Starting phenix.real_space_refine on Sun Feb 25 00:57:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6avo_7010/02_2024/6avo_7010_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6avo_7010/02_2024/6avo_7010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6avo_7010/02_2024/6avo_7010.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6avo_7010/02_2024/6avo_7010.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6avo_7010/02_2024/6avo_7010_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6avo_7010/02_2024/6avo_7010_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 308 5.16 5 C 30168 2.51 5 N 8184 2.21 5 O 9055 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 106": "NH1" <-> "NH2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B ARG 84": "NH1" <-> "NH2" Residue "B ARG 121": "NH1" <-> "NH2" Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 141": "NH1" <-> "NH2" Residue "C PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 30": "NH1" <-> "NH2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 120": "NH1" <-> "NH2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "D PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 30": "NH1" <-> "NH2" Residue "D TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 120": "NH1" <-> "NH2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "E PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 57": "NH1" <-> "NH2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E ARG 121": "NH1" <-> "NH2" Residue "E PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 141": "NH1" <-> "NH2" Residue "F ARG 106": "NH1" <-> "NH2" Residue "F ARG 152": "NH1" <-> "NH2" Residue "F ARG 186": "NH1" <-> "NH2" Residue "G ARG 101": "NH1" <-> "NH2" Residue "G TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 90": "NH1" <-> "NH2" Residue "Q PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 71": "NH1" <-> "NH2" Residue "T TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 153": "NH1" <-> "NH2" Residue "U ARG 79": "NH1" <-> "NH2" Residue "V TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 153": "NH1" <-> "NH2" Residue "W PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 100": "NH1" <-> "NH2" Residue "W TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 167": "OD1" <-> "OD2" Residue "W ASP 167": "OD1" <-> "OD2" Residue "X PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 71": "NH1" <-> "NH2" Residue "Y ARG 25": "NH1" <-> "NH2" Residue "Y ARG 79": "NH1" <-> "NH2" Residue "a PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 100": "NH1" <-> "NH2" Residue "a TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 167": "OD1" <-> "OD2" Residue "a ASP 167": "OD1" <-> "OD2" Residue "b GLU 58": "OE1" <-> "OE2" Residue "b ARG 90": "NH1" <-> "NH2" Residue "b ASP 149": "OD1" <-> "OD2" Residue "b ASP 149": "OD1" <-> "OD2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 47715 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1493 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain: "B" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1609 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "C" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1563 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 4, 'TRANS': 196} Chain: "D" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1563 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 4, 'TRANS': 196} Chain: "E" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1609 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "F" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1493 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain: "G" Number of atoms: 1817 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 234, 1809 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 224} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 234, 1809 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 224} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 1833 Chain: "H" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1753 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 1749 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 232, 1739 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 225} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 232, 1739 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 225} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 1752 Chain: "J" Number of atoms: 1888 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 239, 1866 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 233} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 239, 1866 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 233} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1875 Chain: "K" Number of atoms: 1850 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 240, 1843 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 231} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Conformer: "B" Number of residues, atoms: 240, 1843 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 231} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 1864 Chain: "L" Number of atoms: 1841 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 234, 1818 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 224} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 234, 1818 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 224} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 1825 Chain: "M" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1748 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "N" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1754 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 224} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 27 Chain: "O" Number of atoms: 1843 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 240, 1835 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 240, 1835 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 1855 Chain: "P" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1741 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 10, 'TRANS': 219} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "Q" Number of atoms: 1851 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 239, 1848 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 233} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 239, 1848 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 233} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 1879 Chain: "R" Number of atoms: 1817 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 240, 1812 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 8, 'TRANS': 231} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 240, 1812 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 8, 'TRANS': 231} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 1836 Chain: "S" Number of atoms: 1642 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 213, 1639 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Conformer: "B" Number of residues, atoms: 213, 1639 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 1665 Chain: "T" Number of atoms: 1567 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 196, 1557 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 188} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 196, 1557 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 188} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 1576 Chain: "U" Number of atoms: 1599 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 204, 1582 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 204, 1582 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1591 Chain: "V" Number of atoms: 1581 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 196, 1560 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 188} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 196, 1560 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 188} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 1567 Chain: "W" Number of atoms: 1692 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 216, 1687 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 208} Conformer: "B" Number of residues, atoms: 216, 1687 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 208} bond proxies already assigned to first conformer: 1714 Chain: "X" Number of atoms: 1636 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 213, 1630 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 213, 1630 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 1652 Chain: "Y" Number of atoms: 1604 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: 1605 Chain: "Z" Number of atoms: 1860 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 240, 1850 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Conformer: "B" Number of residues, atoms: 240, 1850 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 bond proxies already assigned to first conformer: 1868 Chain: "a" Number of atoms: 1684 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 216, 1679 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 208} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 216, 1679 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 208} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1706 Chain: "b" Number of atoms: 1788 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 230, 1766 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 219} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 230, 1766 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 219} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 1780 Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Classifications: {'peptide': 1} Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Classifications: {'peptide': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AARG L 18 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG L 18 " occ=0.50 residue: pdb=" N ALYS U 16 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS U 16 " occ=0.50 residue: pdb=" N AHIS V 99 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS V 99 " occ=0.50 residue: pdb=" N AGLU b 58 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU b 58 " occ=0.50 Time building chain proxies: 38.04, per 1000 atoms: 0.80 Number of scatterers: 47715 At special positions: 0 Unit cell: (178.8, 134.4, 138, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 308 16.00 O 9055 8.00 N 8184 7.00 C 30168 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.89 Conformation dependent library (CDL) restraints added in 13.7 seconds 12348 Ramachandran restraints generated. 6174 Oldfield, 0 Emsley, 6174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11462 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 157 helices and 78 sheets defined 34.5% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.31 Creating SS restraints... Processing helix chain 'A' and resid 49 through 70 Processing helix chain 'A' and resid 76 through 88 Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 129 through 133 removed outlier: 3.585A pdb=" N THR A 132 " --> pdb=" O SER A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 141 Processing helix chain 'A' and resid 148 through 165 Processing helix chain 'B' and resid 49 through 69 Processing helix chain 'B' and resid 76 through 89 Processing helix chain 'B' and resid 129 through 141 removed outlier: 4.163A pdb=" N ASP B 132 " --> pdb=" O SER B 129 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 133 " --> pdb=" O GLY B 130 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA B 134 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B 138 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG B 141 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 165 Processing helix chain 'C' and resid 49 through 69 Processing helix chain 'C' and resid 76 through 89 Processing helix chain 'C' and resid 132 through 140 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'D' and resid 49 through 69 Processing helix chain 'D' and resid 76 through 89 Processing helix chain 'D' and resid 132 through 140 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 193 through 200 Processing helix chain 'E' and resid 49 through 69 Processing helix chain 'E' and resid 76 through 89 Processing helix chain 'E' and resid 129 through 141 removed outlier: 4.163A pdb=" N ASP E 132 " --> pdb=" O SER E 129 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA E 133 " --> pdb=" O GLY E 130 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA E 134 " --> pdb=" O GLN E 131 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU E 138 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG E 141 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 165 Processing helix chain 'F' and resid 49 through 70 Processing helix chain 'F' and resid 76 through 88 Processing helix chain 'F' and resid 115 through 117 No H-bonds generated for 'chain 'F' and resid 115 through 117' Processing helix chain 'F' and resid 129 through 133 removed outlier: 3.584A pdb=" N THR F 132 " --> pdb=" O SER F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 141 Processing helix chain 'F' and resid 148 through 165 Processing helix chain 'G' and resid 20 through 31 removed outlier: 3.538A pdb=" N ALA G 28 " --> pdb=" O TYR G 24 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL G 29 " --> pdb=" O ALA G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 98 Processing helix chain 'G' and resid 105 through 118 removed outlier: 3.560A pdb=" N ILE G 118 " --> pdb=" O SER G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 178 removed outlier: 5.368A pdb=" N SER G 177 " --> pdb=" O GLU G 173 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLU G 178 " --> pdb=" O ARG G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 196 Processing helix chain 'G' and resid 228 through 230 No H-bonds generated for 'chain 'G' and resid 228 through 230' Processing helix chain 'H' and resid 22 through 33 removed outlier: 3.825A pdb=" N LYS H 32 " --> pdb=" O ILE H 28 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU H 33 " --> pdb=" O GLU H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 103 removed outlier: 3.717A pdb=" N ASP H 90 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN H 97 " --> pdb=" O VAL H 94 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR H 102 " --> pdb=" O HIS H 99 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR H 103 " --> pdb=" O TRP H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 119 removed outlier: 4.179A pdb=" N LEU H 119 " --> pdb=" O ALA H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 184 Processing helix chain 'H' and resid 191 through 205 Processing helix chain 'H' and resid 231 through 240 removed outlier: 4.631A pdb=" N ASP H 240 " --> pdb=" O GLU H 236 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 28 Processing helix chain 'I' and resid 57 through 59 No H-bonds generated for 'chain 'I' and resid 57 through 59' Processing helix chain 'I' and resid 77 through 98 Processing helix chain 'I' and resid 104 through 120 Processing helix chain 'I' and resid 165 through 175 Processing helix chain 'I' and resid 184 through 197 removed outlier: 4.364A pdb=" N GLU I 197 " --> pdb=" O LYS I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 222 through 232 removed outlier: 3.556A pdb=" N TYR I 228 " --> pdb=" O GLU I 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 32 removed outlier: 3.532A pdb=" N ASN J 32 " --> pdb=" O LYS J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 102 Processing helix chain 'J' and resid 108 through 122 removed outlier: 3.991A pdb=" N TYR J 122 " --> pdb=" O TYR J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 169 through 178 removed outlier: 4.041A pdb=" N LYS J 178 " --> pdb=" O THR J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 183 No H-bonds generated for 'chain 'J' and resid 181 through 183' Processing helix chain 'J' and resid 186 through 200 removed outlier: 4.723A pdb=" N LYS J 191 " --> pdb=" O ARG J 187 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU J 192 " --> pdb=" O ASP J 188 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 243 Processing helix chain 'K' and resid 23 through 34 removed outlier: 4.089A pdb=" N ASN K 33 " --> pdb=" O PHE K 29 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLN K 34 " --> pdb=" O LYS K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 105 Processing helix chain 'K' and resid 111 through 123 Processing helix chain 'K' and resid 172 through 185 removed outlier: 4.187A pdb=" N LYS K 185 " --> pdb=" O LYS K 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 206 Processing helix chain 'K' and resid 232 through 243 Processing helix chain 'L' and resid 20 through 31 removed outlier: 3.538A pdb=" N ALA L 28 " --> pdb=" O TYR L 24 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL L 29 " --> pdb=" O ALA L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 98 Processing helix chain 'L' and resid 105 through 118 removed outlier: 3.560A pdb=" N ILE L 118 " --> pdb=" O SER L 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 165 through 178 removed outlier: 5.367A pdb=" N SER L 177 " --> pdb=" O GLU L 173 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLU L 178 " --> pdb=" O ARG L 174 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 196 Processing helix chain 'M' and resid 22 through 33 removed outlier: 3.825A pdb=" N LYS M 32 " --> pdb=" O ILE M 28 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU M 33 " --> pdb=" O GLU M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 103 removed outlier: 3.716A pdb=" N ASP M 90 " --> pdb=" O THR M 87 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN M 97 " --> pdb=" O VAL M 94 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR M 102 " --> pdb=" O HIS M 99 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR M 103 " --> pdb=" O TRP M 100 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 115 Processing helix chain 'M' and resid 174 through 184 Processing helix chain 'M' and resid 191 through 205 Processing helix chain 'M' and resid 231 through 240 removed outlier: 4.630A pdb=" N ASP M 240 " --> pdb=" O GLU M 236 