outliers outliers start: 114 outliers final: 84 residues processed: 30 average time/residue: 0.9228 time to fit residues: 47.1573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 706 optimal weight: 4.9990 chunk 537 optimal weight: 0.9980 chunk 371 optimal weight: 0.0980 chunk 79 optimal weight: 2.9990 chunk 341 optimal weight: 6.9990 chunk 480 optimal weight: 7.9990 chunk 717 optimal weight: 0.9980 chunk 759 optimal weight: 0.9990 chunk 374 optimal weight: 0.6980 chunk 680 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 88 ASN ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN D 41 GLN D 99 HIS E 4 ASN E 185 ASN G 172 GLN I 156 ASN J 27 GLN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 152 GLN N 66 HIS N 106 GLN N 110 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 S 16 GLN S 31 GLN S 60 GLN S 152 ASN B T 101 ASN U 150 GLN V 153 ASN V 193 ASN W 156 ASN W 161 HIS X 8 GLN Z 160 ASN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 110 GLN c 722 HIS c1644 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3121 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= 0.189 Angle : 0.601 12.970 86269 Z= 0.312 Chirality : 0.043 0.173 9754 Planarity : 0.004 0.055 11057 Dihedral : 5.727 93.503 8819 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.22 % Favored : 95.73 % Rotamer: Outliers : 3.84 % Allowed : 16.18 % Favored : 79.98 % 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 (0.09), residues: 7935 helix: 0.65 (0.09), residues: 3390 sheet: -0.26 (0.13), residues: 1503 loop : -1.22 (0.11), residues: 3042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP T 215 HIS 0.007 0.001 HIS c 227 PHE 0.026 0.001 PHE A 198 TYR 0.022 0.001 TYR Y 153 ARG 0.008 0.000 ARG b 40 *********************** 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 1274 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 1032 time to evaluate : 5.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 242 outliers final: 95 residues processed: 1199 average time/residue: 1.4648 time to fit residues: 2260.6663 Evaluate side-chains 1016 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 921 time to evaluate : 5.233 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 79 residues processed: 16 average time/residue: 0.6773 time to fit residues: 24.5132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 632 optimal weight: 0.3980 chunk 431 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 565 optimal weight: 5.9990 chunk 313 optimal weight: 0.9980 chunk 648 optimal weight: 7.9990 chunk 525 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 387 optimal weight: 8.9990 chunk 681 optimal weight: 0.7980 chunk 191 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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** A 165 ASN B 119 GLN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 ASN E 185 ASN F 201 HIS G 224 ASN H 30 ASN I 156 ASN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 HIS N 106 GLN N 154 GLN N 193 GLN O 101 GLN O 111 GLN P 40 ASN P 84 ASN P 100 GLN Q 122 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 T 63 ASN T 101 ASN U 150 GLN V 193 ASN W 156 ASN X 8 GLN X 61 GLN Z 160 ASN b 7 GLN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 254 GLN c 660 ASN c 707 HIS c 826 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3271 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= 0.213 Angle : 0.605 14.049 86269 Z= 0.312 Chirality : 0.044 0.194 9754 Planarity : 0.004 0.051 11057 Dihedral : 5.549 93.921 8819 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.34 % Favored : 95.62 % Rotamer: Outliers : 3.72 % Allowed : 17.13 % Favored : 79.15 % 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: -0.13 (0.09), residues: 7935 helix: 0.91 (0.09), residues: 3392 sheet: -0.19 (0.13), residues: 1517 loop : -1.10 (0.11), residues: 3026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP T 215 HIS 0.007 0.001 HIS R 186 PHE 0.033 0.002 PHE A 198 TYR 0.021 0.001 TYR Y 153 ARG 0.008 0.000 ARG b 40 *********************** 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 1204 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 970 time to evaluate : 5.326 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 234 outliers final: 111 residues processed: 1135 average time/residue: 1.4986 time to fit residues: 2197.2152 Evaluate side-chains 1019 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 908 time to evaluate : 5.223 Switching outliers to nearest non-outliers outliers start: 111 outliers final: 89 residues processed: 22 average time/residue: 0.7393 time to fit residues: 32.7681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 255 optimal weight: 3.9990 chunk 684 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 446 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 760 optimal weight: 6.9990 chunk 631 optimal weight: 0.7980 chunk 352 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 251 optimal weight: 1.9990 chunk 399 optimal weight: 7.