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 28 Processing helix chain 'N' and resid 57 through 59 No H-bonds generated for 'chain 'N' and resid 57 through 59' Processing helix chain 'N' and resid 77 through 98 Processing helix chain 'N' and resid 104 through 120 Processing helix chain 'N' and resid 165 through 175 Processing helix chain 'N' and resid 184 through 197 removed outlier: 4.364A pdb=" N GLU N 197 " --> pdb=" O LYS N 193 " (cutoff:3.500A) Processing helix chain 'N' and resid 222 through 232 removed outlier: 3.557A pdb=" N TYR N 228 " --> pdb=" O GLU N 224 " (cutoff:3.500A) Processing helix chain 'O' and resid 19 through 30 Processing helix chain 'O' and resid 80 through 101 Processing helix chain 'O' and resid 107 through 123 removed outlier: 3.584A pdb=" N ILE O 117 " --> pdb=" O ALA O 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 168 through 178 Processing helix chain 'O' and resid 186 through 200 Processing helix chain 'O' and resid 230 through 240 Processing helix chain 'P' and resid 19 through 30 Processing helix chain 'P' and resid 58 through 60 No H-bonds generated for 'chain 'P' and resid 58 through 60' Processing helix chain 'P' and resid 79 through 100 Processing helix chain 'P' and resid 106 through 121 removed outlier: 3.980A pdb=" N TYR P 120 " --> pdb=" O VAL P 116 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR P 121 " --> pdb=" O MET P 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 166 through 174 Processing helix chain 'P' and resid 183 through 197 removed outlier: 4.266A pdb=" N SER P 197 " --> pdb=" O THR P 193 " (cutoff:3.500A) Processing helix chain 'P' and resid 222 through 229 Processing helix chain 'Q' and resid 21 through 32 removed outlier: 3.533A pdb=" N ASN Q 32 " --> pdb=" O LYS Q 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 81 through 102 Processing helix chain 'Q' and resid 108 through 122 removed outlier: 3.992A pdb=" N TYR Q 122 " --> pdb=" O TYR Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 169 through 178 removed outlier: 4.041A pdb=" N LYS Q 178 " --> pdb=" O THR Q 174 " (cutoff:3.500A) Processing helix chain 'Q' and resid 181 through 183 No H-bonds generated for 'chain 'Q' and resid 181 through 183' Processing helix chain 'Q' and resid 186 through 200 removed outlier: 4.722A pdb=" N LYS Q 191 " --> pdb=" O ARG Q 187 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU Q 192 " --> pdb=" O ASP Q 188 " (cutoff:3.500A) Processing helix chain 'Q' and resid 229 through 243 Processing helix chain 'R' and resid 23 through 34 removed outlier: 4.090A pdb=" N ASN R 33 " --> pdb=" O PHE R 29 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLN R 34 " --> pdb=" O LYS R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 105 Processing helix chain 'R' and resid 111 through 123 Processing helix chain 'R' and resid 172 through 185 removed outlier: 4.186A pdb=" N LYS R 185 " --> pdb=" O LYS R 181 " (cutoff:3.500A) Processing helix chain 'R' and resid 195 through 206 Processing helix chain 'R' and resid 232 through 243 Processing helix chain 'S' and resid 58 through 79 Processing helix chain 'S' and resid 85 through 98 Processing helix chain 'S' and resid 140 through 152 removed outlier: 4.626A pdb=" N ALA S 143 " --> pdb=" O SER S 140 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLN S 146 " --> pdb=" O ALA S 143 " (cutoff:3.500A) Proline residue: S 147 - end of helix removed outlier: 4.048A pdb=" N GLN S 152 " --> pdb=" O LEU S 149 " (cutoff:3.500A) Processing helix chain 'S' and resid 168 through 183 Processing helix chain 'T' and resid 52 through 71 Processing helix chain 'T' and resid 77 through 90 Processing helix chain 'T' and resid 133 through 146 removed outlier: 4.183A pdb=" N PHE T 137 " --> pdb=" O GLY T 133 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU T 138 " --> pdb=" O TYR T 134 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N SER T 141 " --> pdb=" O PHE T 137 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ILE T 142 " --> pdb=" O LEU T 138 " (cutoff:3.500A) Processing helix chain 'T' and resid 153 through 169 Processing helix chain 'U' and resid 3 through 5 No H-bonds generated for 'chain 'U' and resid 3 through 5' Processing helix chain 'U' and resid 56 through 76 Processing helix chain 'U' and resid 83 through 97 removed outlier: 3.921A pdb=" N LYS U 97 " --> pdb=" O LEU U 93 " (cutoff:3.500A) Processing helix chain 'U' and resid 142 through 152 Processing helix chain 'U' and resid 159 through 175 Processing helix chain 'V' and resid 52 through 71 Processing helix chain 'V' and resid 77 through 90 Processing helix chain 'V' and resid 133 through 146 removed outlier: 4.183A pdb=" N PHE V 137 " --> pdb=" O GLY V 133 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU V 138 " --> pdb=" O TYR V 134 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N SER V 141 " --> pdb=" O PHE V 137 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ILE V 142 " --> pdb=" O LEU V 138 " (cutoff:3.500A) Processing helix chain 'V' and resid 153 through 169 Processing helix chain 'W' and resid 58 through 77 removed outlier: 3.779A pdb=" N LEU W 77 " --> pdb=" O ASP W 73 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 101 Processing helix chain 'W' and resid 140 through 143 Processing helix chain 'W' and resid 146 through 156 Processing helix chain 'W' and resid 162 through 179 Processing helix chain 'W' and resid 210 through 213 Processing helix chain 'X' and resid 58 through 79 Processing helix chain 'X' and resid 85 through 98 Processing helix chain 'X' and resid 140 through 152 removed outlier: 4.625A pdb=" N ALA X 143 " --> pdb=" O SER X 140 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLN X 146 " --> pdb=" O ALA X 143 " (cutoff:3.500A) Proline residue: X 147 - end of helix removed outlier: 4.048A pdb=" N GLN X 152 " --> pdb=" O LEU X 149 " (cutoff:3.500A) Processing helix chain 'X' and resid 168 through 183 Processing helix chain 'Y' and resid 3 through 5 No H-bonds generated for 'chain 'Y' and resid 3 through 5' Processing helix chain 'Y' and resid 56 through 76 Processing helix chain 'Y' and resid 83 through 97 removed outlier: 3.921A pdb=" N LYS Y 97 " --> pdb=" O LEU Y 93 " (cutoff:3.500A) Processing helix chain 'Y' and resid 142 through 152 Processing helix chain 'Y' and resid 159 through 175 Processing helix chain 'Z' and resid 19 through 30 Processing helix chain 'Z' and resid 80 through 101 Processing helix chain 'Z' and resid 107 through 123 removed outlier: 3.584A pdb=" N ILE Z 117 " --> pdb=" O ALA Z 113 " (cutoff:3.500A) Processing helix chain 'Z' and resid 168 through 178 Processing helix chain 'Z' and resid 186 through 200 Processing helix chain 'Z' and resid 230 through 240 Processing helix chain 'a' and resid 58 through 77 removed outlier: 3.778A pdb=" N LEU a 77 " --> pdb=" O ASP a 73 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 101 Processing helix chain 'a' and resid 140 through 143 Processing helix chain 'a' and resid 146 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 19 through 30 Processing helix chain 'b' and resid 58 through 60 No H-bonds generated for 'chain 'b' and resid 58 through 60' Processing helix chain 'b' and resid 79 through 100 Processing helix chain 'b' and resid 106 through 121 removed outlier: 3.980A pdb=" N TYR b 120 " --> pdb=" O VAL b 116 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR b 121 " --> pdb=" O MET b 117 " (cutoff:3.500A) Processing helix chain 'b' and resid 166 through 174 Processing helix chain 'b' and resid 183 through 197 removed outlier: 4.266A pdb=" N SER b 197 " --> pdb=" O THR b 193 " (cutoff:3.500A) Processing helix chain 'b' and resid 222 through 229 Processing sheet with id= A, first strand: chain 'A' and resid 3 through 7 Processing sheet with id= B, first strand: chain 'A' and resid 34 through 36 removed outlier: 3.600A pdb=" N ALA A 44 " --> pdb=" O MET A 99 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 173 through 175 Processing sheet with id= D, first strand: chain 'A' and resid 20 through 22 removed outlier: 5.333A pdb=" N ALA A 22 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N VAL A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 2 through 4 Processing sheet with id= F, first strand: chain 'B' and resid 42 through 44 Processing sheet with id= G, first strand: chain 'B' and resid 175 through 178 removed outlier: 3.812A pdb=" N ALA B 175 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 125 through 129 Processing sheet with id= I, first strand: chain 'C' and resid 41 through 43 Processing sheet with id= J, first strand: chain 'C' and resid 20 through 22 removed outlier: 6.231A pdb=" N ALA C 22 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ILE C 26 " --> pdb=" O ALA C 22 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 173 through 177 Processing sheet with id= L, first strand: chain 'D' and resid 125 through 129 Processing sheet with id= M, first strand: chain 'D' and resid 41 through 43 Processing sheet with id= N, first strand: chain 'D' and resid 20 through 22 removed outlier: 6.229A pdb=" N ALA D 22 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ILE D 26 " --> pdb=" O ALA D 22 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 173 through 177 Processing sheet with id= P, first strand: chain 'E' and resid 2 through 4 Processing sheet with id= Q, first strand: chain 'E' and resid 42 through 44 Processing sheet with id= R, first strand: chain 'E' and resid 175 through 178 removed outlier: 3.811A pdb=" N ALA E 175 " --> pdb=" O LEU E 186 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 3 through 7 Processing sheet with id= T, first strand: chain 'F' and resid 34 through 36 removed outlier: 3.601A pdb=" N ALA F 44 " --> pdb=" O MET F 99 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 173 through 175 Processing sheet with id= V, first strand: chain 'F' and resid 20 through 22 removed outlier: 5.334A pdb=" N ALA F 22 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N VAL F 26 " --> pdb=" O ALA F 22 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 35 through 39 removed outlier: 3.521A pdb=" N GLY G 213 " --> pdb=" O LEU G 46 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 153 through 155 removed outlier: 3.529A pdb=" N ILE G 70 " --> pdb=" O ASP G 67 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE G 72 " --> pdb=" O HIS G 65 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N HIS G 65 " --> pdb=" O ILE G 72 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'H' and resid 167 through 170 removed outlier: 3.544A pdb=" N GLY H 39 " --> pdb=" O ARG H 168 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL H 50 " --> pdb=" O GLU H 216 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'H' and resid 163 through 165 removed outlier: 4.058A pdb=" N LEU H 153 " --> pdb=" O CYS H 165 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N CYS H 76 " --> pdb=" O GLU H 69 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLU H 69 " --> pdb=" O CYS H 76 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N MET H 78 " --> pdb=" O ILE H 67 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE H 67 " --> pdb=" O MET H 78 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'I' and resid 32 through 36 removed outlier: 3.646A pdb=" N VAL I 42 " --> pdb=" O VAL I 35 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'I' and resid 153 through 155 removed outlier: 3.616A pdb=" N VAL I 69 " --> pdb=" O ASP I 66 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N MET I 71 " --> pdb=" O ALA I 64 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ALA I 64 " --> pdb=" O MET I 71 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'J' and resid 162 through 165 removed outlier: 3.556A pdb=" N GLY J 44 " --> pdb=" O CYS J 41 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 50 through 52 Processing sheet with id= AE, first strand: chain 'J' and resid 73 through 77 removed outlier: 4.080A pdb=" N TYR J 158 " --> pdb=" O MET J 150 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'K' and resid 165 through 169 removed outlier: 3.625A pdb=" N ALA K 41 " --> pdb=" O THR K 166 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR K 38 " --> pdb=" O GLN K 53 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN K 53 " --> pdb=" O THR K 38 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL K 217 " --> pdb=" O LEU K 230 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'K' and resid 76 through 79 removed outlier: 3.624A pdb=" N ILE K 141 " --> pdb=" O GLY K 77 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'L' and resid 35 through 39 removed outlier: 3.521A pdb=" N GLY L 213 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'L' and resid 153 through 155 removed outlier: 3.529A pdb=" N ILE L 70 " --> pdb=" O ASP L 67 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE L 72 " --> pdb=" O HIS L 65 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N HIS L 65 " --> pdb=" O ILE L 72 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'M' and resid 167 through 170 removed outlier: 3.544A pdb=" N GLY M 39 " --> pdb=" O ARG M 168 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL M 50 " --> pdb=" O GLU M 216 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'M' and resid 163 through 165 removed outlier: 4.057A pdb=" N LEU M 153 " --> pdb=" O CYS M 165 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N CYS M 76 " --> pdb=" O GLU M 69 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLU M 69 " --> pdb=" O CYS M 76 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N MET M 78 " --> pdb=" O ILE M 67 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE M 67 " --> pdb=" O MET M 78 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'N' and resid 32 through 36 removed outlier: 3.646A pdb=" N VAL N 42 " --> pdb=" O VAL N 35 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'N' and resid 153 through 155 removed outlier: 3.616A pdb=" N VAL N 69 " --> pdb=" O ASP N 66 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N MET N 71 " --> pdb=" O ALA N 64 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ALA N 64 " --> pdb=" O MET N 71 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'O' and resid 161 through 164 removed outlier: 3.514A pdb=" N LEU O 44 " --> pdb=" O ILE O 37 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'O' and resid 65 through 67 Processing sheet with id= AP, first strand: chain 'P' and resid 159 through 162 Processing sheet with id= AQ, first strand: chain 'P' and resid 133 through 138 Processing sheet with id= AR, first strand: chain 'Q' and resid 162 through 165 removed outlier: 3.556A pdb=" N GLY Q 44 " --> pdb=" O CYS Q 41 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'Q' and resid 50 through 52 Processing sheet with id= AT, first strand: chain 'Q' and resid 73 through 77 removed outlier: 4.080A pdb=" N TYR Q 158 " --> pdb=" O MET Q 150 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'R' and resid 165 through 169 removed outlier: 3.626A pdb=" N ALA R 41 " --> pdb=" O THR R 166 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR R 38 " --> pdb=" O GLN R 53 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN R 53 " --> pdb=" O THR R 38 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL R 217 " --> pdb=" O LEU R 230 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'R' and resid 76 through 79 removed outlier: 3.623A pdb=" N ILE R 141 " --> pdb=" O GLY R 77 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'S' and resid 135 through 138 Processing sheet with id= AX, first strand: chain 'S' and resid 43 through 45 removed outlier: 3.573A pdb=" N ILE S 109 " --> pdb=" O GLY S 53 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'S' and resid 29 through 31 removed outlier: 4.020A pdb=" N THR S 37 " --> pdb=" O LEU S 29 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLU S 31 " --> pdb=" O ILE S 35 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE S 35 " --> pdb=" O GLU S 31 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'T' and resid 129 through 131 removed outlier: 3.599A pdb=" N GLY T 6 " --> pdb=" O ALA T 130 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE T 7 " --> pdb=" O LEU T 14 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'T' and resid 124 through 127 removed outlier: 3.645A pdb=" N ALA T 125 " --> pdb=" O TYR T 117 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU T 115 " --> pdb=" O ALA T 127 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP T 108 " --> pdb=" O GLY T 112 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR T 116 " --> pdb=" O LEU T 104 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE T 42 " --> pdb=" O SER T 39 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU T 44 " --> pdb=" O LYS T 37 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LYS T 37 " --> pdb=" O LEU T 44 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N CYS T 46 " --> pdb=" O MET T 35 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N MET T 35 " --> pdb=" O CYS T 46 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'U' and resid 12 through 14 removed outlier: 3.537A pdb=" N VAL U 19 " --> pdb=" O ILE U 189 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL U 184 " --> pdb=" O LEU U 199 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'U' and resid 41 through 43 removed outlier: 3.699A pdb=" N PHE U 42 " --> pdb=" O ILE U 50 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'U' and resid 27 through 29 removed outlier: 6.593A pdb=" N ILE U 29 " --> pdb=" O MET U 33 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N MET U 33 " --> pdb=" O ILE U 29 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'V' and resid 129 through 131 removed outlier: 3.598A pdb=" N GLY V 6 " --> pdb=" O ALA V 130 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE V 7 " --> pdb=" O LEU V 14 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'V' and resid 124 through 127 removed outlier: 3.645A pdb=" N ALA V 125 " --> pdb=" O TYR V 117 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU V 115 " --> pdb=" O ALA V 127 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP V 108 " --> pdb=" O GLY V 112 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR V 116 " --> pdb=" O LEU V 104 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE V 42 " --> pdb=" O SER V 39 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU V 44 " --> pdb=" O LYS V 37 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LYS V 37 " --> pdb=" O LEU V 44 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N CYS V 46 " --> pdb=" O MET V 35 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N MET V 35 " --> pdb=" O CYS V 46 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'W' and resid 136 through 138 Processing sheet with id= BH, first strand: chain 'W' and resid 53 through 55 removed outlier: 3.717A pdb=" N SER W 54 " --> pdb=" O THR W 109 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR W 109 " --> pdb=" O SER W 54 " (cutoff:3.500A) No H-bonds generated for sheet with id= BH Processing sheet with id= BI, first strand: chain 'W' and resid 113 through 116 removed outlier: 3.742A pdb=" N ALA W 116 " --> pdb=" O GLU W 119 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU W 119 " --> pdb=" O ALA W 116 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'W' and resid 123 through 125 Processing sheet with id= BK, first strand: chain 'W' and resid 42 through 46 removed outlier: 6.444A pdb=" N THR W 49 " --> pdb=" O VAL W 45 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'X' and resid 135 through 138 Processing sheet with id= BM, first strand: chain 'X' and resid 43 through 45 removed outlier: 3.572A pdb=" N ILE X 109 " --> pdb=" O GLY X 53 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'X' and resid 29 through 31 removed outlier: 4.020A pdb=" N THR X 37 " --> pdb=" O LEU X 29 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLU X 31 " --> pdb=" O ILE X 35 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE X 35 " --> pdb=" O GLU X 31 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'Y' and resid 12 through 14 removed outlier: 3.538A pdb=" N VAL Y 19 " --> pdb=" O ILE Y 189 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL Y 184 " --> pdb=" O LEU Y 199 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'Y' and resid 41 through 43 removed outlier: 3.699A pdb=" N PHE Y 42 " --> pdb=" O ILE Y 50 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'Y' and resid 27 through 29 removed outlier: 6.593A pdb=" N ILE Y 29 " --> pdb=" O MET Y 33 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N MET Y 33 " --> pdb=" O ILE Y 29 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'Z' and resid 161 through 164 removed outlier: 3.514A pdb=" N LEU Z 44 " --> pdb=" O ILE Z 37 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'Z' and resid 65 through 67 Processing sheet with id= BT, first strand: chain 'a' and resid 136 through 138 Processing sheet with id= BU, first strand: chain 'a' and resid 53 through 55 removed outlier: 3.717A pdb=" N SER a 54 " --> pdb=" O THR a 109 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR a 109 " --> pdb=" O SER a 54 " (cutoff:3.500A) No H-bonds generated for sheet with id= BU Processing sheet with id= BV, first strand: chain 'a' and resid 113 through 116 removed outlier: 3.742A pdb=" N ALA a 116 " --> pdb=" O GLU a 119 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU a 119 " --> pdb=" O ALA a 116 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'a' and resid 123 through 125 Processing sheet with id= BX, first strand: chain 'a' and resid 42 through 46 removed outlier: 6.445A pdb=" N THR a 49 " --> pdb=" O VAL a 45 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'b' and resid 159 through 162 Processing sheet with id= BZ, first strand: chain 'b' and resid 133 through 138 2132 hydrogen bonds defined for protein. 5971 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: 17.29 Time building geometry restraints manager: 19.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 8021 1.31 - 1.44: 12608 1.44 - 1.56: 27483 1.56 - 1.69: 0 1.69 - 1.82: 503 Bond restraints: 48615 Sorted by residual: bond pdb=" CAD BZ7 C 301 " pdb=" CAE BZ7 C 301 " ideal model delta sigma weight residual 1.388 1.527 -0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" CAD BZ7 D 301 " pdb=" CAE BZ7 D 301 " ideal model delta sigma weight residual 1.388 1.527 -0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" CAA BZ7 D 301 " pdb=" CAF BZ7 D 301 " ideal model delta sigma weight residual 1.389 1.527 -0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" CAA BZ7 C 301 " pdb=" CAF BZ7 C 301 " ideal model delta sigma weight residual 1.389 1.527 -0.138 2.00e-02 2.50e+03 4.74e+01 bond pdb=" CAB BZ7 D 301 " pdb=" CAC BZ7 D 301 " ideal model delta sigma weight residual 1.393 1.528 -0.135 2.00e-02 2.50e+03 4.53e+01 ... (remaining 48610 not shown) Histogram of bond angle deviations from ideal: 98.29 - 105.68: 894 105.68 - 113.08: 27051 113.08 - 120.47: 19950 120.47 - 127.87: 17680 127.87 - 135.27: 285 Bond angle restraints: 65860 Sorted by residual: angle pdb=" C BLYS U 16 " pdb=" N ASN U 17 " pdb=" CA ASN U 17 " ideal model delta sigma weight residual 120.23 135.27 -15.04 1.67e+00 3.59e-01 8.11e+01 angle pdb=" N LEU I 208 " pdb=" CA LEU I 208 " pdb=" C LEU I 208 " ideal model delta sigma weight residual 108.65 117.67 -9.02 1.85e+00 2.92e-01 2.38e+01 angle pdb=" N LEU N 208 " pdb=" CA LEU N 208 " pdb=" C LEU N 208 " ideal model delta sigma weight residual 108.65 117.64 -8.99 1.85e+00 2.92e-01 2.36e+01 angle pdb=" N LYS I 47 " pdb=" CA LYS I 47 " pdb=" CB LYS I 47 " ideal model delta sigma weight residual 114.17 108.74 5.43 1.14e+00 7.69e-01 2.27e+01 angle pdb=" N LYS N 47 " pdb=" CA LYS N 47 " pdb=" CB LYS N 47 " ideal model delta sigma weight residual 114.17 108.75 5.42 1.14e+00 7.69e-01 2.26e+01 ... (remaining 65855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.40: 28802 26.40 - 52.81: 383 52.81 - 79.21: 55 79.21 - 105.61: 15 105.61 - 132.02: 2 Dihedral angle restraints: 29257 sinusoidal: 11277 harmonic: 17980 Sorted by residual: dihedral pdb=" CA LYS I 204 " pdb=" C LYS I 204 " pdb=" N ASN I 205 " pdb=" CA ASN I 205 " ideal model delta harmonic sigma weight residual -180.00 -77.82 -102.18 0 5.00e+00 4.00e-02 4.18e+02 dihedral pdb=" CA ILE Z 52 " pdb=" C ILE Z 52 " pdb=" N HIS Z 53 " pdb=" CA HIS Z 53 " ideal model delta harmonic sigma weight residual -180.00 -82.00 -98.00 0 5.00e+00 4.00e-02 3.84e+02 dihedral pdb=" CA ILE O 52 " pdb=" C ILE O 52 " pdb=" N HIS O 53 " pdb=" CA HIS O 53 " ideal model delta harmonic sigma weight residual -180.00 -82.05 -97.95 0 5.00e+00 4.00e-02 3.84e+02 ... (remaining 29254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 7017 0.092 - 0.184: 438 0.184 - 0.276: 4 0.276 - 0.367: 0 0.367 - 0.459: 1 Chirality restraints: 7460 Sorted by residual: chirality pdb=" CA ASN N 221 " pdb=" N ASN N 221 " pdb=" C ASN N 221 " pdb=" CB ASN N 221 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.27e+00 chirality pdb=" CA LEU N 208 " pdb=" N LEU N 208 " pdb=" C LEU N 208 " pdb=" CB LEU N 208 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA LEU I 208 " pdb=" N LEU I 208 " pdb=" C LEU I 208 " pdb=" CB LEU I 208 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 7457 not shown) Planarity restraints: 8519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN I 221 " -0.056 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO I 222 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO I 222 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO I 222 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 101 " 0.020 2.00e-02 2.50e+03 1.91e-02 9.13e+00 pdb=" CG TRP K 101 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP K 101 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP K 101 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP K 101 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP K 101 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP K 101 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 101 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 101 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP K 101 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 101 " -0.020 2.00e-02 2.50e+03 1.90e-02 9.00e+00 pdb=" CG TRP R 101 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP R 101 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP R 101 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP R 101 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP R 101 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 101 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 101 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 101 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP R 101 " 0.001 2.00e-02 2.50e+03 ... (remaining 8516 not shown) Histogram of nonbonded interaction distances: 0.97 - 1.76: 6 1.76 - 2.54: 444 2.54 - 3.33: 62758 3.33 - 4.11: 116818 4.11 - 4.90: 225265 Warning: very small nonbonded interaction distances. Nonbonded interactions: 405291 Sorted by model distance: nonbonded pdb=" CD1 LEU N 220 " pdb=" CD1 ILE N 225 " model vdw 0.972 3.880 nonbonded pdb=" CD1 LEU N 220 " pdb=" CG1 ILE N 225 " model vdw 1.365 3.860 nonbonded pdb=" CD1 ILE R 32 " pdb=" SG CYS R 137 " model vdw 1.688 3.820 nonbonded pdb=" CB GLN R 193 " pdb=" OE1 GLU R 196 " model vdw 1.721 3.440 nonbonded pdb=" O GLN M 114 " pdb=" OD1 ASN M 118 " model vdw 1.741 3.040 ... (remaining 405286 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' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'G' and (resid 4 through 17 or resid 19 through 64 or resid 66 through 10 \ 0 or resid 102 through 151 or resid 153 through 188 or (resid 189 and (name N or \ name CA or name C or name O or name CB )) or resid 190 through 216 or (resid 21 \ 7 through 218 and (name N or name CA or name C or name O or name CB )) or resid \ 219 through 237)) selection = (chain 'L' and (resid 4 through 17 or resid 19 through 50 or (resid 51 through 5 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 56 through 5 \ 8 or (resid 59 and (name N or name CA or name C or name O or name CB )) or resid \ 60 through 64 or resid 66 through 100 or resid 102 through 151 or resid 153 thr \ ough 207 or (resid 208 and (name N or name CA or name C or name O or name CB )) \ or resid 209 through 237)) } ncs_group { reference = (chain 'H' and (resid 9 through 125 or (resid 126 through 129 and (name N or nam \ e CA or name C or name O or name CB )) or resid 130 through 174 or (resid 175 an \ d (name N or name CA or name C or name O or name CB )) or resid 176 through 206 \ or (resid 207 through 209 and (name N or name CA or name C or name O or name CB \ )) or resid 210 through 230 or (resid 231 and (name N or name CA or name C or na \ me O or name CB )) or resid 232 through 241)) selection = (chain 'M' and (resid 9 through 171 or (resid 172 through 173 and (name N or nam \ e CA or name C or name O or name CB )) or resid 174 through 186 or (resid 187 an \ d (name N or name CA or name C or name O or name CB )) or resid 188 through 191 \ or (resid 192 and (name N or name CA or name C or name O or name CB )) or resid \ 193 through 195 or (resid 196 and (name N or name CA or name C or name O or name \ CB )) or resid 197 through 208 or (resid 209 and (name N or name CA or name C o \ r name O or name CB )) or resid 210 through 240 or (resid 241 and (name N or nam \ e CA or name C or name O or name CB or name CG1 or name CG2 or name CD1)))) } ncs_group { reference = (chain 'I' and (resid 2 through 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB )) or resid 62 through 84 or resid 86 through 181 or (resi \ d 182 and (name N or name CA or name C or name O or name CB )) or resid 183 thro \ ugh 220 or resid 222 through 233)) selection = (chain 'N' and (resid 2 through 84 or resid 86 through 169 or (resid 170 and (na \ me N or name CA or name C or name O or name CB )) or resid 171 through 195 or (r \ esid 196 and (name N or name CA or name C or name O or name CB )) or resid 197 t \ hrough 198 or (resid 199 through 200 and (name N or name CA or name C or name O \ or name CB )) or resid 201 through 205 or (resid 206 through 207 and (name N or \ name CA or name C or name O or name CB )) or resid 208 through 220 or resid 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 na \ me O or name CB )) or resid 233)) } ncs_group { reference = (chain 'J' and (resid 6 through 41 or (resid 42 and (name N or name CA or name C \ or name O or name CB )) or resid 43 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 throu \ gh 138 or resid 140 through 168 or resid 170 through 186 or (resid 187 and (name \ N or name CA or name C or name O or name CB )) or resid 188 through 231 or resi \ d 233 or (resid 234 through 235 and (name N or name CA or name C or name O or na \ me CB )) or resid 236 through 243 or (resid 244 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'Q' and (resid 6 through 132 or resid 134 through 138 or resid 140 throug \ h 168 or resid 170 through 204 or (resid 205 and (name N or name CA or name C or \ name O or name CB )) or resid 206 through 231 or resid 233 through 244)) } ncs_group { reference = (chain 'K' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 48 or resid 50 through 54 or (resid 55 and (name \ N or name CA or name C or name O or name CB )) or resid 56 through 58 or (resid \ 59 and (name N or name CA or name C or name O or name CB )) or resid 60 through \ 79 or resid 81 through 88 or resid 90 through 146 or (resid 147 and (name N or \ name CA or name C or name O or name CB )) or resid 148 through 169 or (resid 170 \ through 171 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 72 through 183 or (resid 184 and (name N or name CA or name C or name O or name \ CB )) or resid 185 or (resid 186 and (name N or name CA or name C or name O or n \ ame CB )) or resid 191 through 208 or (resid 209 and (name N or name CA or name \ C or name O or name CB )) or resid 210 through 225 or (resid 226 and (name N or \ name CA or name C or name O or name CB )) or resid 227 through 245)) selection = (chain 'R' and (resid 2 through 44 or (resid 45 and (name N or name CA or name C \ or name O or name CB )) or resid 46 through 48 or resid 50 through 79 or resid \ 81 through 88 or resid 90 through 195 or (resid 196 and (name N or name CA or na \ me C or name O or name CB )) or resid 197 through 245)) } ncs_group { reference = (chain 'O' and (resid 2 through 6 or resid 8 through 24 or resid 26 through 53 o \ r (resid 54 and (name N or name CA or name C or name O or name CB )) or resid 55 \ through 91 or resid 93 through 180 or (resid 181 and (name N or name CA or name \ C or name O or name CB )) or resid 182 or (resid 183 and (name N or name CA or \ name C or name O or name CB )) or resid 184 through 201 or (resid 202 through 20 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 204 through \ 241)) selection = (chain 'Z' and (resid 2 through 6 or resid 8 through 24 or resid 26 through 50 o \ r (resid 51 through 52 and (name N or name CA or name C or name O or name CB )) \ or resid 53 through 91 or resid 93 through 225 or (resid 226 and (name N or name \ CA or name C or name O or name CB )) or resid 227 through 228 or (resid 229 and \ (name N or name CA or name C or name O or name CB )) or resid 230 or (resid 231 \ through 232 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 33 through 237 or (resid 238 through 239 and (name N or name CA or name C or nam \ e O or name CB )) or resid 240 through 241)) } ncs_group { reference = (chain 'P' and (resid 3 through 57 or (resid 59 and (name N or name CA or name C \ or name O or name CB )) or resid 60 through 87 or resid 89 through 139 or (resi \ d 140 and (name N or name CA or name C or name O or name CB )) or resid 141 thro \ ugh 148 or resid 150 through 194 or (resid 195 and (name N or name CA or name C \ or name O or name CB )) or resid 196 through 198 or (resid 199 and (name N or na \ me CA or name C or name O or name CB )) or resid 200 through 232)) selection = (chain 'b' and (resid 3 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 49 or (resid 50 through 52 and (nam \ e N or name CA or name C or name O or name CB )) or resid 53 or (resid 54 and (n \ ame N or name CA or name C or name O or name CB )) or resid 55 through 57 or res \ id 59 through 68 or (resid 69 and (name N or name CA or name C or name O or name \ CB )) or resid 70 through 87 or resid 89 through 148 or resid 150 through 163 o \ r (resid 164 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 65 through 173 or (resid 174 through 175 and (name N or name CA or name C or nam \ e O or name CB )) or resid 176 or (resid 177 and (name N or name CA or name C or \ name O or name CB )) or resid 178 through 187 or (resid 188 and (name N or name \ CA or name C or name O or name CB )) or resid 189 through 232)) } ncs_group { reference = (chain 'S' and (resid 1 through 2 or resid 4 through 17 or (resid 18 and (name N \ or name CA or name C or name O or name CB )) or resid 19 through 42 or resid 44 \ through 172 or (resid 173 and (name N or name CA or name C or name O or name CB \ )) or resid 174 through 199 or (resid 200 and (name N or name CA or name C or n \ ame O or name CB )) or resid 201 through 213)) selection = (chain 'X' and (resid 1 through 2 or resid 4 through 42 or resid 44 through 159 \ or (resid 160 through 162 and (name N or name CA or name C or name O or name CB \ )) or resid 163 through 213)) } ncs_group { reference = (chain 'T' and (resid 2 through 23 or (resid 24 and (name N or name CA or name C \ or name O or name CB )) or resid 25 through 26 or resid 28 through 45 or resid \ 47 through 98 or resid 100 through 153 or (resid 154 through 156 and (name N or \ name CA or name C or name O or name CB )) or resid 157 through 196)) selection = (chain 'V' and (resid 2 through 26 or resid 28 through 45 or resid 47 through 98 \ or resid 100 through 110 or (resid 111 and (name N or name CA or name C or name \ O or name CB )) or resid 112 through 154 or (resid 155 through 156 and (name N \ or name CA or name C or name O or name CB )) or resid 157 through 196)) } ncs_group { reference = (chain 'U' and (resid 1 through 12 or resid 14 through 15 or resid 17 through 24 \ or resid 26 through 204)) selection = (chain 'Y' and (resid 1 through 12 or resid 14 through 15 or resid 17 through 24 \ or resid 26 through 160 or (resid 161 and (name N or name CA or name C or name \ O or name CB )) or resid 162 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)) } ncs_group { reference = (chain 'W' and (resid 1 through 155 or (resid 156 and (name N or name CA or name \ C or name O or name CB )) or resid 157 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)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 6.750 Check model and map are aligned: 0.700 Set scattering table: 0.450 Process input model: 139.690 Find NCS groups from input model: 4.910 Set up NCS constraints: 0.430 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 157.