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 ASN E 185 ASN G 193 GLN ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 ASN I 156 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 Q 122 ASN ** 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 60 GLN T 101 ASN U 150 GLN V 193 ASN W 156 ASN X 8 GLN Z 160 ASN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 254 GLN c 607 GLN c 611 ASN ** c 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 707 HIS c 818 HIS c1644 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 63716 Z= 0.325 Angle : 0.662 13.054 86269 Z= 0.341 Chirality : 0.046 0.223 9754 Planarity : 0.005 0.051 11057 Dihedral : 5.713 95.939 8819 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.58 % Favored : 95.37 % Rotamer: Outliers : 3.79 % Allowed : 17.64 % Favored : 78.57 % 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: -0.13 (0.09), residues: 7935 helix: 0.86 (0.09), residues: 3409 sheet: -0.18 (0.13), residues: 1532 loop : -1.05 (0.11), residues: 2994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP c1688 HIS 0.007 0.001 HIS c1044 PHE 0.037 0.002 PHE A 198 TYR 0.024 0.002 TYR Y 153 ARG 0.010 0.001 ARG V 72 *********************** 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 1155 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 915 time to evaluate : 5.366 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 240 outliers final: 122 residues processed: 1090 average time/residue: 1.5202 time to fit residues: 2183.2466 Evaluate side-chains 1013 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 891 time to evaluate : 5.282 Switching outliers to nearest non-outliers outliers start: 122 outliers final: 101 residues processed: 21 average time/residue: 0.7690 time to fit residues: 33.0550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 733 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 433 optimal weight: 3.9990 chunk 555 optimal weight: 0.9980 chunk 430 optimal weight: 5.9990 chunk 640 optimal weight: 0.0070 chunk 424 optimal weight: 0.7980 chunk 757 optimal weight: 3.9990 chunk 474 optimal weight: 0.6980 chunk 461 optimal weight: 2.9990 chunk 349 optimal weight: 8.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- 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 51 ASN B 119 GLN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN E 185 ASN G 12 HIS G 224 ASN H 30 ASN I 156 ASN ** 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 122 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 U 150 GLN V 193 ASN W 156 ASN X 8 GLN X 61 GLN Z 160 ASN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 66 GLN c 254 GLN c 707 HIS ** c1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3466 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= 0.202 Angle : 0.595 12.938 86269 Z= 0.309 Chirality : 0.043 0.242 9754 Planarity : 0.004 0.046 11057 Dihedral : 5.455 96.050 8819 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.28 % Favored : 95.68 % Rotamer: Outliers : 3.14 % Allowed : 18.47 % Favored : 78.39 % 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: 0.08 (0.09), residues: 7935 helix: 1.07 (0.09), residues: 3411 sheet: -0.09 (0.13), residues: 1519 loop : -0.99 (0.11), residues: 3005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP c1688 HIS 0.007 0.001 HIS R 186 PHE 0.040 0.001 PHE A 198 TYR 0.019 0.001 TYR c 714 ARG 0.009 0.000 ARG b 40 *********************** 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 1145 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 949 time to evaluate : 5.324 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 196 outliers final: 119 residues processed: 1092 average time/residue: 1.4754 time to fit residues: 2080.6598 Evaluate side-chains 1021 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 902 time to evaluate : 5.266 Switching outliers to nearest non-outliers outliers start: 119 outliers final: 100 residues processed: 19 average time/residue: 0.8724 time to fit residues: 31.7519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 468 optimal weight: 0.5980 chunk 302 optimal weight: 3.9990 chunk 452 optimal weight: 3.9990 chunk 228 optimal weight: 0.9990 chunk 148 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 chunk 481 optimal weight: 0.6980 chunk 516 optimal weight: 2.9990 chunk 374 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 595 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 B 119 GLN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN E 4 ASN E 166 GLN E 185 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 ASN I 156 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 177 GLN P 198 ASN Q 120 GLN Q 122 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 X 61 GLN X 65 GLN Z 160 ASN b 7 GLN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 66 GLN c 707 HIS ** c1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c1644 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 63716 Z= 0.217 Angle : 0.602 12.844 86269 Z= 0.312 Chirality : 0.044 0.314 9754 Planarity : 0.004 0.046 11057 Dihedral : 5.389 96.262 8819 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.41 % Favored : 95.56 % Rotamer: Outliers : 2.84 % Allowed : 19.20 % Favored : 77.96 % 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: 0.18 (0.09), residues: 7935 helix: 1.18 (0.09), residues: 3403 sheet: -0.05 (0.13), residues: 1528 loop : -0.96 (0.11), residues: 3004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP c1688 HIS 0.007 0.001 HIS R 186 PHE 0.043 0.002 PHE A 198 TYR 0.020 0.001 TYR T 58 ARG 0.009 0.000 ARG O 142 *********************** 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 1112 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 936 time to evaluate : 5.337 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 176 outliers final: 119 residues processed: 1069 average time/residue: 1.4997 time to fit residues: 2073.4758 Evaluate side-chains 1011 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 892 time to evaluate : 5.260 Switching outliers to nearest non-outliers outliers start: 119 outliers final: 106 residues processed: 15 average time/residue: 0.6349 time to fit residues: 23.0075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 689 optimal weight: 1.9990 chunk 725 optimal weight: 0.7980 chunk 662 optimal weight: 1.9990 chunk 705 optimal weight: 0.8980 chunk 424 optimal weight: 0.7980 chunk 307 optimal weight: 2.9990 chunk 554 optimal weight: 0.8980 chunk 216 optimal weight: 0.8980 chunk 637 optimal weight: 3.9990 chunk 667 optimal weight: 0.9980 chunk 703 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 185 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 GLN H 30 ASN I 156 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 