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 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 : 0.009 0.139 48615 Z= 0.565 Angle : 0.931 15.036 65860 Z= 0.539 Chirality : 0.048 0.459 7460 Planarity : 0.005 0.083 8519 Dihedral : 9.760 132.017 17795 Min Nonbonded Distance : 0.972 Molprobity Statistics. All-atom Clashscore : 35.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.31 % Favored : 90.56 % Rotamer: Outliers : 0.82 % Allowed : 1.77 % Favored : 97.41 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.41 (0.09), residues: 6174 helix: -1.81 (0.09), residues: 2232 sheet: -2.61 (0.12), residues: 1394 loop : -2.28 (0.11), residues: 2548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.005 TRP K 101 HIS 0.020 0.002 HIS Y 161 PHE 0.025 0.003 PHE I 127 TYR 0.036 0.003 TYR C 134 ARG 0.011 0.001 ARG T 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12348 Ramachandran restraints generated. 6174 Oldfield, 0 Emsley, 6174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12348 Ramachandran restraints generated. 6174 Oldfield, 0 Emsley, 6174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1857 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1831 time to evaluate : 4.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.8030 (mtp) cc_final: 0.7736 (mmm) REVERT: A 32 ASP cc_start: 0.7593 (t0) cc_final: 0.7299 (p0) REVERT: A 72 GLU cc_start: 0.7483 (tt0) cc_final: 0.7256 (tt0) REVERT: A 143 LYS cc_start: 0.8160 (mptp) cc_final: 0.7881 (mmtp) REVERT: A 179 THR cc_start: 0.8882 (p) cc_final: 0.8640 (t) REVERT: B 1 THR cc_start: 0.8520 (m) cc_final: 0.7959 (p) REVERT: B 19 ARG cc_start: 0.7985 (ttm170) cc_final: 0.7330 (ttm170) REVERT: B 44 CYS cc_start: 0.8371 (m) cc_final: 0.8104 (m) REVERT: B 51 ASP cc_start: 0.8299 (m-30) cc_final: 0.7923 (m-30) REVERT: B 57 ARG cc_start: 0.7670 (ttp-110) cc_final: 0.7201 (ttp-170) REVERT: B 99 ILE cc_start: 0.9600 (tt) cc_final: 0.9288 (tt) REVERT: C 46 SER cc_start: 0.8527 (t) cc_final: 0.8071 (p) REVERT: C 141 SER cc_start: 0.8333 (m) cc_final: 0.8106 (p) REVERT: D 134 TYR cc_start: 0.7971 (m-10) cc_final: 0.7598 (m-80) REVERT: D 141 SER cc_start: 0.8443 (m) cc_final: 0.7830 (t) REVERT: D 146 ASN cc_start: 0.7003 (t0) cc_final: 0.6649 (t0) REVERT: E 1 THR cc_start: 0.8418 (m) cc_final: 0.7897 (p) REVERT: E 19 ARG cc_start: 0.7894 (ttm170) cc_final: 0.7689 (ttm170) REVERT: E 25 VAL cc_start: 0.8733 (t) cc_final: 0.8430 (m) REVERT: E 44 CYS cc_start: 0.8140 (m) cc_final: 0.7774 (m) REVERT: E 202 TYR cc_start: 0.8378 (m-10) cc_final: 0.8108 (m-10) REVERT: E 203 HIS cc_start: 0.7346 (t70) cc_final: 0.6883 (t-90) REVERT: E 217 LYS cc_start: 0.8142 (tmtm) cc_final: 0.7884 (tptt) REVERT: F 32 ASP cc_start: 0.7543 (t0) cc_final: 0.7220 (p0) REVERT: F 88 TYR cc_start: 0.8348 (t80) cc_final: 0.8133 (t80) REVERT: F 143 LYS cc_start: 0.8393 (mptp) cc_final: 0.7879 (pttm) REVERT: F 179 THR cc_start: 0.8860 (p) cc_final: 0.8504 (t) REVERT: G 39 LYS cc_start: 0.9013 (pttt) cc_final: 0.8602 (ptpt) REVERT: G 118 ILE cc_start: 0.8931 (mt) cc_final: 0.8634 (mt) REVERT: G 137 TYR cc_start: 0.8606 (t80) cc_final: 0.8168 (t80) REVERT: G 155 ASP cc_start: 0.8464 (t70) cc_final: 0.8148 (t70) REVERT: G 157 ARG cc_start: 0.7844 (mtp180) cc_final: 0.7171 (mtm110) REVERT: G 175 HIS cc_start: 0.7609 (m-70) cc_final: 0.6566 (m170) REVERT: G 186 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6937 (mt-10) REVERT: I 66 ASP cc_start: 0.7940 (t0) cc_final: 0.7603 (t0) REVERT: I 71 MET cc_start: 0.8752 (ptm) cc_final: 0.8439 (ptm) REVERT: I 116 GLN cc_start: 0.8437 (tm-30) cc_final: 0.7987 (tp40) REVERT: I 214 ASP cc_start: 0.7372 (m-30) cc_final: 0.7061 (m-30) REVERT: J 28 LYS cc_start: 0.8219 (mtpt) cc_final: 0.7805 (ttmm) REVERT: J 58 TYR cc_start: 0.8004 (m-80) cc_final: 0.7400 (m-80) REVERT: J 70 ASP cc_start: 0.8590 (t0) cc_final: 0.8372 (t0) REVERT: J 118 TYR cc_start: 0.8052 (t80) cc_final: 0.7311 (m-80) REVERT: J 120 HIS cc_start: 0.8684 (t-90) cc_final: 0.8341 (t70) REVERT: J 150 MET cc_start: 0.8162 (tmm) cc_final: 0.7554 (ttp) REVERT: J 175 GLU cc_start: 0.8293 (tp30) cc_final: 0.7837 (mm-30) REVERT: J 179 LEU cc_start: 0.8830 (mt) cc_final: 0.8406 (mp) REVERT: J 215 TRP cc_start: 0.8515 (p90) cc_final: 0.8075 (p90) REVERT: K 60 LEU cc_start: 0.8743 (mt) cc_final: 0.8365 (mt) REVERT: K 185 LYS cc_start: 0.8100 (mttt) cc_final: 0.7537 (ttpt) REVERT: K 235 ILE cc_start: 0.7211 (mt) cc_final: 0.6799 (mt) REVERT: L 39 LYS cc_start: 0.8977 (pttt) cc_final: 0.8619 (ptpt) REVERT: L 118 ILE cc_start: 0.8896 (mt) cc_final: 0.8489 (mt) REVERT: L 137 TYR cc_start: 0.8628 (t80) cc_final: 0.8159 (t80) REVERT: L 156 CYS cc_start: 0.7715 (m) cc_final: 0.7321 (m) REVERT: L 175 HIS cc_start: 0.7400 (m-70) cc_final: 0.7074 (m170) REVERT: L 232 PHE cc_start: 0.7532 (m-80) cc_final: 0.7188 (m-80) REVERT: L 233 LEU cc_start: 0.6159 (OUTLIER) cc_final: 0.5877 (tt) REVERT: L 234 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.6907 (pm20) REVERT: M 121 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7812 (tt) REVERT: M 133 MET cc_start: 0.7117 (mmt) cc_final: 0.6864 (mtm) REVERT: M 211 ASN cc_start: 0.7894 (p0) cc_final: 0.7673 (t0) REVERT: N 28 LYS cc_start: 0.7420 (mtmt) cc_final: 0.7197 (mtmt) REVERT: N 66 ASP cc_start: 0.7723 (t0) cc_final: 0.7175 (t0) REVERT: N 116 GLN cc_start: 0.8160 (tm-30) cc_final: 0.7920 (tm-30) REVERT: N 120 GLN cc_start: 0.8747 (tt0) cc_final: 0.8464 (tt0) REVERT: N 196 LEU cc_start: 0.8663 (mt) cc_final: 0.8388 (pp) REVERT: N 201 SER cc_start: 0.6075 (OUTLIER) cc_final: 0.5513 (p) REVERT: N 214 ASP cc_start: 0.7042 (m-30) cc_final: 0.6762 (m-30) REVERT: O 72 MET cc_start: 0.7870 (mtp) cc_final: 0.7513 (ttt) REVERT: O 89 GLU cc_start: 0.8167 (tp30) cc_final: 0.7716 (tp30) REVERT: O 141 LYS cc_start: 0.8580 (pttt) cc_final: 0.8344 (ptpp) REVERT: P 90 ARG cc_start: 0.9024 (mtt180) cc_final: 0.8708 (mtt180) REVERT: P 118 GLN cc_start: 0.9243 (tm-30) cc_final: 0.8800 (tm-30) REVERT: P 181 LEU cc_start: 0.8162 (tp) cc_final: 0.7553 (pp) REVERT: P 195 LYS cc_start: 0.8335 (tppt) cc_final: 0.8129 (ttpt) REVERT: P 201 GLN cc_start: 0.8755 (tp-100) cc_final: 0.8550 (tp40) REVERT: P 226 LYS cc_start: 0.7436 (ttpt) cc_final: 0.7102 (tptt) REVERT: Q 7 TYR cc_start: 0.6063 (m-80) cc_final: 0.5304 (m-80) REVERT: Q 13 THR cc_start: 0.9072 (m) cc_final: 0.8651 (p) REVERT: Q 28 LYS cc_start: 0.7996 (mtpt) cc_final: 0.7614 (ttmm) REVERT: Q 58 TYR cc_start: 0.7880 (m-80) cc_final: 0.7393 (m-80) REVERT: Q 70 ASP cc_start: 0.8373 (t0) cc_final: 0.7972 (t0) REVERT: Q 215 TRP cc_start: 0.8516 (p90) cc_final: 0.8011 (p90) REVERT: Q 223 ARG cc_start: 0.8123 (tpp80) cc_final: 0.7770 (tpp80) REVERT: R 113 MET cc_start: 0.8172 (mmm) cc_final: 0.7952 (mmm) REVERT: R 130 GLU cc_start: 0.7272 (pm20) cc_final: 0.6238 (pm20) REVERT: R 131 MET cc_start: 0.8342 (pmm) cc_final: 0.7856 (pmm) REVERT: R 185 LYS cc_start: 0.8103 (mttt) cc_final: 0.7236 (tmmt) REVERT: R 235 ILE cc_start: 0.7096 (mt) cc_final: 0.6838 (mt) REVERT: S 106 VAL cc_start: 0.9442 (t) cc_final: 0.9192 (m) REVERT: S 118 LYS cc_start: 0.8502 (mttp) cc_final: 0.8099 (ttmm) REVERT: S 193 LEU cc_start: 0.8897 (tp) cc_final: 0.8634 (tp) REVERT: S 204 ARG cc_start: 0.7958 (ttp80) cc_final: 0.7364 (ptp90) REVERT: S 212 LYS cc_start: 0.7501 (mptp) cc_final: 0.6336 (ptmt) REVERT: T 8 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8492 (tm-30) REVERT: T 20 VAL cc_start: 0.9009 (t) cc_final: 0.8213 (t) REVERT: T 33 ASP cc_start: 0.7622 (t0) cc_final: 0.7408 (m-30) REVERT: T 115 LEU cc_start: 0.8926 (tp) cc_final: 0.8629 (tt) REVERT: T 166 GLU cc_start: 0.7785 (tp30) cc_final: 0.7581 (tp30) REVERT: U 3 MET cc_start: 0.8353 (mmm) cc_final: 0.7988 (mmm) REVERT: U 4 SER cc_start: 0.8302 (p) cc_final: 0.7689 (t) REVERT: U 124 ASP cc_start: 0.7867 (p0) cc_final: 0.7630 (p0) REVERT: U 145 MET cc_start: 0.8729 (mtm) cc_final: 0.8475 (mtm) REVERT: U 175 ASP cc_start: 0.7638 (m-30) cc_final: 0.7249 (m-30) REVERT: U 182 MET cc_start: 0.8234 (mmm) cc_final: 0.8028 (mmt) REVERT: U 193 LYS cc_start: 0.8655 (pttt) cc_final: 0.8419 (pttt) REVERT: V 28 MET cc_start: 0.6997 (mtp) cc_final: 0.6730 (mtt) REVERT: V 144 ASP cc_start: 0.6982 (m-30) cc_final: 0.6779 (m-30) REVERT: W 27 LEU cc_start: 0.9073 (tp) cc_final: 0.8848 (tt) REVERT: W 79 ASP cc_start: 0.6903 (p0) cc_final: 0.6370 (m-30) REVERT: W 210 ASP cc_start: 0.7860 (m-30) cc_final: 0.7536 (m-30) REVERT: X 30 SER cc_start: 0.9311 (m) cc_final: 0.8970 (t) REVERT: X 31 GLU cc_start: 0.7531 (tt0) cc_final: 0.7266 (tt0) REVERT: X 181 SER cc_start: 0.8191 (m) cc_final: 0.7968 (p) REVERT: X 203 ILE cc_start: 0.9160 (mt) cc_final: 0.8945 (mt) REVERT: Y 3 MET cc_start: 0.8418 (mmm) cc_final: 0.7939 (mmm) REVERT: Y 76 LYS cc_start: 0.8490 (ttmt) cc_final: 0.8076 (ttpt) REVERT: Y 148 MET cc_start: 0.8617 (mmm) cc_final: 0.8259 (mmm) REVERT: Y 156 ASN cc_start: 0.8353 (m-40) cc_final: 0.8100 (t0) REVERT: Z 72 MET cc_start: 0.7710 (mtp) cc_final: 0.7319 (mtm) REVERT: Z 89 GLU cc_start: 0.8156 (tp30) cc_final: 0.7457 (tp30) REVERT: Z 140 ASP cc_start: 0.8377 (p0) cc_final: 0.8108 (p0) REVERT: Z 218 ARG cc_start: 0.8233 (mmm160) cc_final: 0.7983 (mmm160) REVERT: a 27 LEU cc_start: 0.9182 (tp) cc_final: 0.8967 (tt) REVERT: a 79 ASP cc_start: 0.5847 (p0) cc_final: 0.5349 (m-30) REVERT: a 83 TYR cc_start: 0.9142 (m-10) cc_final: 0.8298 (m-10) REVERT: a 208 ASN cc_start: 0.8265 (t0) cc_final: 0.7681 (t0) REVERT: a 210 ASP cc_start: 0.7901 (m-30) cc_final: 0.7562 (m-30) REVERT: b 17 LYS cc_start: 0.8426 (tptt) cc_final: 0.7850 (tptt) REVERT: b 90 ARG cc_start: 0.9005 (mtt180) cc_final: 0.8800 (mtt180) REVERT: b 118 GLN cc_start: 0.9099 (tm-30) cc_final: 0.8752 (tm-30) REVERT: b 123 SER cc_start: 0.8836 (t) cc_final: 0.8588 (t) REVERT: b 201 GLN cc_start: 0.8693 (tp-100) cc_final: 0.8477 (tp40) REVERT: b 226 LYS cc_start: 0.7592 (ttpt) cc_final: 0.7252 (tptt) outliers start: 26 outliers final: 11 residues processed: 1853 average time/residue: 0.6841 time to fit residues: 1994.3633 Evaluate side-chains 1223 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1208 time to evaluate : 5.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 234 GLU Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain M residue 121 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain R residue 191 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 513 optimal weight: 0.6980 chunk 460 optimal weight: 8.9990 chunk 255 optimal weight: 0.9980 chunk 157 optimal weight: 5.9990 chunk 310 optimal weight: 9.9990 chunk 246 optimal weight: 4.9990 chunk 476 optimal weight: 0.8980 chunk 184 optimal weight: 1.9990 chunk 289 optimal weight: 0.9990 chunk 354 optimal weight: 4.9990 chunk 552 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 38 HIS A 81 ASN A 97 HIS B 9 GLN B 109 GLN B 203 HIS ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 HIS D 10 HIS D 175 ASN E 9 GLN E 109 GLN E 172 ASN F 28 ASN F 38 HIS F 97 HIS ** G 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 23 GLN ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 HIS H 155 HIS H 224 GLN ** I 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 221 ASN K 53 GLN K 100 ASN L 65 HIS A M 23 GLN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 155 HIS M 224 GLN N 175 ASN N 205 ASN ** O 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 240 HIS P 108 GLN Q 147 GLN R 33 ASN R 75 ASN R 100 ASN S 8 ASN ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 163 HIS ** T 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 174 ASN ** U 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 30 GLN V 27 GLN B V 174 ASN W 213 HIS ** X 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 157 ASN ** Y 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 30 GLN Y 168 GLN ** Z 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 240 HIS a 213 HIS b 108 GLN b 111 GLN ** b 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 48615 Z= 0.229 Angle : 0.678 12.953 65860 Z= 0.352 Chirality : 0.045 0.257 7460 Planarity : 0.005 0.049 8519 Dihedral : 7.110 126.363 6932 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.06 % Favored : 95.86 % Rotamer: Outliers : 2.51 % Allowed : 11.78 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.10), residues: 6174 helix: 0.52 (0.11), residues: 2264 sheet: -1.74 (0.13), residues: 1390 loop : -1.67 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP J 215 HIS 0.011 0.001 HIS D 165 PHE 0.023 0.002 PHE I 73 TYR 0.025 0.002 TYR P 166 ARG 0.009 0.001 ARG Z 17 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12348 Ramachandran restraints generated. 6174 Oldfield, 0 Emsley, 6174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12348 Ramachandran restraints generated. 6174 Oldfield, 0 Emsley, 6174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1583 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1470 time to evaluate : 5.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.7608 (t0) cc_final: 0.7131 (p0) REVERT: A 77 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8430 (tp) REVERT: A 153 ARG cc_start: 0.7521 (tpt170) cc_final: 0.7273 (tpt170) REVERT: A 157 ASP cc_start: 0.8468 (m-30) cc_final: 0.8096 (m-30) REVERT: B 1 THR cc_start: 0.7982 (m) cc_final: 0.7778 (t) REVERT: B 51 ASP cc_start: 0.8085 (m-30) cc_final: 0.7714 (m-30) REVERT: B 188 THR cc_start: 0.8310 (p) cc_final: 0.8015 (t) REVERT: C 46 SER cc_start: 0.8494 (t) cc_final: 0.8253 (t) REVERT: C 54 TYR cc_start: 0.9136 (t80) cc_final: 0.8918 (t80) REVERT: C 58 LEU cc_start: 0.8923 (tp) cc_final: 0.8630 (tt) REVERT: C 141 SER cc_start: 0.8321 (m) cc_final: 0.8074 (t) REVERT: C 179 MET cc_start: 0.7406 (tpt) cc_final: 0.7183 (tpp) REVERT: D 133 THR cc_start: 0.8035 (p) cc_final: 0.7621 (p) REVERT: D 141 SER cc_start: 0.8492 (m) cc_final: 0.7966 (t) REVERT: D 146 ASN cc_start: 0.7172 (t0) cc_final: 0.6702 (t0) REVERT: D 197 HIS cc_start: 0.7062 (m-70) cc_final: 0.6729 (m90) REVERT: E 25 VAL cc_start: 0.8300 (t) cc_final: 0.8071 (m) REVERT: E 39 PRO cc_start: 0.9065 (Cg_exo) cc_final: 0.8843 (Cg_endo) REVERT: E 217 LYS cc_start: 0.8370 (tmtm) cc_final: 0.8082 (tptt) REVERT: F 14 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7852 (mmm) REVERT: F 32 ASP cc_start: 0.7692 (t0) cc_final: 0.7198 (p0) REVERT: F 99 MET cc_start: 0.7580 (mpp) cc_final: 0.7246 (mtm) REVERT: G 39 LYS cc_start: 0.8666 (pttt) cc_final: 0.8221 (ptpt) REVERT: G 133 LEU cc_start: 0.8528 (mt) cc_final: 0.8279 (mp) REVERT: G 137 TYR cc_start: 0.8277 (t80) cc_final: 0.7772 (t80) REVERT: G 175 HIS cc_start: 0.6973 (m-70) cc_final: 0.6427 (m-70) REVERT: G 220 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7672 (mt-10) REVERT: H 135 ARG cc_start: 0.8888 (ptt90) cc_final: 0.8644 (ptt-90) REVERT: H 156 MET cc_start: 0.6502 (ttp) cc_final: 0.6102 (tmm) REVERT: I 13 ASP cc_start: 0.8298 (p0) cc_final: 0.7910 (p0) REVERT: J 7 TYR cc_start: 0.6455 (m-80) cc_final: 0.6050 (m-80) REVERT: J 10 SER cc_start: 0.8963 (t) cc_final: 0.8557 (m) REVERT: J 93 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7543 (tm-30) REVERT: J 197 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7812 (tp) REVERT: K 53 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7620 (mt0) REVERT: K 150 GLN cc_start: 0.8427 (mm-40) cc_final: 0.7871 (mt0) REVERT: K 185 LYS cc_start: 0.8075 (mttt) cc_final: 0.7552 (ttpt) REVERT: K 232 GLU cc_start: 0.5842 (mm-30) cc_final: 0.5528 (mm-30) REVERT: K 235 ILE cc_start: 0.7072 (mt) cc_final: 0.6850 (mt) REVERT: L 39 LYS cc_start: 0.8573 (pttt) cc_final: 0.8255 (ptpt) REVERT: L 118 ILE cc_start: 0.8602 (mt) cc_final: 0.8365 (tp) REVERT: L 137 TYR cc_start: 0.8426 (t80) cc_final: 0.7862 (t80) REVERT: L 142 PRO cc_start: 0.8712 (Cg_exo) cc_final: 0.8327 (Cg_endo) REVERT: L 155 ASP cc_start: 0.8361 (t70) cc_final: 0.7835 (t0) REVERT: L 156 CYS cc_start: 0.7494 (m) cc_final: 0.7271 (m) REVERT: L 209 ASN cc_start: 0.7400 (p0) cc_final: 0.7083 (p0) REVERT: L 234 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6901 (pm20) REVERT: N 13 ASP cc_start: 0.8372 (p0) cc_final: 0.8040 (p0) REVERT: N 139 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7241 (p0) REVERT: N 214 ASP cc_start: 0.6797 (m-30) cc_final: 0.6542 (m-30) REVERT: N 224 GLU cc_start: 0.7391 (tm-30) cc_final: 0.6525 (tm-30) REVERT: O 8 ARG cc_start: 0.8112 (mtt90) cc_final: 0.7845 (mtt90) REVERT: O 72 MET cc_start: 0.7550 (mtp) cc_final: 0.6777 (mtm) REVERT: O 140 ASP cc_start: 0.8061 (p0) cc_final: 0.7774 (p0) REVERT: O 217 THR cc_start: 0.8612 (p) cc_final: 0.8410 (p) REVERT: P 113 VAL cc_start: 0.8304 (t) cc_final: 0.8062 (p) REVERT: P 117 MET cc_start: 0.8962 (ttm) cc_final: 0.8646 (ttm) REVERT: P 118 GLN cc_start: 0.9176 (tm-30) cc_final: 0.8525 (tm-30) REVERT: P 138 TRP cc_start: 0.7994 (t-100) cc_final: 0.7478 (t-100) REVERT: P 181 LEU cc_start: 0.8227 (tp) cc_final: 0.7442 (pp) REVERT: P 195 LYS cc_start: 0.8147 (tppt) cc_final: 0.7883 (ttpt) REVERT: P 201 GLN cc_start: 0.8705 (tp-100) cc_final: 0.8403 (tp40) REVERT: Q 7 TYR cc_start: 0.6134 (m-80) cc_final: 0.5729 (m-80) REVERT: Q 80 LEU cc_start: 0.8767 (tp) cc_final: 0.8515 (tp) REVERT: Q 94 GLU cc_start: 0.8158 (tp30) cc_final: 0.7904 (tp30) REVERT: Q 108 LEU cc_start: 0.9103 (tp) cc_final: 0.8679 (tt) REVERT: Q 118 TYR cc_start: 0.7656 (t80) cc_final: 0.7434 (m-80) REVERT: Q 191 LYS cc_start: 0.8377 (mtmm) cc_final: 0.7564 (mptt) REVERT: R 150 GLN cc_start: 0.8508 (mm-40) cc_final: 0.8170 (mt0) REVERT: R 185 LYS cc_start: 0.8166 (mttt) cc_final: 0.7240 (tmmt) REVERT: S 39 ASP cc_start: 0.7666 (t0) cc_final: 0.7388 (t0) REVERT: S 106 VAL cc_start: 0.9262 (t) cc_final: 0.8994 (m) REVERT: S 172 MET cc_start: 0.7274 (mmm) cc_final: 0.6983 (mmm) REVERT: T 8 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8387 (tm-30) REVERT: T 27 GLN cc_start: 0.8383 (mt0) cc_final: 0.7987 (mm-40) REVERT: T 52 ASP cc_start: 0.8255 (m-30) cc_final: 0.8037 (m-30) REVERT: T 65 GLN cc_start: 0.7423 (mm-40) cc_final: 0.7214 (mp10) REVERT: T 166 GLU cc_start: 0.7826 (tp30) cc_final: 0.7622 (tp30) REVERT: U 4 SER cc_start: 0.8115 (p) cc_final: 0.7724 (t) REVERT: U 33 MET cc_start: 0.8757 (tmm) cc_final: 0.8181 (ttp) REVERT: U 44 MET cc_start: 0.8455 (mmm) cc_final: 0.8080 (mmm) REVERT: U 92 ASN cc_start: 0.9306 (t0) cc_final: 0.8868 (t0) REVERT: U 157 MET cc_start: 0.7966 (mtp) cc_final: 0.7761 (mtt) REVERT: V 166 GLU cc_start: 0.8259 (tp30) cc_final: 0.8007 (tp30) REVERT: W 27 LEU cc_start: 0.9134 (tp) cc_final: 0.8826 (tt) REVERT: W 147 GLN cc_start: 0.7783 (tp40) cc_final: 0.7269 (tp40) REVERT: W 208 ASN cc_start: 0.8433 (t0) cc_final: 0.7791 (t0) REVERT: X 106 VAL cc_start: 0.9244 (t) cc_final: 0.9016 (m) REVERT: X 181 SER cc_start: 0.8076 (m) cc_final: 0.7828 (p) REVERT: X 201 GLU cc_start: 0.6914 (mp0) cc_final: 0.6714 (mp0) REVERT: Y 3 MET cc_start: 0.8511 (mmm) cc_final: 0.8264 (mmm) REVERT: Y 33 MET cc_start: 0.9103 (tmm) cc_final: 0.8598 (ttt) REVERT: Y 76 LYS cc_start: 0.8467 (ttmt) cc_final: 0.8069 (ttpp) REVERT: Y 148 MET cc_start: 0.8765 (mmm) cc_final: 0.8451 (mmm) REVERT: Y 150 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7431 (tp30) REVERT: Y 168 GLN cc_start: 0.7023 (mm110) cc_final: 0.6735 (mm-40) REVERT: Y 175 ASP cc_start: 0.7321 (m-30) cc_final: 0.7072 (m-30) REVERT: Y 182 MET cc_start: 0.8192 (mmt) cc_final: 0.7834 (mmt) REVERT: Y 193 LYS cc_start: 0.8901 (pttt) cc_final: 0.8648 (pttp) REVERT: Z 8 ARG cc_start: 0.8094 (mtt90) cc_final: 0.7321 (mtt90) REVERT: Z 10 THR cc_start: 0.9107 (p) cc_final: 0.8540 (t) REVERT: Z 48 GLU cc_start: 0.6653 (tt0) cc_final: 0.6314 (tt0) REVERT: Z 72 MET cc_start: 0.7250 (mtp) cc_final: 0.6857 (ttt) REVERT: Z 127 LYS cc_start: 0.8689 (mmtp) cc_final: 0.8477 (mmmt) REVERT: Z 140 ASP cc_start: 0.8173 (p0) cc_final: 0.7871 (p0) REVERT: Z 174 MET cc_start: 0.6875 (mmp) cc_final: 0.6388 (mmm) REVERT: Z 177 GLN cc_start: 0.7223 (mm110) cc_final: 0.6883 (mm110) REVERT: Z 194 ILE cc_start: 0.8273 (mm) cc_final: 0.7808 (mt) REVERT: Z 229 LYS cc_start: 0.8057 (mptm) cc_final: 0.7821 (mptm) REVERT: Z 232 GLU cc_start: 0.6903 (mp0) cc_final: 0.6498 (mp0) REVERT: a 16 PHE cc_start: 0.9238 (p90) cc_final: 0.9000 (p90) REVERT: a 27 LEU cc_start: 0.9232 (tp) cc_final: 0.8918 (tt) REVERT: a 127 MET cc_start: 0.7849 (ptp) cc_final: 0.7496 (ptm) REVERT: a 147 GLN cc_start: 0.7679 (tp40) cc_final: 0.7356 (tp40) REVERT: a 197 VAL cc_start: 0.9030 (t) cc_final: 0.8789 (t) REVERT: a 208 ASN cc_start: 0.8213 (t0) cc_final: 0.7756 (t0) REVERT: a 210 ASP cc_start: 0.8090 (m-30) cc_final: 0.7848 (m-30) REVERT: b 17 LYS cc_start: 0.8164 (tptt) cc_final: 0.7701 (tptt) REVERT: b 117 MET cc_start: 0.8842 (ttm) cc_final: 0.8597 (ttm) REVERT: b 118 GLN cc_start: 0.9096 (tm-30) cc_final: 0.8562 (tm-30) REVERT: b 201 GLN cc_start: 0.8627 (tp-100) cc_final: 0.8367 (tp40) outliers start: 113 outliers final: 59 residues processed: 1524 average time/residue: 0.5923 time to fit residues: 1486.5970 Evaluate side-chains 1242 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1176 time to evaluate : 5.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 119 TYR Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 93 GLU Chi-restraints excluded: chain J residue 143 ASN Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 197 ILE Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 53 GLN Chi-restraints excluded: chain L residue 9 ASP Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 234 GLU Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain M residue 121 LEU Chi-restraints excluded: chain M residue 206 MET Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 122 ASN Chi-restraints excluded: chain N residue 139 ASP Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 34 SER Chi-restraints excluded: chain P residue 115 SER Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 143 ASN Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 156 VAL Chi-restraints excluded: chain R residue 191 PHE Chi-restraints excluded: chain S residue 48 ASP Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 151 SER Chi-restraints excluded: chain W residue 195 LYS Chi-restraints excluded: chain W residue 205 THR Chi-restraints excluded: chain Y residue 151 SER Chi-restraints excluded: chain a residue 195 LYS Chi-restraints excluded: chain a residue 205 THR Chi-restraints excluded: chain b residue 13 SER Chi-restraints excluded: chain b residue 28 VAL Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 167 VAL Chi-restraints excluded: chain b residue 212 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 306 optimal weight: 2.9990 chunk 171 optimal weight: 9.9990 chunk 459 optimal weight: 4.9990 chunk 375 optimal weight: 10.0000 chunk 152 optimal weight: 4.9990 chunk 553 optimal weight: 1.9990 chunk 597 optimal weight: 6.9990 chunk 492 optimal weight: 0.6980 chunk 548 optimal weight: 0.7980 chunk 188 optimal weight: 0.8980 chunk 443 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 HIS C 198 GLN ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN F 81 ASN G 175 HIS H 23 GLN I 120 GLN J 63 ASN K 75 ASN K 238 HIS L 143 HIS M 98 ASN M 99 HIS M 224 GLN ** O 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 198 ASN ** Q 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 75 ASN R 238 HIS ** S 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 30 GLN U 168 GLN V 55 GLN X 8 ASN ** X 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 51 ASN ** Z 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 89 HIS b 94 GLN ** b 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 48615 Z= 0.256 Angle : 0.654 12.893 65860 Z= 0.338 Chirality : 0.044 0.241 7460 Planarity : 0.004 0.050 8519 Dihedral : 6.744 126.519 6917 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.83 % Favored : 95.14 % Rotamer: Outliers : 3.17 % Allowed : 15.19 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.79 (0.11), residues: 6174 helix: 0.99 (0.11), residues: 2264 sheet: -1.30 (0.13), residues: 1366 loop : -1.41 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP J 215 HIS 0.008 0.001 HIS X 77 PHE 0.022 0.002 PHE M 162 TYR 0.021 0.002 TYR C 40 ARG 0.010 0.001 ARG Z 17 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12348 Ramachandran restraints generated. 6174 Oldfield, 0 Emsley, 6174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12348 Ramachandran restraints generated. 6174 Oldfield, 0 Emsley, 6174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1391 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1246 time to evaluate : 4.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.8148 (mmm) cc_final: 0.7826 (mmm) REVERT: A 32 ASP cc_start: 0.7605 (t0) cc_final: 0.7105 (p0) REVERT: A 45 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7647 (mt) REVERT: A 157 ASP cc_start: 0.8301 (m-30) cc_final: 0.8043 (m-30) REVERT: B 51 ASP cc_start: 0.8040 (m-30) cc_final: 0.7656 (m-30) REVERT: B 135 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8402 (mt) REVERT: B 174 ASP cc_start: 0.8014 (t0) cc_final: 0.7775 (t0) REVERT: B 185 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7925 (tt) REVERT: B 188 THR cc_start: 0.8370 (p) cc_final: 0.8011 (t) REVERT: C 46 SER cc_start: 0.8565 (t) cc_final: 0.8131 (p) REVERT: C 54 TYR cc_start: 0.9096 (t80) cc_final: 0.8869 (t80) REVERT: C 139 MET cc_start: 0.7108 (mtp) cc_final: 0.6830 (ttm) REVERT: C 141 SER cc_start: 0.8332 (m) cc_final: 0.8117 (t) REVERT: C 179 MET cc_start: 0.7353 (tpt) cc_final: 0.7116 (tpp) REVERT: D 45 MET cc_start: 0.7160 (mtt) cc_final: 0.6869 (mtt) REVERT: D 90 TYR cc_start: 0.8621 (m-10) cc_final: 0.8377 (m-80) REVERT: D 133 THR cc_start: 0.7896 (p) cc_final: 0.7495 (p) REVERT: D 141 SER cc_start: 0.8751 (m) cc_final: 0.8141 (t) REVERT: D 146 ASN cc_start: 0.7174 (t0) cc_final: 0.6867 (t0) REVERT: D 194 ASP cc_start: 0.7729 (m-30) cc_final: 0.7421 (t0) REVERT: E 25 VAL cc_start: 0.8435 (t) cc_final: 0.8225 (m) REVERT: E 51 ASP cc_start: 0.7999 (m-30) cc_final: 0.7605 (m-30) REVERT: E 54 MET cc_start: 0.7854 (mmt) cc_final: 0.7627 (tpt) REVERT: E 174 ASP cc_start: 0.7738 (t0) cc_final: 0.7530 (t0) REVERT: E 217 LYS cc_start: 0.8591 (tmtm) cc_final: 0.8290 (tptt) REVERT: F 14 MET cc_start: 0.7978 (mmm) cc_final: 0.7709 (mmm) REVERT: F 32 ASP cc_start: 0.7701 (t0) cc_final: 0.7084 (p0) REVERT: F 99 MET cc_start: 0.7880 (mpp) cc_final: 0.7558 (mtm) REVERT: G 39 LYS cc_start: 0.8752 (pttt) cc_final: 0.8151 (ptpt) REVERT: G 118 ILE cc_start: 0.8970 (mt) cc_final: 0.7798 (tp) REVERT: G 122 ARG cc_start: 0.7356 (mpt180) cc_final: 0.6944 (mpt180) REVERT: G 137 TYR cc_start: 0.8396 (t80) cc_final: 0.7873 (t80) REVERT: G 142 PRO cc_start: 0.8761 (Cg_exo) cc_final: 0.8402 (Cg_endo) REVERT: G 176 MET cc_start: 0.7425 (tmm) cc_final: 0.6926 (tmm) REVERT: G 178 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7835 (mt-10) REVERT: G 184 LEU cc_start: 0.8430 (tp) cc_final: 0.8103 (tp) REVERT: G 209 ASN cc_start: 0.7875 (p0) cc_final: 0.7538 (p0) REVERT: H 156 MET cc_start: 0.6376 (ttp) cc_final: 0.6149 (tmm) REVERT: H 193 GLU cc_start: 0.5565 (tt0) cc_final: 0.5009 (tp30) REVERT: I 13 ASP cc_start: 0.7927 (p0) cc_final: 0.7703 (p0) REVERT: I 27 LYS cc_start: 0.8549 (mtpp) cc_final: 0.8323 (ttmm) REVERT: I 214 ASP cc_start: 0.7049 (m-30) cc_final: 0.6811 (m-30) REVERT: J 7 TYR cc_start: 0.6713 (m-80) cc_final: 0.6450 (m-80) REVERT: J 94 GLU cc_start: 0.8361 (tp30) cc_final: 0.7749 (tp30) REVERT: J 118 TYR cc_start: 0.7923 (t80) cc_final: 0.7372 (m-80) REVERT: J 149 TYR cc_start: 0.7906 (m-80) cc_final: 0.7600 (m-80) REVERT: J 215 TRP cc_start: 0.8236 (p90) cc_final: 0.7417 (p90) REVERT: K 143 ILE cc_start: 0.7669 (mm) cc_final: 0.7308 (mm) REVERT: K 185 LYS cc_start: 0.8041 (mttt) cc_final: 0.7518 (ttpt) REVERT: K 235 ILE cc_start: 0.7063 (mt) cc_final: 0.6781 (mt) REVERT: L 39 LYS cc_start: 0.8700 (pttt) cc_final: 0.8218 (ptpt) REVERT: L 118 ILE cc_start: 0.8804 (mt) cc_final: 0.8550 (mt) REVERT: L 137 TYR cc_start: 0.8355 (t80) cc_final: 0.7774 (t80) REVERT: L 142 PRO cc_start: 0.8645 (Cg_exo) cc_final: 0.8300 (Cg_endo) REVERT: L 155 ASP cc_start: 0.8426 (t70) cc_final: 0.8081 (t0) REVERT: L 156 CYS cc_start: 0.7840 (m) cc_final: 0.6984 (p) REVERT: L 176 MET cc_start: 0.6449 (ptt) cc_final: 0.6238 (tmm) REVERT: M 91 LYS cc_start: 0.8202 (tptm) cc_final: 0.7663 (tptm) REVERT: M 121 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7991 (tt) REVERT: N 28 LYS cc_start: 0.7636 (mttt) cc_final: 0.7354 (mtpt) REVERT: N 68 ASN cc_start: 0.8559 (p0) cc_final: 0.8264 (p0) REVERT: N 139 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.7254 (p0) REVERT: N 214 ASP cc_start: 0.6861 (m-30) cc_final: 0.6620 (m-30) REVERT: O 10 THR cc_start: 0.8906 (p) cc_final: 0.8472 (t) REVERT: O 72 MET cc_start: 0.7741 (mtp) cc_final: 0.7187 (mtm) REVERT: O 140 ASP cc_start: 0.7983 (p0) cc_final: 0.7715 (p0) REVERT: P 117 MET cc_start: 0.8950 (ttm) cc_final: 0.8581 (ttm) REVERT: P 118 GLN cc_start: 0.9187 (tm-30) cc_final: 0.8433 (tm-30) REVERT: P 138 TRP cc_start: 0.8109 (t-100) cc_final: 0.7467 (t-100) REVERT: P 181 LEU cc_start: 0.8165 (tp) cc_final: 0.7508 (pp) REVERT: P 226 LYS cc_start: 0.7189 (ttpt) cc_final: 0.6917 (tptt) REVERT: Q 10 SER cc_start: 0.9125 (t) cc_final: 0.8738 (m) REVERT: Q 108 LEU cc_start: 0.9092 (tp) cc_final: 0.8615 (tt) REVERT: Q 118 TYR cc_start: 0.7692 (t80) cc_final: 0.7465 (m-80) REVERT: Q 150 MET cc_start: 0.8237 (tmm) cc_final: 0.7440 (ttt) REVERT: Q 191 LYS cc_start: 0.8348 (mtmm) cc_final: 0.7535 (mptt) REVERT: Q 215 TRP cc_start: 0.8271 (p90) cc_final: 0.7681 (p90) REVERT: R 66 VAL cc_start: 0.8684 (t) cc_final: 0.8406 (p) REVERT: R 185 LYS cc_start: 0.8184 (mttt) cc_final: 0.7383 (tmmt) REVERT: S 39 ASP cc_start: 0.7415 (t0) cc_final: 0.7200 (t0) REVERT: S 106 VAL cc_start: 0.9259 (t) cc_final: 0.9002 (m) REVERT: T 3 TYR cc_start: 0.8734 (t80) cc_final: 0.8480 (t80) REVERT: T 8 GLN cc_start: 0.8662 (tm-30) cc_final: 0.8342 (tp40) REVERT: T 27 GLN cc_start: 0.8408 (mt0) cc_final: 0.8032 (mm-40) REVERT: T 104 LEU cc_start: 0.8954 (tt) cc_final: 0.8532 (tt) REVERT: T 191 LEU cc_start: 0.6479 (tp) cc_final: 0.6251 (tt) REVERT: U 3 MET cc_start: 0.8552 (mmm) cc_final: 0.8201 (mmm) REVERT: U 4 SER cc_start: 0.7982 (p) cc_final: 0.7752 (t) REVERT: U 33 MET cc_start: 0.9011 (tmm) cc_final: 0.8475 (ttt) REVERT: U 148 MET cc_start: 0.8777 (mmm) cc_final: 0.8547 (mmm) REVERT: V 152 SER cc_start: 0.7687 (m) cc_final: 0.7446 (m) REVERT: V 166 GLU cc_start: 0.8281 (tp30) cc_final: 0.7982 (tp30) REVERT: W 122 LEU cc_start: 0.9369 (tt) cc_final: 0.9067 (tt) REVERT: X 19 ASP cc_start: 0.8219 (p0) cc_final: 0.7989 (p0) REVERT: X 201 GLU cc_start: 0.6969 (mp0) cc_final: 0.6755 (mp0) REVERT: Y 33 MET cc_start: 0.9069 (tmm) cc_final: 0.8540 (ttt) REVERT: Y 74 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7389 (tm-30) REVERT: Y 76 LYS cc_start: 0.8490 (ttmt) cc_final: 0.7924 (ttpp) REVERT: Y 97 LYS cc_start: 0.8456 (mmtp) cc_final: 0.8198 (mptt) REVERT: Y 148 MET cc_start: 0.8856 (mmm) cc_final: 0.8458 (mmm) REVERT: Y 150 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7466 (tp30) REVERT: Y 156 ASN cc_start: 0.8183 (OUTLIER) cc_final: 0.7853 (t0) REVERT: Y 182 MET cc_start: 0.8003 (mmt) cc_final: 0.7736 (mmt) REVERT: Y 193 LYS cc_start: 0.8955 (pttt) cc_final: 0.8743 (pttp) REVERT: Y 197 ARG cc_start: 0.7684 (mtm-85) cc_final: 0.7369 (mtm180) REVERT: Z 8 ARG cc_start: 0.8119 (mtt90) cc_final: 0.7363 (mtt90) REVERT: Z 10 THR cc_start: 0.9145 (p) cc_final: 0.8662 (t) REVERT: Z 72 MET cc_start: 0.7409 (mtp) cc_final: 0.6745 (ttt) REVERT: Z 140 ASP cc_start: 0.8236 (p0) cc_final: 0.8031 (p0) REVERT: Z 174 MET cc_start: 0.6986 (mmp) cc_final: 0.6743 (mmm) REVERT: Z 194 ILE cc_start: 0.8122 (mm) cc_final: 0.7726 (mt) REVERT: Z 232 GLU cc_start: 0.6893 (mp0) cc_final: 0.6594 (mp0) REVERT: a 104 ASN cc_start: 0.7599 (t0) cc_final: 0.7278 (t0) REVERT: a 127 MET cc_start: 0.8009 (ptp) cc_final: 0.7705 (ptm) REVERT: a 147 GLN cc_start: 0.7594 (tp40) cc_final: 0.7389 (tp40) REVERT: a 208 ASN cc_start: 0.8259 (t0) cc_final: 0.7834 (t0) REVERT: a 210 ASP cc_start: 0.8023 (m-30) cc_final: 0.7779 (m-30) REVERT: b 117 MET cc_start: 0.8880 (ttm) cc_final: 0.8564 (ttm) REVERT: b 118 GLN cc_start: 0.9058 (tm-30) cc_final: 0.8515 (tm-30) REVERT: b 174 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7797 (tm-30) REVERT: b 201 GLN cc_start: 0.8629 (tp-100) cc_final: 0.8355 (tp40) REVERT: b 202 MET cc_start: 0.7379 (mtm) cc_final: 0.7118 (mtm) REVERT: b 224 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7992 (mt-10) outliers start: 145 outliers final: 106 residues processed: 1322 average time/residue: 0.5853 time to fit residues: 1282.3237 Evaluate side-chains 1251 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1139 time to evaluate : 5.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 119 TYR Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 86 ASN Chi-restraints excluded: chain G residue 161 ILE Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 227 HIS Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain I residue 122 ASN Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 143 ASN Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 175 GLU Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain L residue 9 ASP Chi-restraints excluded: chain L residue 226 ASP Chi-restraints excluded: chain M residue 43 SER Chi-restraints excluded: chain M residue 121 LEU Chi-restraints excluded: chain M residue 206 MET Chi-restraints excluded: chain M residue 209 LYS Chi-restraints excluded: chain M residue 216 GLU Chi-restraints excluded: chain M residue 227 HIS Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 122 ASN Chi-restraints excluded: chain N residue 129 ILE Chi-restraints excluded: chain N residue 139 ASP Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 115 SER Chi-restraints excluded: chain P residue 119 GLU Chi-restraints excluded: chain P residue 121 THR Chi-restraints excluded: chain P residue 165 ASN Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 223 THR Chi-restraints excluded: chain P residue 229 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 81 LEU Chi-restraints excluded: chain Q residue 143 ASN Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 156 VAL Chi-restraints excluded: chain R residue 191 PHE Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 48 ASP Chi-restraints excluded: chain T residue 33 ASP Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 72 LEU Chi-restraints excluded: chain U residue 151 SER Chi-restraints excluded: chain U residue 164 GLU Chi-restraints excluded: chain V residue 30 ASP Chi-restraints excluded: chain V residue 33 ASP Chi-restraints excluded: chain V residue 41 LYS Chi-restraints excluded: chain W residue 96 MET Chi-restraints excluded: chain W residue 189 ILE Chi-restraints excluded: chain W residue 195 LYS Chi-restraints excluded: chain W residue 205 THR Chi-restraints excluded: chain W residue 207 THR Chi-restraints excluded: chain X residue 48 ASP Chi-restraints excluded: chain X residue 78 SER Chi-restraints excluded: chain X residue 169 ASP Chi-restraints excluded: chain Y residue 36 THR Chi-restraints excluded: chain Y residue 156 ASN Chi-restraints excluded: chain a residue 189 ILE Chi-restraints excluded: chain a residue 195 LYS Chi-restraints excluded: chain a residue 205 THR Chi-restraints excluded: chain a residue 207 THR Chi-restraints excluded: chain b residue 13 SER Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 167 VAL Chi-restraints excluded: chain b residue 212 CYS Chi-restraints excluded: chain b residue 229 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 546 optimal weight: 0.5980 chunk 415 optimal weight: 5.9990 chunk 287 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 263 optimal weight: 6.9990 chunk 371 optimal weight: 10.0000 chunk 555 optimal weight: 5.9990 chunk 587 optimal weight: 0.6980 chunk 290 optimal weight: 4.9990 chunk 526 optimal weight: 0.9990 chunk 158 optimal weight: 8.