O 111 GLN O 168 ASN P 40 ASN P 84 ASN P 100 GLN P 177 GLN Q 122 ASN ** R 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 186 HIS R 221 GLN S 16 GLN S 60 GLN S 166 GLN U 150 GLN V 57 GLN V 193 ASN W 156 ASN X 8 GLN X 61 GLN Z 160 ASN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 66 GLN c 707 HIS ** c1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 63716 Z= 0.186 Angle : 0.589 12.838 86269 Z= 0.305 Chirality : 0.043 0.315 9754 Planarity : 0.004 0.047 11057 Dihedral : 5.292 96.294 8819 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.23 % Favored : 95.73 % Rotamer: Outliers : 2.42 % Allowed : 19.81 % 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: 0.27 (0.09), residues: 7935 helix: 1.27 (0.09), residues: 3410 sheet: -0.01 (0.13), residues: 1524 loop : -0.93 (0.11), residues: 3001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP c1688 HIS 0.007 0.001 HIS R 186 PHE 0.044 0.001 PHE A 198 TYR 0.020 0.001 TYR U 159 ARG 0.010 0.000 ARG V 72 *********************** 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 1078 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 930 time to evaluate : 5.402 Fit side-chains revert: symmetry clash outliers start: 148 outliers final: 112 residues processed: 1052 average time/residue: 1.5255 time to fit residues: 2095.0642 Evaluate side-chains 1007 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 895 time to evaluate : 5.292 Switching outliers to nearest non-outliers outliers start: 112 outliers final: 103 residues processed: 11 average time/residue: 1.0300 time to fit residues: 23.5221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 463 optimal weight: 0.4980 chunk 746 optimal weight: 0.0010 chunk 455 optimal weight: 3.9990 chunk 354 optimal weight: 5.9990 chunk 518 optimal weight: 0.9990 chunk 783 optimal weight: 3.9990 chunk 720 optimal weight: 0.5980 chunk 623 optimal weight: 0.9990 chunk 64 optimal weight: 0.0870 chunk 481 optimal weight: 5.9990 chunk 382 optimal weight: 0.8980 overall best weight: 0.4164 ------------------------------------------------------------------------------- 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** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN ** 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 193 GLN H 30 ASN I 156 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 O 111 GLN ** O 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 201 GLN P 40 ASN P 84 ASN P 100 GLN P 177 GLN Q 122 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 68 HIS U 150 GLN V 57 GLN V 193 ASN W 156 ASN X 8 GLN X 61 GLN Z 160 ASN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 66 GLN c 254 GLN c 707 HIS c 712 GLN ** c1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c1644 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 63716 Z= 0.156 Angle : 0.574 16.033 86269 Z= 0.297 Chirality : 0.042 0.311 9754 Planarity : 0.004 0.062 11057 Dihedral : 5.134 95.785 8819 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.27 % Favored : 95.70 % Rotamer: Outliers : 2.17 % Allowed : 20.24 % Favored : 77.59 % 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: 1.42 (0.09), residues: 3396 sheet: 0.00 (0.13), residues: 1517 loop : -0.90 (0.11), residues: 3022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP c1688 HIS 0.007 0.001 HIS R 186 PHE 0.043 0.001 PHE A 198 TYR 0.020 0.001 TYR U 159 ARG 0.014 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 1119 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 988 time to evaluate : 5.630 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 131 outliers final: 95 residues processed: 1101 average time/residue: 1.4813 time to fit residues: 2126.4337 Evaluate side-chains 1014 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 919 time to evaluate : 5.266 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 91 residues processed: 6 average time/residue: 1.1139 time to fit residues: 16.4904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 191 optimal weight: 0.9980 chunk 574 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 173 optimal weight: 7.9990 chunk 624 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 641 optimal weight: 5.9990 chunk 79 optimal weight: 0.3980 chunk 115 optimal weight: 4.9990 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** B 84 ASN ** 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 H 30 ASN I 156 ASN 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 O 111 GLN P 40 ASN P 84 ASN P 100 GLN P 177 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 186 HIS S 60 GLN S 166 GLN U 150 GLN V 57 GLN V 193 ASN W 156 ASN X 8 GLN X 27 GLN X 61 GLN Z 160 ASN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 66 GLN c 254 GLN ** c 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 707 HIS c1017 GLN ** c1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.138068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.116519 restraints weight = 220361.316| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.75 r_work: 0.3293 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 63716 Z= 0.193 Angle : 0.592 14.319 86269 Z= 0.305 Chirality : 0.043 0.312 9754 Planarity : 0.004 0.059 11057 Dihedral : 5.145 96.061 8819 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.38 % Favored : 95.58 % Rotamer: Outliers : 2.10 % Allowed : 20.76 % Favored : 77.14 % 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: 0.43 (0.10), residues: 7935 helix: 1.44 (0.09), residues: 3399 sheet: 0.03 (0.13), residues: 1515 loop : -0.87 (0.11), residues: 3021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP c1688 HIS 0.008 0.001 HIS R 186 PHE 0.044 0.001 PHE A 198 TYR 0.018 0.001 TYR V 189 ARG 0.015 0.000 ARG C 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29441.98 seconds wall clock time: 506 minutes 47.72 seconds (30407.72 seconds total)