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 HIS C 198 GLN ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 GLN E 114 HIS G 143 HIS G 175 HIS ** I 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 120 GLN J 63 ASN K 53 GLN K 75 ASN ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 224 GLN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 198 ASN R 75 ASN ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 168 GLN ** V 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 99 HIS B W 89 HIS ** X 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 168 GLN Z 40 ASN ** Z 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 240 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 48615 Z= 0.355 Angle : 0.701 13.165 65860 Z= 0.363 Chirality : 0.046 0.225 7460 Planarity : 0.005 0.054 8519 Dihedral : 6.647 120.162 6912 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.77 % Favored : 94.19 % Rotamer: Outliers : 4.01 % Allowed : 16.27 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.73 (0.11), residues: 6174 helix: 0.94 (0.11), residues: 2274 sheet: -1.19 (0.13), residues: 1411 loop : -1.31 (0.12), residues: 2489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP J 215 HIS 0.009 0.001 HIS X 77 PHE 0.029 0.002 PHE M 162 TYR 0.022 0.002 TYR V 73 ARG 0.010 0.001 ARG Z 17 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12348 Ramachandran restraints generated. 6174 Oldfield, 0 Emsley, 6174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12348 Ramachandran restraints generated. 6174 Oldfield, 0 Emsley, 6174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1355 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1168 time to evaluate : 5.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.7667 (t0) cc_final: 0.7074 (p0) REVERT: A 42 TYR cc_start: 0.8708 (m-80) cc_final: 0.8504 (m-10) REVERT: B 57 ARG cc_start: 0.8286 (ttp80) cc_final: 0.8066 (ttp-170) REVERT: B 132 ASP cc_start: 0.7891 (m-30) cc_final: 0.7330 (m-30) REVERT: B 135 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8425 (mm) REVERT: B 173 VAL cc_start: 0.9148 (OUTLIER) cc_final: 0.8883 (m) REVERT: B 174 ASP cc_start: 0.7969 (t0) cc_final: 0.7744 (t0) REVERT: B 185 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8017 (tt) REVERT: B 188 THR cc_start: 0.8531 (p) cc_final: 0.8217 (t) REVERT: C 46 SER cc_start: 0.8643 (t) cc_final: 0.8283 (p) REVERT: C 54 TYR cc_start: 0.9094 (t80) cc_final: 0.8825 (t80) REVERT: C 97 MET cc_start: 0.8280 (ttt) cc_final: 0.8023 (ptm) REVERT: C 115 ASP cc_start: 0.7755 (t70) cc_final: 0.7341 (t70) REVERT: C 119 THR cc_start: 0.8532 (OUTLIER) cc_final: 0.8303 (p) REVERT: C 139 MET cc_start: 0.7374 (mtp) cc_final: 0.6782 (ttp) REVERT: C 141 SER cc_start: 0.8465 (m) cc_final: 0.8217 (t) REVERT: D 45 MET cc_start: 0.7236 (mtt) cc_final: 0.6963 (mtt) REVERT: D 54 TYR cc_start: 0.9084 (t80) cc_final: 0.8805 (t80) REVERT: D 90 TYR cc_start: 0.8628 (m-10) cc_final: 0.7327 (m-10) REVERT: D 115 ASP cc_start: 0.8233 (t70) cc_final: 0.7981 (t70) REVERT: D 140 ASP cc_start: 0.7470 (m-30) cc_final: 0.7207 (m-30) REVERT: D 141 SER cc_start: 0.8557 (m) cc_final: 0.8038 (t) REVERT: D 146 ASN cc_start: 0.7317 (t0) cc_final: 0.6975 (t0) REVERT: E 25 VAL cc_start: 0.8636 (t) cc_final: 0.8370 (m) REVERT: E 51 ASP cc_start: 0.8120 (m-30) cc_final: 0.7552 (m-30) REVERT: E 173 VAL cc_start: 0.9165 (OUTLIER) cc_final: 0.8943 (m) REVERT: E 174 ASP cc_start: 0.7773 (t0) cc_final: 0.7526 (t0) REVERT: F 14 MET cc_start: 0.8074 (mmm) cc_final: 0.7837 (mmm) REVERT: F 32 ASP cc_start: 0.7704 (t0) cc_final: 0.7112 (p0) REVERT: F 118 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.6541 (ptm) REVERT: G 39 LYS cc_start: 0.8764 (pttt) cc_final: 0.8273 (ptpt) REVERT: G 118 ILE cc_start: 0.8977 (mt) cc_final: 0.8317 (tp) REVERT: G 122 ARG cc_start: 0.7400 (mpt180) cc_final: 0.7060 (mpt180) REVERT: G 137 TYR cc_start: 0.8223 (t80) cc_final: 0.7838 (t80) REVERT: G 142 PRO cc_start: 0.8652 (Cg_exo) cc_final: 0.8388 (Cg_endo) REVERT: G 178 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7972 (mt-10) REVERT: G 206 THR cc_start: 0.8466 (t) cc_final: 0.8146 (m) REVERT: H 193 GLU cc_start: 0.5631 (tt0) cc_final: 0.5331 (tp30) REVERT: I 27 LYS cc_start: 0.8622 (mtpp) cc_final: 0.8412 (ttmm) REVERT: I 46 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7603 (tm-30) REVERT: I 214 ASP cc_start: 0.7137 (m-30) cc_final: 0.6909 (m-30) REVERT: I 226 GLU cc_start: 0.4915 (mp0) cc_final: 0.4596 (mp0) REVERT: J 7 TYR cc_start: 0.7038 (m-80) cc_final: 0.6806 (m-80) REVERT: J 75 MET cc_start: 0.7963 (tpp) cc_final: 0.7693 (ttm) REVERT: J 94 GLU cc_start: 0.8382 (tp30) cc_final: 0.7832 (tp30) REVERT: J 118 TYR cc_start: 0.7925 (t80) cc_final: 0.7394 (m-10) REVERT: J 147 GLN cc_start: 0.8382 (mt0) cc_final: 0.8083 (mt0) REVERT: K 80 MET cc_start: 0.8518 (mmm) cc_final: 0.7493 (mmm) REVERT: K 185 LYS cc_start: 0.8183 (mttt) cc_final: 0.7521 (ttpt) REVERT: K 235 ILE cc_start: 0.7159 (mt) cc_final: 0.6841 (mt) REVERT: L 39 LYS cc_start: 0.8891 (pttt) cc_final: 0.8402 (ptpt) REVERT: L 137 TYR cc_start: 0.8338 (t80) cc_final: 0.7894 (t80) REVERT: L 156 CYS cc_start: 0.7728 (m) cc_final: 0.7397 (m) REVERT: M 93 ARG cc_start: 0.8174 (mtt180) cc_final: 0.7822 (mtt180) REVERT: M 107 MET cc_start: 0.8155 (ttt) cc_final: 0.7833 (tpt) REVERT: M 121 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7985 (tt) REVERT: N 5 ARG cc_start: 0.7931 (mmm-85) cc_final: 0.7724 (mmm-85) REVERT: N 28 LYS cc_start: 0.7648 (mttt) cc_final: 0.7375 (mtpt) REVERT: N 68 ASN cc_start: 0.8372 (p0) cc_final: 0.7942 (p0) REVERT: N 139 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7385 (p0) REVERT: N 214 ASP cc_start: 0.6996 (m-30) cc_final: 0.6697 (m-30) REVERT: O 8 ARG cc_start: 0.7993 (mtt90) cc_final: 0.7558 (mtt90) REVERT: O 26 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6988 (mt-10) REVERT: O 48 GLU cc_start: 0.6808 (tm-30) cc_final: 0.6607 (tm-30) REVERT: O 224 VAL cc_start: 0.8604 (t) cc_final: 0.8260 (m) REVERT: P 117 MET cc_start: 0.8982 (ttm) cc_final: 0.8641 (ttm) REVERT: P 118 GLN cc_start: 0.9178 (tm-30) cc_final: 0.8514 (tm-30) REVERT: P 138 TRP cc_start: 0.8232 (t-100) cc_final: 0.7551 (t-100) REVERT: P 151 SER cc_start: 0.8346 (p) cc_final: 0.7957 (t) REVERT: P 181 LEU cc_start: 0.8221 (tp) cc_final: 0.7787 (pp) REVERT: P 199 GLU cc_start: 0.8015 (mp0) cc_final: 0.7637 (pm20) REVERT: Q 118 TYR cc_start: 0.7958 (t80) cc_final: 0.7459 (m-10) REVERT: Q 144 ASP cc_start: 0.7825 (m-30) cc_final: 0.7600 (m-30) REVERT: Q 150 MET cc_start: 0.8061 (tmm) cc_final: 0.7366 (ttt) REVERT: Q 215 TRP cc_start: 0.8199 (p90) cc_final: 0.7358 (p90) REVERT: R 61 LEU cc_start: 0.8747 (mm) cc_final: 0.8502 (mp) REVERT: R 185 LYS cc_start: 0.8304 (mttt) cc_final: 0.7754 (ttpt) REVERT: S 3 SER cc_start: 0.8545 (t) cc_final: 0.8197 (p) REVERT: S 106 VAL cc_start: 0.9315 (t) cc_final: 0.9042 (m) REVERT: S 174 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7829 (mm) REVERT: T 27 GLN cc_start: 0.8432 (mt0) cc_final: 0.8098 (mm-40) REVERT: T 52 ASP cc_start: 0.8534 (m-30) cc_final: 0.8282 (m-30) REVERT: T 150 THR cc_start: 0.8614 (p) cc_final: 0.8325 (t) REVERT: T 191 LEU cc_start: 0.6335 (tp) cc_final: 0.6068 (tp) REVERT: U 3 MET cc_start: 0.8509 (mmm) cc_final: 0.7929 (mmm) REVERT: U 4 SER cc_start: 0.8029 (p) cc_final: 0.7663 (t) REVERT: U 33 MET cc_start: 0.9023 (tmm) cc_final: 0.8592 (ttt) REVERT: U 148 MET cc_start: 0.8770 (mmm) cc_final: 0.8520 (mmm) REVERT: U 168 GLN cc_start: 0.7637 (mm110) cc_final: 0.7434 (mm-40) REVERT: V 49 GLU cc_start: 0.7174 (tt0) cc_final: 0.6932 (tt0) REVERT: V 166 GLU cc_start: 0.8287 (tp30) cc_final: 0.7951 (tp30) REVERT: W 103 MET cc_start: 0.8278 (mmm) cc_final: 0.8033 (tpp) REVERT: W 127 MET cc_start: 0.8189 (ptp) cc_final: 0.7786 (ptm) REVERT: W 147 GLN cc_start: 0.7951 (tp40) cc_final: 0.7597 (tp40) REVERT: W 173 MET cc_start: 0.8408 (mmm) cc_final: 0.8116 (mmt) REVERT: X 2 PHE cc_start: 0.6746 (t80) cc_final: 0.6540 (t80) REVERT: X 201 GLU cc_start: 0.7204 (mp0) cc_final: 0.6978 (mp0) REVERT: Y 33 MET cc_start: 0.9048 (tmm) cc_final: 0.8656 (ttt) REVERT: Y 44 MET cc_start: 0.8315 (mmm) cc_final: 0.7902 (mmm) REVERT: Y 76 LYS cc_start: 0.8545 (ttmt) cc_final: 0.8301 (ttpt) REVERT: Y 148 MET cc_start: 0.8849 (mmm) cc_final: 0.8586 (mmm) REVERT: Y 156 ASN cc_start: 0.8216 (OUTLIER) cc_final: 0.7855 (t0) REVERT: Y 197 ARG cc_start: 0.7706 (mtm-85) cc_final: 0.7395 (mtm180) REVERT: Z 8 ARG cc_start: 0.8140 (mtt90) cc_final: 0.7355 (mtt90) REVERT: Z 140 ASP cc_start: 0.8322 (p0) cc_final: 0.7927 (p0) REVERT: Z 174 MET cc_start: 0.7043 (mmp) cc_final: 0.6745 (mmm) REVERT: Z 232 GLU cc_start: 0.7110 (mp0) cc_final: 0.6634 (mp0) REVERT: a 79 ASP cc_start: 0.6019 (p0) cc_final: 0.5756 (m-30) REVERT: a 104 ASN cc_start: 0.7700 (t0) cc_final: 0.7310 (t0) REVERT: a 127 MET cc_start: 0.8064 (ptp) cc_final: 0.7765 (ptm) REVERT: a 147 GLN cc_start: 0.7696 (tp40) cc_final: 0.7411 (tp40) REVERT: a 208 ASN cc_start: 0.8254 (t0) cc_final: 0.7895 (t0) REVERT: a 210 ASP cc_start: 0.8006 (m-30) cc_final: 0.7789 (m-30) REVERT: b 117 MET cc_start: 0.8937 (ttm) cc_final: 0.8609 (ttm) REVERT: b 118 GLN cc_start: 0.9095 (tm-30) cc_final: 0.8543 (tm-30) REVERT: b 138 TRP cc_start: 0.8248 (t-100) cc_final: 0.7634 (t-100) REVERT: b 174 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7473 (tm-30) REVERT: b 228 TYR cc_start: 0.7426 (m-80) cc_final: 0.7067 (m-10) outliers start: 187 outliers final: 134 residues processed: 1273 average time/residue: 0.6074 time to fit residues: 1282.7391 Evaluate side-chains 1270 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1126 time to evaluate : 5.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 119 TYR Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 86 ASN Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 227 HIS Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 122 ASN Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 143 ASN Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 53 GLN Chi-restraints excluded: chain K residue 143 ILE Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain L residue 9 ASP Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 139 ASP Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 226 ASP Chi-restraints excluded: chain M residue 43 SER Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 121 LEU Chi-restraints excluded: chain M residue 206 MET Chi-restraints excluded: chain M residue 216 GLU Chi-restraints excluded: chain M residue 227 HIS Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 122 ASN Chi-restraints excluded: chain N residue 129 ILE Chi-restraints excluded: chain N residue 139 ASP Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 115 SER Chi-restraints excluded: chain P residue 119 GLU Chi-restraints excluded: chain P residue 121 THR Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 207 ILE Chi-restraints excluded: chain P residue 221 THR Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 81 LEU Chi-restraints excluded: chain Q residue 143 ASN Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 156 VAL Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 48 ASP Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 78 SER Chi-restraints excluded: chain S residue 113 LEU Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain T residue 33 ASP Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 72 LEU Chi-restraints excluded: chain U residue 164 GLU Chi-restraints excluded: chain V residue 30 ASP Chi-restraints excluded: chain V residue 33 ASP Chi-restraints excluded: chain V residue 41 LYS Chi-restraints excluded: chain V residue 101 ASN Chi-restraints excluded: chain V residue 182 ILE Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 25 ASP Chi-restraints excluded: chain W residue 84 SER Chi-restraints excluded: chain W residue 96 MET Chi-restraints excluded: chain W residue 189 ILE Chi-restraints excluded: chain W residue 205 THR Chi-restraints excluded: chain W residue 207 THR Chi-restraints excluded: chain X residue 48 ASP Chi-restraints excluded: chain X residue 68 ILE Chi-restraints excluded: chain X residue 78 SER Chi-restraints excluded: chain X residue 181 SER Chi-restraints excluded: chain Y residue 18 CYS Chi-restraints excluded: chain Y residue 36 THR Chi-restraints excluded: chain Y residue 133 ASP Chi-restraints excluded: chain Y residue 151 SER Chi-restraints excluded: chain Y residue 156 ASN Chi-restraints excluded: chain Z residue 172 VAL Chi-restraints excluded: chain a residue 10 SER Chi-restraints excluded: chain a residue 25 ASP Chi-restraints excluded: chain a residue 74 GLU Chi-restraints excluded: chain a residue 192 VAL Chi-restraints excluded: chain a residue 195 LYS Chi-restraints excluded: chain a residue 207 THR Chi-restraints excluded: chain b residue 13 SER Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 167 VAL Chi-restraints excluded: chain b residue 212 CYS Chi-restraints excluded: chain b residue 229 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 489 optimal weight: 0.9980 chunk 333 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 437 optimal weight: 4.9990 chunk 242 optimal weight: 0.0470 chunk 501 optimal weight: 4.9990 chunk 406 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 300 optimal weight: 1.9990 chunk 527 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 overall best weight: 1.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 HIS K 53 GLN K 75 ASN ** L 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 109 GLN O 198 ASN ** P 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 75 ASN R 90 GLN S 77 HIS ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 189 HIS X 8 ASN X 108 ASN ** X 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 161 HIS Y 168 GLN Z 109 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 48615 Z= 0.231 Angle : 0.631 12.971 65860 Z= 0.326 Chirality : 0.044 0.189 7460 Planarity : 0.004 0.052 8519 Dihedral : 6.274 111.957 6910 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.35 % Favored : 95.61 % Rotamer: Outliers : 3.75 % Allowed : 17.43 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.11), residues: 6174 helix: 1.19 (0.11), residues: 2290 sheet: -0.96 (0.14), residues: 1359 loop : -1.23 (0.12), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP J 215 HIS 0.006 0.001 HIS V 132 PHE 0.025 0.002 PHE M 162 TYR 0.023 0.002 TYR N 153 ARG 0.012 0.001 ARG Z 17 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12348 Ramachandran restraints generated. 6174 Oldfield, 0 Emsley, 6174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12348 Ramachandran restraints generated. 6174 Oldfield, 0 Emsley, 6174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1369 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1195 time to evaluate : 5.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.7617 (t0) cc_final: 0.7032 (p0) REVERT: A 42 TYR cc_start: 0.8584 (m-80) cc_final: 0.8364 (m-10) REVERT: B 1 THR cc_start: 0.8064 (m) cc_final: 0.7849 (t) REVERT: B 51 ASP cc_start: 0.7923 (m-30) cc_final: 0.7517 (m-30) REVERT: B 132 ASP cc_start: 0.7746 (m-30) cc_final: 0.7296 (m-30) REVERT: B 135 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8313 (mm) REVERT: B 173 VAL cc_start: 0.9154 (OUTLIER) cc_final: 0.8881 (m) REVERT: B 174 ASP cc_start: 0.7960 (t0) cc_final: 0.7732 (t0) REVERT: B 185 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7869 (tt) REVERT: B 188 THR cc_start: 0.8474 (p) cc_final: 0.8176 (t) REVERT: C 46 SER cc_start: 0.8637 (t) cc_final: 0.8284 (p) REVERT: C 54 TYR cc_start: 0.9124 (t80) cc_final: 0.8880 (t80) REVERT: C 97 MET cc_start: 0.8288 (ttt) cc_final: 0.8031 (ptm) REVERT: C 139 MET cc_start: 0.7111 (mtp) cc_final: 0.6526 (ttp) REVERT: C 141 SER cc_start: 0.8662 (m) cc_final: 0.8359 (t) REVERT: C 179 MET cc_start: 0.7591 (tpp) cc_final: 0.7291 (tpp) REVERT: C 197 HIS cc_start: 0.7643 (m-70) cc_final: 0.7352 (m-70) REVERT: D 46 SER cc_start: 0.8743 (t) cc_final: 0.8311 (p) REVERT: D 54 TYR cc_start: 0.9051 (t80) cc_final: 0.8819 (t80) REVERT: D 90 TYR cc_start: 0.8516 (m-10) cc_final: 0.8223 (m-80) REVERT: D 115 ASP cc_start: 0.8191 (t70) cc_final: 0.7922 (t70) REVERT: D 141 SER cc_start: 0.8612 (m) cc_final: 0.8108 (t) REVERT: D 146 ASN cc_start: 0.7190 (t0) cc_final: 0.6862 (t0) REVERT: E 25 VAL cc_start: 0.8495 (t) cc_final: 0.8284 (m) REVERT: E 51 ASP cc_start: 0.8054 (m-30) cc_final: 0.7810 (m-30) REVERT: E 131 GLN cc_start: 0.7505 (pm20) cc_final: 0.6665 (pm20) REVERT: E 173 VAL cc_start: 0.9127 (OUTLIER) cc_final: 0.8885 (m) REVERT: E 174 ASP cc_start: 0.7926 (t0) cc_final: 0.7584 (t0) REVERT: F 32 ASP cc_start: 0.7640 (t0) cc_final: 0.7026 (p0) REVERT: F 107 GLU cc_start: 0.7493 (tm-30) cc_final: 0.7260 (tm-30) REVERT: G 39 LYS cc_start: 0.8696 (pttt) cc_final: 0.8198 (ptpt) REVERT: G 118 ILE cc_start: 0.8959 (mt) cc_final: 0.8298 (tp) REVERT: G 122 ARG cc_start: 0.7407 (mpt180) cc_final: 0.7088 (mpt180) REVERT: G 137 TYR cc_start: 0.8178 (t80) cc_final: 0.7807 (t80) REVERT: G 142 PRO cc_start: 0.8695 (Cg_exo) cc_final: 0.8490 (Cg_endo) REVERT: G 175 HIS cc_start: 0.7069 (m90) cc_final: 0.6868 (m-70) REVERT: G 176 MET cc_start: 0.7675 (tmm) cc_final: 0.7277 (tmm) REVERT: G 206 THR cc_start: 0.8240 (t) cc_final: 0.7890 (m) REVERT: G 234 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.5431 (pp20) REVERT: H 156 MET cc_start: 0.6394 (ttp) cc_final: 0.5959 (tmm) REVERT: H 193 GLU cc_start: 0.5970 (tt0) cc_final: 0.5680 (tp30) REVERT: I 27 LYS cc_start: 0.8546 (mtpp) cc_final: 0.8337 (ttmm) REVERT: I 46 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7446 (tm-30) REVERT: I 214 ASP cc_start: 0.7063 (m-30) cc_final: 0.6768 (m-30) REVERT: J 75 MET cc_start: 0.7874 (tpp) cc_final: 0.7583 (ttm) REVERT: J 94 GLU cc_start: 0.8322 (tp30) cc_final: 0.7912 (tp30) REVERT: J 118 TYR cc_start: 0.7853 (t80) cc_final: 0.7482 (m-10) REVERT: K 66 VAL cc_start: 0.8615 (t) cc_final: 0.8246 (p) REVERT: K 80 MET cc_start: 0.8494 (mmm) cc_final: 0.7532 (mmm) REVERT: K 143 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7341 (mm) REVERT: K 185 LYS cc_start: 0.8083 (mttt) cc_final: 0.7484 (ttpt) REVERT: K 235 ILE cc_start: 0.7132 (mt) cc_final: 0.6896 (mt) REVERT: L 39 LYS cc_start: 0.8807 (pttt) cc_final: 0.8317 (ptpt) REVERT: L 137 TYR cc_start: 0.8210 (t80) cc_final: 0.7883 (t80) REVERT: L 156 CYS cc_start: 0.7652 (m) cc_final: 0.7292 (m) REVERT: L 176 MET cc_start: 0.7467 (ttp) cc_final: 0.7065 (tmm) REVERT: M 71 ASP cc_start: 0.8082 (t70) cc_final: 0.7406 (m-30) REVERT: M 93 ARG cc_start: 0.8164 (mtt180) cc_final: 0.7871 (mtt180) REVERT: M 156 MET cc_start: 0.6441 (ttp) cc_final: 0.5912 (tmm) REVERT: N 5 ARG cc_start: 0.7934 (mmm-85) cc_final: 0.7716 (mmm-85) REVERT: N 68 ASN cc_start: 0.8315 (p0) cc_final: 0.7889 (p0) REVERT: N 139 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7292 (p0) REVERT: N 214 ASP cc_start: 0.6970 (m-30) cc_final: 0.6689 (m-30) REVERT: O 8 ARG cc_start: 0.8060 (mtt90) cc_final: 0.7651 (mtt90) REVERT: O 38 LEU cc_start: 0.7064 (tp) cc_final: 0.6819 (tp) REVERT: O 89 GLU cc_start: 0.8046 (tp30) cc_final: 0.6726 (tp30) REVERT: O 224 VAL cc_start: 0.8577 (t) cc_final: 0.8288 (m) REVERT: P 117 MET cc_start: 0.8868 (ttm) cc_final: 0.8559 (ttm) REVERT: P 118 GLN cc_start: 0.9139 (tm-30) cc_final: 0.8464 (tm-30) REVERT: P 121 THR cc_start: 0.9180 (OUTLIER) cc_final: 0.8973 (t) REVERT: P 138 TRP cc_start: 0.8103 (t-100) cc_final: 0.7501 (t-100) REVERT: P 151 SER cc_start: 0.8348 (p) cc_final: 0.7915 (t) REVERT: P 181 LEU cc_start: 0.8131 (tp) cc_final: 0.7690 (pp) REVERT: P 224 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8173 (mp0) REVERT: Q 94 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7865 (tt0) REVERT: Q 118 TYR cc_start: 0.7700 (t80) cc_final: 0.7429 (m-10) REVERT: Q 180 GLN cc_start: 0.7973 (tp-100) cc_final: 0.7569 (tm-30) REVERT: Q 215 TRP cc_start: 0.8158 (p90) cc_final: 0.7419 (p90) REVERT: R 66 VAL cc_start: 0.8675 (t) cc_final: 0.8432 (p) REVERT: R 185 LYS cc_start: 0.8218 (mttt) cc_final: 0.7703 (ttpt) REVERT: S 106 VAL cc_start: 0.9245 (t) cc_final: 0.8975 (m) REVERT: S 158 MET cc_start: 0.5884 (mmm) cc_final: 0.5337 (mmt) REVERT: S 174 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7797 (mm) REVERT: T 1 MET cc_start: 0.8208 (tmm) cc_final: 0.7653 (tmm) REVERT: T 27 GLN cc_start: 0.8268 (mt0) cc_final: 0.7856 (mm-40) REVERT: T 52 ASP cc_start: 0.8619 (m-30) cc_final: 0.8380 (m-30) REVERT: T 150 THR cc_start: 0.8619 (p) cc_final: 0.8320 (t) REVERT: U 4 SER cc_start: 0.7958 (p) cc_final: 0.7756 (t) REVERT: U 14 LYS cc_start: 0.8392 (ttpt) cc_final: 0.8028 (ttpt) REVERT: U 33 MET cc_start: 0.9055 (tmm) cc_final: 0.8628 (ttt) REVERT: U 148 MET cc_start: 0.8788 (mmm) cc_final: 0.8507 (mmm) REVERT: V 23 SER cc_start: 0.6773 (m) cc_final: 0.6551 (p) REVERT: V 145 ARG cc_start: 0.7610 (tpt170) cc_final: 0.6962 (tpm170) REVERT: V 166 GLU cc_start: 0.8196 (tp30) cc_final: 0.7814 (tp30) REVERT: W 103 MET cc_start: 0.8103 (mmm) cc_final: 0.7898 (tpp) REVERT: W 122 LEU cc_start: 0.9368 (tt) cc_final: 0.9018 (tt) REVERT: W 147 GLN cc_start: 0.7931 (tp40) cc_final: 0.7492 (tp40) REVERT: W 173 MET cc_start: 0.8423 (mmm) cc_final: 0.8138 (mmt) REVERT: Y 4 SER cc_start: 0.8414 (OUTLIER) cc_final: 0.7762 (t) REVERT: Y 33 MET cc_start: 0.8986 (tmm) cc_final: 0.8561 (ttt) REVERT: Y 76 LYS cc_start: 0.8473 (ttmt) cc_final: 0.8219 (ttpt) REVERT: Y 146 TYR cc_start: 0.8642 (m-80) cc_final: 0.8354 (m-80) REVERT: Y 148 MET cc_start: 0.8834 (mmm) cc_final: 0.8509 (mmm) REVERT: Y 156 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.7918 (t0) REVERT: Y 193 LYS cc_start: 0.9000 (pttt) cc_final: 0.8744 (pttp) REVERT: Y 197 ARG cc_start: 0.7687 (mtm-85) cc_final: 0.7426 (mtm180) REVERT: Z 72 MET cc_start: 0.7434 (mtp) cc_final: 0.6875 (ttt) REVERT: Z 140 ASP cc_start: 0.8256 (p0) cc_final: 0.7956 (p0) REVERT: Z 177 GLN cc_start: 0.7159 (mm110) cc_final: 0.6882 (mm110) REVERT: Z 194 ILE cc_start: 0.8182 (mm) cc_final: 0.7777 (mt) REVERT: Z 232 GLU cc_start: 0.6861 (mp0) cc_final: 0.6612 (mp0) REVERT: a 79 ASP cc_start: 0.5887 (p0) cc_final: 0.5552 (m-30) REVERT: a 127 MET cc_start: 0.7985 (ptp) cc_final: 0.7734 (ptm) REVERT: a 213 HIS cc_start: 0.7956 (m-70) cc_final: 0.7746 (m-70) REVERT: b 38 LYS cc_start: 0.8168 (ttpp) cc_final: 0.7882 (ttpt) REVERT: b 117 MET cc_start: 0.8838 (ttm) cc_final: 0.8563 (ttm) REVERT: b 118 GLN cc_start: 0.9012 (tm-30) cc_final: 0.8531 (tm-30) REVERT: b 138 TRP cc_start: 0.8058 (t-100) cc_final: 0.7566 (t-100) REVERT: b 174 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7476 (tm-30) REVERT: b 175 LYS cc_start: 0.8445 (ptpp) cc_final: 0.8101 (ptpt) outliers start: 174 outliers final: 129 residues processed: 1288 average time/residue: 0.5642 time to fit residues: 1203.0781 Evaluate side-chains 1249 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1108 time to evaluate : 4.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 119 TYR Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 86 ASN Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 227 HIS Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 122 ASN Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 143 ASN Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 137 CYS Chi-restraints excluded: chain K residue 143 ILE Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain L residue 9 ASP Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 226 ASP Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 121 LEU Chi-restraints excluded: chain M residue 206 MET Chi-restraints excluded: chain M residue 209 LYS Chi-restraints excluded: chain M residue 216 GLU Chi-restraints excluded: chain M residue 227 HIS Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 122 ASN Chi-restraints excluded: chain N residue 129 ILE Chi-restraints excluded: chain N residue 139 ASP Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 47 THR Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 115 SER Chi-restraints excluded: chain P residue 119 GLU Chi-restraints excluded: chain P residue 121 THR Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 207 ILE Chi-restraints excluded: chain P residue 229 LEU Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 81 LEU Chi-restraints excluded: chain Q residue 94 GLU Chi-restraints excluded: chain Q residue 143 ASN Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 156 VAL Chi-restraints excluded: chain Q residue 226 ILE Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain S residue 48 ASP Chi-restraints excluded: chain S residue 78 SER Chi-restraints excluded: chain S residue 113 LEU Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain T residue 33 ASP Chi-restraints excluded: chain T residue 41 LYS Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 164 GLU Chi-restraints excluded: chain V residue 30 ASP Chi-restraints excluded: chain V residue 33 ASP Chi-restraints excluded: chain V residue 39 SER Chi-restraints excluded: chain V residue 41 LYS Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 25 ASP Chi-restraints excluded: chain W residue 96 MET Chi-restraints excluded: chain W residue 189 ILE Chi-restraints excluded: chain W residue 205 THR Chi-restraints excluded: chain W residue 207 THR Chi-restraints excluded: chain X residue 8 ASN Chi-restraints excluded: chain X residue 12 ILE Chi-restraints excluded: chain X residue 48 ASP Chi-restraints excluded: chain X residue 78 SER Chi-restraints excluded: chain X residue 169 ASP Chi-restraints excluded: chain Y residue 4 SER Chi-restraints excluded: chain Y residue 18 CYS Chi-restraints excluded: chain Y residue 36 THR Chi-restraints excluded: chain Y residue 133 ASP Chi-restraints excluded: chain Y residue 156 ASN Chi-restraints excluded: chain a residue 10 SER Chi-restraints excluded: chain a residue 25 ASP Chi-restraints excluded: chain a residue 84 SER Chi-restraints excluded: chain a residue 189 ILE Chi-restraints excluded: chain a residue 192 VAL Chi-restraints excluded: chain a residue 205 THR Chi-restraints excluded: chain a residue 207 THR Chi-restraints excluded: chain b residue 13 SER Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 167 VAL Chi-restraints excluded: chain b residue 212 CYS Chi-restraints excluded: chain b residue 229 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 197 optimal weight: 8.9990 chunk 529 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 345 optimal weight: 10.0000 chunk 145 optimal weight: 0.8980 chunk 588 optimal weight: 4.9990 chunk 488 optimal weight: 5.9990 chunk 272 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 194 optimal weight: 0.3980 chunk 308 optimal weight: 7.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 GLN K 75 ASN ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 198 ASN P 62 HIS R 75 ASN R 90 GLN S 77 HIS ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 168 GLN ** V 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 30 GLN Y 168 GLN ** Z 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 48615 Z= 0.350 Angle : 0.692 13.250 65860 Z= 0.356 Chirality : 0.046 0.175 7460 Planarity : 0.005 0.060 8519 Dihedral : 6.228 102.868 6910 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.76 % Favored : 94.21 % Rotamer: Outliers : 4.33 % Allowed : 17.71 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.50 (0.11), residues: 6174 helix: 1.10 (0.11), residues: 2282 sheet: -1.07 (0.13), residues: 1407 loop : -1.15 (0.12), residues: 2485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP Q 215 HIS 0.007 0.001 HIS V 132 PHE 0.025 0.002 PHE M 162 TYR 0.025 0.002 TYR D 153 ARG 0.012 0.001 ARG O 17 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12348 Ramachandran restraints generated. 6174 Oldfield, 0 Emsley, 6174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12348 Ramachandran restraints generated. 6174 Oldfield, 0 Emsley, 6174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1346 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1143 time to evaluate : 5.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.7684 (t0) cc_final: 0.7031 (p0) REVERT: A 42 TYR cc_start: 0.8702 (m-80) cc_final: 0.8411 (m-10) REVERT: A 126 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8408 (pt) REVERT: B 51 ASP cc_start: 0.7900 (m-30) cc_final: 0.7630 (m-30) REVERT: B 132 ASP cc_start: 0.7699 (m-30) cc_final: 0.7236 (m-30) REVERT: B 135 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8456 (mm) REVERT: B 173 VAL cc_start: 0.9148 (OUTLIER) cc_final: 0.8904 (m) REVERT: B 188 THR cc_start: 0.8577 (p) cc_final: 0.8298 (t) REVERT: C 46 SER cc_start: 0.8737 (t) cc_final: 0.8391 (p) REVERT: C 54 TYR cc_start: 0.9056 (t80) cc_final: 0.8796 (t80) REVERT: C 97 MET cc_start: 0.8396 (ttt) cc_final: 0.8007 (ptm) REVERT: C 139 MET cc_start: 0.7356 (mtp) cc_final: 0.7095 (ttm) REVERT: C 141 SER cc_start: 0.8679 (m) cc_final: 0.8307 (t) REVERT: C 146 ASN cc_start: 0.7118 (t0) cc_final: 0.6842 (t0) REVERT: D 46 SER cc_start: 0.8726 (t) cc_final: 0.8337 (p) REVERT: D 54 TYR cc_start: 0.9094 (t80) cc_final: 0.8835 (t80) REVERT: D 90 TYR cc_start: 0.8428 (m-80) cc_final: 0.7530 (m-10) REVERT: D 115 ASP cc_start: 0.8140 (t70) cc_final: 0.7839 (t70) REVERT: D 141 SER cc_start: 0.8640 (m) cc_final: 0.8260 (t) REVERT: D 146 ASN cc_start: 0.7243 (t0) cc_final: 0.6918 (t0) REVERT: D 154 ASP cc_start: 0.7947 (t0) cc_final: 0.7530 (t0) REVERT: E 173 VAL cc_start: 0.9167 (OUTLIER) cc_final: 0.8912 (m) REVERT: F 32 ASP cc_start: 0.7625 (t0) cc_final: 0.7073 (p0) REVERT: F 118 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7621 (ppp) REVERT: G 39 LYS cc_start: 0.8765 (pttt) cc_final: 0.8314 (ptpt) REVERT: G 137 TYR cc_start: 0.8188 (t80) cc_final: 0.7901 (t80) REVERT: G 206 THR cc_start: 0.8431 (t) cc_final: 0.8098 (m) REVERT: G 234 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.5441 (pp20) REVERT: H 41 GLN cc_start: 0.6832 (OUTLIER) cc_final: 0.6066 (tp40) REVERT: H 156 MET cc_start: 0.6523 (ttp) cc_final: 0.6004 (tmm) REVERT: H 193 GLU cc_start: 0.6045 (tt0) cc_final: 0.5670 (tp30) REVERT: I 27 LYS cc_start: 0.8615 (mtpp) cc_final: 0.8394 (ttmm) REVERT: I 46 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7569 (tm-30) REVERT: I 214 ASP cc_start: 0.7307 (m-30) cc_final: 0.7017 (m-30) REVERT: I 227 LYS cc_start: 0.4413 (pttm) cc_final: 0.4184 (pttm) REVERT: J 58 TYR cc_start: 0.7784 (m-80) cc_final: 0.7299 (m-80) REVERT: J 75 MET cc_start: 0.7982 (tpp) cc_final: 0.7751 (ttm) REVERT: J 94 GLU cc_start: 0.8362 (tp30) cc_final: 0.7935 (tp30) REVERT: J 118 TYR cc_start: 0.7990 (t80) cc_final: 0.7493 (m-10) REVERT: K 53 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.7263 (mt0) REVERT: K 66 VAL cc_start: 0.8749 (t) cc_final: 0.8404 (p) REVERT: K 80 MET cc_start: 0.8613 (mmm) cc_final: 0.7553 (mmm) REVERT: K 185 LYS cc_start: 0.8153 (mttt) cc_final: 0.7570 (ttpt) REVERT: K 235 ILE cc_start: 0.7166 (mt) cc_final: 0.6903 (mt) REVERT: L 39 LYS cc_start: 0.8917 (pttt) cc_final: 0.8389 (ptpt) REVERT: L 137 TYR cc_start: 0.8230 (t80) cc_final: 0.7950 (t80) REVERT: L 148 CYS cc_start: 0.8215 (m) cc_final: 0.7932 (m) REVERT: L 156 CYS cc_start: 0.7635 (m) cc_final: 0.7334 (m) REVERT: L 176 MET cc_start: 0.7348 (ttp) cc_final: 0.6918 (tmm) REVERT: M 93 ARG cc_start: 0.8299 (mtt180) cc_final: 0.7817 (mtt180) REVERT: M 156 MET cc_start: 0.6526 (ttp) cc_final: 0.5976 (tmm) REVERT: M 201 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8401 (tt) REVERT: N 5 ARG cc_start: 0.8014 (mmm-85) cc_final: 0.7692 (mmm-85) REVERT: N 214 ASP cc_start: 0.6920 (m-30) cc_final: 0.6536 (m-30) REVERT: O 8 ARG cc_start: 0.8011 (mtt90) cc_final: 0.7619 (mtt90) REVERT: O 89 GLU cc_start: 0.8261 (tp30) cc_final: 0.7983 (tp30) REVERT: O 224 VAL cc_start: 0.8559 (t) cc_final: 0.8259 (m) REVERT: P 117 MET cc_start: 0.8854 (ttm) cc_final: 0.8486 (ttm) REVERT: P 118 GLN cc_start: 0.9155 (tm-30) cc_final: 0.8472 (tm-30) REVERT: P 138 TRP cc_start: 0.8248 (t-100) cc_final: 0.7591 (t-100) REVERT: P 149 ASP cc_start: 0.7704 (m-30) cc_final: 0.7295 (m-30) REVERT: P 151 SER cc_start: 0.8371 (p) cc_final: 0.7944 (t) REVERT: P 181 LEU cc_start: 0.8136 (tp) cc_final: 0.7726 (pp) REVERT: P 201 GLN cc_start: 0.8655 (tp40) cc_final: 0.8428 (tp40) REVERT: Q 94 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7774 (tt0) REVERT: Q 169 ARG cc_start: 0.7365 (ttp80) cc_final: 0.6994 (ttp80) REVERT: R 66 VAL cc_start: 0.8771 (t) cc_final: 0.8508 (p) REVERT: R 185 LYS cc_start: 0.8297 (mttt) cc_final: 0.7547 (tmmt) REVERT: S 106 VAL cc_start: 0.9308 (t) cc_final: 0.9021 (m) REVERT: S 158 MET cc_start: 0.5932 (mmm) cc_final: 0.5404 (mmt) REVERT: S 172 MET cc_start: 0.7671 (tpt) cc_final: 0.7201 (mmm) REVERT: S 174 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7872 (mm) REVERT: T 3 TYR cc_start: 0.8548 (t80) cc_final: 0.8344 (t80) REVERT: T 27 GLN cc_start: 0.8042 (mt0) cc_final: 0.7627 (mm-40) REVERT: T 52 ASP cc_start: 0.8610 (m-30) cc_final: 0.8331 (m-30) REVERT: T 69 MET cc_start: 0.8220 (mmm) cc_final: 0.7800 (mmt) REVERT: T 150 THR cc_start: 0.8654 (p) cc_final: 0.8431 (t) REVERT: U 4 SER cc_start: 0.8047 (p) cc_final: 0.7673 (t) REVERT: U 14 LYS cc_start: 0.8479 (ttpt) cc_final: 0.8261 (ttpt) REVERT: U 33 MET cc_start: 0.9063 (tmm) cc_final: 0.8715 (ttt) REVERT: U 97 LYS cc_start: 0.8026 (mttt) cc_final: 0.7723 (mttt) REVERT: V 52 ASP cc_start: 0.8692 (m-30) cc_final: 0.8104 (m-30) REVERT: V 166 GLU cc_start: 0.8274 (tp30) cc_final: 0.8033 (tp30) REVERT: W 127 MET cc_start: 0.8139 (ptp) cc_final: 0.7857 (ptm) REVERT: W 147 GLN cc_start: 0.8013 (tp40) cc_final: 0.7453 (tp40) REVERT: X 115 GLU cc_start: 0.7372 (mp0) cc_final: 0.7102 (mp0) REVERT: Y 33 MET cc_start: 0.8982 (tmm) cc_final: 0.8617 (ttt) REVERT: Y 44 MET cc_start: 0.8415 (mmm) cc_final: 0.8067 (mtp) REVERT: Y 76 LYS cc_start: 0.8512 (ttmt) cc_final: 0.8167 (ttpt) REVERT: Y 98 ARG cc_start: 0.8288 (tpt90) cc_final: 0.8051 (tpt-90) REVERT: Y 148 MET cc_start: 0.8820 (mmm) cc_final: 0.8509 (mmm) REVERT: Y 156 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.8052 (t0) REVERT: Y 193 LYS cc_start: 0.9056 (pttt) cc_final: 0.8767 (pttp) REVERT: Y 197 ARG cc_start: 0.7679 (mtm-85) cc_final: 0.7295 (mtm180) REVERT: Z 140 ASP cc_start: 0.8329 (p0) cc_final: 0.7844 (p0) REVERT: Z 194 ILE cc_start: 0.8283 (mm) cc_final: 0.7876 (mt) REVERT: Z 217 THR cc_start: 0.8204 (m) cc_final: 0.8002 (m) REVERT: a 79 ASP cc_start: 0.5919 (p0) cc_final: 0.5500 (m-30) REVERT: a 104 ASN cc_start: 0.7745 (t0) cc_final: 0.7363 (t0) REVERT: a 127 MET cc_start: 0.8093 (ptp) cc_final: 0.7822 (ptm) REVERT: b 38 LYS cc_start: 0.8278 (ttpp) cc_final: 0.7993 (ttpt) REVERT: b 78 MET cc_start: 0.7848 (ptp) cc_final: 0.7496 (ptp) REVERT: b 117 MET cc_start: 0.8881 (ttm) cc_final: 0.8596 (ttm) REVERT: b 118 GLN cc_start: 0.9068 (tm-30) cc_final: 0.8561 (tm-30) REVERT: b 138 TRP cc_start: 0.8255 (t-100) cc_final: 0.7647 (t-100) REVERT: b 174 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7513 (tm-30) REVERT: b 175 LYS cc_start: 0.8534 (ptpp) cc_final: 0.8167 (ptpt) outliers start: 203 outliers final: 157 residues processed: 1260 average time/residue: 0.6164 time to fit residues: 1286.9665 Evaluate side-chains 1277 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1108 time to evaluate : 5.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 119 TYR Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 86 ASN Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain H residue 41 GLN Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 227 HIS Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 122 ASN Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 143 ASN Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 53 GLN Chi-restraints excluded: chain K residue 143 ILE Chi-restraints excluded: chain K residue 176 THR Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain L residue 9 ASP Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 159 MET Chi-restraints excluded: chain L residue 226 ASP Chi-restraints excluded: chain M residue 43 SER Chi-restraints excluded: chain M residue 121 LEU Chi-restraints excluded: chain M residue 163 VAL Chi-restraints excluded: chain M residue 201 ILE Chi-restraints excluded: chain M residue 206 MET Chi-restraints excluded: chain M residue 216 GLU Chi-restraints excluded: chain M residue 227 HIS Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 122 ASN Chi-restraints excluded: chain N residue 129 ILE Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain N residue 227 LYS Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 78 MET Chi-restraints excluded: chain P residue 115 SER Chi-restraints excluded: chain P residue 119 GLU Chi-restraints excluded: chain P residue 160 THR Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 207 ILE Chi-restraints excluded: chain P residue 229 LEU Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 81 LEU Chi-restraints excluded: chain Q residue 94 GLU Chi-restraints excluded: chain Q residue 143 ASN Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 156 VAL Chi-restraints excluded: chain Q residue 226 ILE Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 48 ASP Chi-restraints excluded: chain S residue 78 SER Chi-restraints excluded: chain S residue 113 LEU Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain T residue 33 ASP Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 84 TYR Chi-restraints excluded: chain U residue 164 GLU Chi-restraints excluded: chain V residue 30 ASP Chi-restraints excluded: chain V residue 33 ASP Chi-restraints excluded: chain V residue 39 SER Chi-restraints excluded: chain V residue 41 LYS Chi-restraints excluded: chain V residue 101 ASN Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 25 ASP Chi-restraints excluded: chain W residue 43 MET Chi-restraints excluded: chain W residue 84 SER Chi-restraints excluded: chain W residue 96 MET Chi-restraints excluded: chain W residue 189 ILE Chi-restraints excluded: chain W residue 205 THR Chi-restraints excluded: chain W residue 207 THR Chi-restraints excluded: chain X residue 12 ILE Chi-restraints excluded: chain X residue 48 ASP Chi-restraints excluded: chain X residue 78 SER Chi-restraints excluded: chain X residue 169 ASP Chi-restraints excluded: chain X residue 174 LEU Chi-restraints excluded: chain Y residue 4 SER Chi-restraints excluded: chain Y residue 18 CYS Chi-restraints excluded: chain Y residue 36 THR Chi-restraints excluded: chain Y residue 84 TYR Chi-restraints excluded: chain Y residue 156 ASN Chi-restraints excluded: chain Z residue 172 VAL Chi-restraints excluded: chain a residue 10 SER Chi-restraints excluded: chain a residue 25 ASP Chi-restraints excluded: chain a residue 84 SER Chi-restraints excluded: chain a residue 189 ILE Chi-restraints excluded: chain a residue 192 VAL Chi-restraints excluded: chain a residue 205 THR Chi-restraints excluded: chain a residue 207 THR Chi-restraints excluded: chain b residue 13 SER Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 115 SER Chi-restraints excluded: chain b residue 167 VAL Chi-restraints excluded: chain b residue 212 CYS Chi-restraints excluded: chain b residue 229 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 567 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 335 optimal weight: 1.9990 chunk 429 optimal weight: 10.0000 chunk 332 optimal weight: 2.9990 chunk 495 optimal weight: 0.6980 chunk 328 optimal weight: 2.9990 chunk 586 optimal weight: 1.9990 chunk 366 optimal weight: 0.9980 chunk 357 optimal weight: 0.0470 chunk 270 optimal weight: 8.9990 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 9 GLN E 145 ASN K 53 GLN K 75 ASN ** L 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 ASN N 120 GLN O 109 GLN O 198 ASN R 75 ASN R 90 GLN S 77 HIS S 108 ASN ** S 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 71 ASN T 110 HIS ** T 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 168 GLN ** X 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 168 GLN Z 84 ASN a 213 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 48615 Z= 0.201 Angle : 0.624 14.868 65860 Z= 0.320 Chirality : 0.043 0.165 7460 Planarity : 0.004 0.052 8519 Dihedral : 5.666 79.225 6910 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.96 % Favored : 96.02 % Rotamer: Outliers : 3.53 % Allowed : 18.88 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.11), residues: 6174 helix: 1.44 (0.11), residues: 2256 sheet: -0.85 (0.14), residues: 1405 loop : -1.03 (0.12), residues: 2513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP J 215 HIS 0.006 0.001 HIS W 89 PHE 0.022 0.001 PHE M 162 TYR 0.025 0.001 TYR N 153 ARG 0.012 0.001 ARG Z 226 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12348 Ramachandran restraints generated. 6174 Oldfield, 0 Emsley, 6174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12348 Ramachandran restraints generated. 6174 Oldfield, 0 Emsley, 6174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1358 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1196 time to evaluate : 5.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.7584 (t0) cc_final: 0.6959 (p0) REVERT: A 42 TYR cc_start: 0.8540 (m-80) cc_final: 0.8274 (m-10) REVERT: B 51 ASP cc_start: 0.7831 (m-30) cc_final: 0.7530 (m-30) REVERT: B 132 ASP cc_start: 0.7564 (m-30) cc_final: 0.7360 (m-30) REVERT: B 135 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8282 (mm) REVERT: B 188 THR cc_start: 0.8523 (p) cc_final: 0.8210 (t) REVERT: C 46 SER cc_start: 0.8727 (t) cc_final: 0.8387 (p) REVERT: C 54 TYR cc_start: 0.9076 (t80) cc_final: 0.8830 (t80) REVERT: C 97 MET cc_start: 0.8353 (ttt) cc_final: 0.7847 (ptm) REVERT: C 139 MET cc_start: 0.7063 (mtp) cc_final: 0.6651 (ttp) REVERT: C 141 SER cc_start: 0.8674 (m) cc_final: 0.8374 (t) REVERT: C 146 ASN cc_start: 0.7075 (t0) cc_final: 0.6791 (t0) REVERT: C 179 MET cc_start: 0.7810 (tpp) cc_final: 0.6099 (tpp) REVERT: C 184 TRP cc_start: 0.7051 (p-90) cc_final: 0.6705 (p-90) REVERT: D 46 SER cc_start: 0.8746 (t) cc_final: 0.8318 (p) REVERT: D 54 TYR cc_start: 0.9033 (t80) cc_final: 0.8747 (t80) REVERT: D 90 TYR cc_start: 0.8326 (m-80) cc_final: 0.7665 (m-10) REVERT: D 115 ASP cc_start: 0.8127 (t70) cc_final: 0.7840 (t70) REVERT: D 141 SER cc_start: 0.8749 (m) cc_final: 0.8203 (p) REVERT: D 154 ASP cc_start: 0.7858 (t0) cc_final: 0.7523 (t0) REVERT: E 131 GLN cc_start: 0.7565 (pm20) cc_final: 0.7161 (pm20) REVERT: E 173 VAL cc_start: 0.9137 (OUTLIER) cc_final: 0.8875 (m) REVERT: F 32 ASP cc_start: 0.7531 (t0) cc_final: 0.6975 (p0) REVERT: G 39 LYS cc_start: 0.8662 (pttt) cc_final: 0.8249 (ptpt) REVERT: G 137 TYR cc_start: 0.8053 (t80) cc_final: 0.7844 (t80) REVERT: G 159 MET cc_start: 0.7189 (tpt) cc_final: 0.6656 (mmm) REVERT: G 206 THR cc_start: 0.8224 (t) cc_final: 0.7760 (p) REVERT: G 234 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.5283 (pp20) REVERT: H 156 MET cc_start: 0.6523 (ttp) cc_final: 0.6048 (tmm) REVERT: H 193 GLU cc_start: 0.5959 (tt0) cc_final: 0.5640 (tp30) REVERT: I 13 ASP cc_start: 0.7747 (p0) cc_final: 0.6913 (p0) REVERT: I 46 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7420 (tm-30) REVERT: I 137 ASP cc_start: 0.6088 (m-30) cc_final: 0.5830 (m-30) REVERT: I 227 LYS cc_start: 0.4842 (pttm) cc_final: 0.4565 (pttm) REVERT: J 58 TYR cc_start: 0.7638 (m-80) cc_final: 0.7197 (m-80) REVERT: J 75 MET cc_start: 0.7991 (tpp) cc_final: 0.7786 (ttm) REVERT: J 94 GLU cc_start: 0.8326 (tp30) cc_final: 0.7777 (tp30) REVERT: J 118 TYR cc_start: 0.7717 (t80) cc_final: 0.7434 (m-10) REVERT: K 66 VAL cc_start: 0.8552 (t) cc_final: 0.8284 (p) REVERT: K 100 ASN cc_start: 0.8758 (t0) cc_final: 0.8545 (t0) REVERT: K 143 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7384 (mm) REVERT: L 39 LYS cc_start: 0.8775 (pttt) cc_final: 0.8284 (ptpt) REVERT: L 137 TYR cc_start: 0.8148 (t80) cc_final: 0.7789 (t80) REVERT: L 142 PRO cc_start: 0.8570 (Cg_exo) cc_final: 0.8236 (Cg_endo) REVERT: L 156 CYS cc_start: 0.7723 (m) cc_final: 0.7500 (m) REVERT: L 176 MET cc_start: 0.7554 (ttp) cc_final: 0.7120 (tmm) REVERT: L 234 GLU cc_start: 0.7203 (pm20) cc_final: 0.6574 (pm20) REVERT: M 71 ASP cc_start: 0.7831 (t70) cc_final: 0.7246 (m-30) REVERT: M 156 MET cc_start: 0.6310 (ttp) cc_final: 0.5888 (tmm) REVERT: M 201 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8383 (tt) REVERT: N 5 ARG cc_start: 0.7957 (mmm-85) cc_final: 0.7659 (mmm-85) REVERT: N 24 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7942 (tp30) REVERT: O 8 ARG cc_start: 0.7839 (mtt90) cc_final: 0.7475 (mtt90) REVERT: O 38 LEU cc_start: 0.7001 (tp) cc_final: 0.6728 (tp) REVERT: O 72 MET cc_start: 0.7965 (ttm) cc_final: 0.6825 (mtm) REVERT: O 224 VAL cc_start: 0.8544 (t) cc_final: 0.8336 (m) REVERT: P 23 TYR cc_start: 0.8307 (m-80) cc_final: 0.7988 (m-80) REVERT: P 117 MET cc_start: 0.8700 (ttm) cc_final: 0.8409 (ttm) REVERT: P 118 GLN cc_start: 0.9130 (tm-30) cc_final: 0.8526 (tm-30) REVERT: P 138 TRP cc_start: 0.8050 (t-100) cc_final: 0.7525 (t-100) REVERT: P 151 SER cc_start: 0.8319 (p) cc_final: 0.7949 (t) REVERT: P 157 TRP cc_start: 0.8910 (m100) cc_final: 0.8684 (m100) REVERT: P 181 LEU cc_start: 0.8075 (tp) cc_final: 0.7714 (pp) REVERT: P 224 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8033 (mp0) REVERT: Q 118 TYR cc_start: 0.7730 (t80) cc_final: 0.7242 (m-10) REVERT: Q 144 ASP cc_start: 0.7696 (m-30) cc_final: 0.7443 (m-30) REVERT: Q 169 ARG cc_start: 0.7282 (ttp80) cc_final: 0.6902 (ttp80) REVERT: R 185 LYS cc_start: 0.8180 (mttt) cc_final: 0.7654 (ttpt) REVERT: S 158 MET cc_start: 0.5324 (mmm) cc_final: 0.4609 (mmt) REVERT: S 172 MET cc_start: 0.7701 (tpt) cc_final: 0.7240 (mmm) REVERT: S 174 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7831 (mm) REVERT: T 3 TYR cc_start: 0.8593 (t80) cc_final: 0.8055 (t80) REVERT: T 52 ASP cc_start: 0.8626 (m-30) cc_final: 0.8383 (m-30) REVERT: T 69 MET cc_start: 0.8079 (mmm) cc_final: 0.7678 (mmt) REVERT: T 150 THR cc_start: 0.8582 (p) cc_final: 0.8352 (t) REVERT: T 166 GLU cc_start: 0.7767 (tp30) cc_final: 0.7553 (tp30) REVERT: U 4 SER cc_start: 0.7959 (p) cc_final: 0.7729 (t) REVERT: U 14 LYS cc_start: 0.8455 (ttpt) cc_final: 0.8173 (ttpt) REVERT: U 33 MET cc_start: 0.9041 (tmm) cc_final: 0.8674 (ttt) REVERT: U 49 TYR cc_start: 0.8919 (m-10) cc_final: 0.8701 (m-10) REVERT: U 97 LYS cc_start: 0.7649 (mttt) cc_final: 0.7444 (mttt) REVERT: U 148 MET cc_start: 0.8732 (mmm) cc_final: 0.8518 (mmm) REVERT: V 38 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.7119 (mtt) REVERT: V 52 ASP cc_start: 0.8701 (m-30) cc_final: 0.8278 (m-30) REVERT: V 166 GLU cc_start: 0.8284 (tp30) cc_final: 0.8067 (tp30) REVERT: W 147 GLN cc_start: 0.7933 (tp40) cc_final: 0.7362 (tp40) REVERT: Y 4 SER cc_start: 0.8234 (OUTLIER) cc_final: 0.7595 (t) REVERT: Y 33 MET cc_start: 0.8947 (tmm) cc_final: 0.8475 (ttt) REVERT: Y 76 LYS cc_start: 0.8537 (ttmt) cc_final: 0.8148 (ttpt) REVERT: Y 98 ARG cc_start: 0.8286 (tpt90) cc_final: 0.7985 (tpt-90) REVERT: Y 105 GLU cc_start: 0.9136 (mp0) cc_final: 0.8885 (mp0) REVERT: Y 146 TYR cc_start: 0.8626 (m-80) cc_final: 0.8386 (m-80) REVERT: Y 148 MET cc_start: 0.8824 (mmm) cc_final: 0.8467 (mmm) REVERT: Y 156 ASN cc_start: 0.8223 (OUTLIER) cc_final: 0.8019 (t0) REVERT: Y 193 LYS cc_start: 0.9028 (pttt) cc_final: 0.8744 (pttp) REVERT: Y 197 ARG cc_start: 0.7722 (mtm-85) cc_final: 0.7389 (mtm180) REVERT: Z 72 MET cc_start: 0.7407 (mtp) cc_final: 0.6962 (ttt) REVERT: Z 140 ASP cc_start: 0.7923 (p0) cc_final: 0.7600 (p0) REVERT: a 147 GLN cc_start: 0.7816 (tp40) cc_final: 0.7324 (tp40) REVERT: b 38 LYS cc_start: 0.8156 (ttpp) cc_final: 0.7887 (ttpt) REVERT: b 117 MET cc_start: 0.8799 (ttm) cc_final: 0.8515 (ttm) REVERT: b 118 GLN cc_start: 0.8965 (tm-30) cc_final: 0.8500 (tm-30) REVERT: b 138 TRP cc_start: 0.8044 (t-100) cc_final: 0.7534 (t-100) REVERT: b 174 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7569 (tm-30) REVERT: b 175 LYS cc_start: 0.8472 (ptpp) cc_final: 0.8091 (ptpt) outliers start: 162 outliers final: 119 residues processed: 1281 average time/residue: 0.5907 time to fit residues: 1253.1178 Evaluate side-chains 1238 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 1110 time to evaluate : 5.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 119 TYR Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 217 LYS Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 227 HIS Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 143 ASN Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 137 CYS Chi-restraints excluded: chain K residue 143 ILE Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain L residue 9 ASP Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 159 MET Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 163 VAL Chi-restraints excluded: chain M residue 201 ILE Chi-restraints excluded: chain M residue 206 MET Chi-restraints excluded: chain M residue 209 LYS Chi-restraints excluded: chain M residue 216 GLU Chi-restraints excluded: chain M residue 227 HIS Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 122 ASN Chi-restraints excluded: chain N residue 129 ILE Chi-restraints excluded: chain N residue 227 LYS Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 78 MET Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 207 ILE Chi-restraints excluded: chain P residue 221 THR Chi-restraints excluded: chain P residue 229 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 81 LEU Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 156 VAL Chi-restraints excluded: chain Q residue 226 ILE Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain S residue 48 ASP Chi-restraints excluded: chain S residue 78 SER Chi-restraints excluded: chain S residue 113 LEU Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain T residue 33 ASP Chi-restraints excluded: chain T residue 191 LEU Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain V residue 38 MET Chi-restraints excluded: chain V residue 41 LYS Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 25 ASP Chi-restraints excluded: chain W residue 43 MET Chi-restraints excluded: chain W residue 96 MET Chi-restraints excluded: chain W residue 189 ILE Chi-restraints excluded: chain W residue 205 THR Chi-restraints excluded: chain X residue 48 ASP Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 78 SER Chi-restraints excluded: chain X residue 174 LEU Chi-restraints excluded: chain X residue 181 SER Chi-restraints excluded: chain Y residue 4 SER Chi-restraints excluded: chain Y residue 18 CYS Chi-restraints excluded: chain Y residue 84 TYR Chi-restraints excluded: chain Y residue 156 ASN Chi-restraints excluded: chain Z residue 19 TYR Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain a residue 10 SER Chi-restraints excluded: chain a residue 25 ASP Chi-restraints excluded: chain a residue 84 SER Chi-restraints excluded: chain a residue 192 VAL Chi-restraints excluded: chain a residue 205 THR Chi-restraints excluded: chain b residue 13 SER Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain b residue 167 VAL Chi-restraints excluded: chain b residue 212 CYS Chi-restraints excluded: chain b residue 229 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 362 optimal weight: 0.6980 chunk 234 optimal weight: 2.9990 chunk 349 optimal weight: 10.0000 chunk 176 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 372 optimal weight: 10.0000 chunk 399 optimal weight: 7.9990 chunk 289 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 460 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 HIS ** H 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 ASN ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 109 GLN O 198 ASN ** Q 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 75 ASN R 90 GLN S 77 HIS ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 152 GLN T 71 ASN T 110 HIS ** T 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 168 GLN V 71 ASN ** V 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 48615 Z= 0.246 Angle : 0.653 13.602 65860 Z= 0.333 Chirality : 0.044 0.225 7460 Planarity : 0.004 0.054 8519 Dihedral : 5.505 79.570 6908 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.65 % Favored : 95.32 % Rotamer: Outliers : 3.65 % Allowed : 19.64 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.11), residues: 6174 helix: 1.45 (0.11), residues: 2254 sheet: -0.81 (0.14), residues: 1391 loop : -1.00 (0.12), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP J 215 HIS 0.006 0.001 HIS V 132 PHE 0.034 0.002 PHE W 187 TYR 0.026 0.002 TYR N 153 ARG 0.014 0.001 ARG O 17 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12348 Ramachandran restraints generated. 6174 Oldfield, 0 Emsley, 6174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12348 Ramachandran restraints generated. 6174 Oldfield, 0 Emsley, 6174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1323 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1155 time to evaluate : 5.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.7577 (t0) cc_final: 0.6957 (p0) REVERT: A 42 TYR cc_start: 0.8558 (m-80) cc_final: 0.8299 (m-10) REVERT: A 163 MET cc_start: 0.7827 (ptt) cc_final: 0.7584 (ptt) REVERT: B 51 ASP cc_start: 0.7897 (m-30) cc_final: 0.7552 (m-30) REVERT: B 135 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8298 (mm) REVERT: B 188 THR cc_start: 0.8501 (p) cc_final: 0.8250 (t) REVERT: C 46 SER cc_start: 0.8760 (t) cc_final: 0.8405 (p) REVERT: C 97 MET cc_start: 0.8397 (ttt) cc_final: 0.8019 (ptm) REVERT: C 139 MET cc_start: 0.6957 (mtp) cc_final: 0.6587 (ttm) REVERT: C 141 SER cc_start: 0.8904 (m) cc_final: 0.8629 (t) REVERT: C 146 ASN cc_start: 0.7057 (t0) cc_final: 0.6855 (t0) REVERT: C 179 MET cc_start: 0.7892 (tpp) cc_final: 0.6146 (tpp) REVERT: C 184 TRP cc_start: 0.7050 (p-90) cc_final: 0.6646 (p-90) REVERT: D 46 SER cc_start: 0.8740 (t) cc_final: 0.8314 (p) REVERT: D 54 TYR cc_start: 0.9040 (t80) cc_final: 0.8788 (t80) REVERT: D 90 TYR cc_start: 0.8370 (m-80) cc_final: 0.7629 (m-10) REVERT: D 115 ASP cc_start: 0.8123 (t70) cc_final: 0.7814 (t70) REVERT: D 141 SER cc_start: 0.8512 (m) cc_final: 0.8051 (p) REVERT: D 179 MET cc_start: 0.7861 (tmm) cc_final: 0.7471 (tpt) REVERT: E 131 GLN cc_start: 0.7506 (pm20) cc_final: 0.7071 (pm20) REVERT: F 32 ASP cc_start: 0.7519 (t0) cc_final: 0.6950 (p0) REVERT: G 39 LYS cc_start: 0.8713 (pttt) cc_final: 0.8267 (ptpt) REVERT: G 206 THR cc_start: 0.8251 (t) cc_final: 0.7760 (p) REVERT: G 234 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.5331 (pp20) REVERT: H 156 MET cc_start: 0.6587 (ttp) cc_final: 0.6037 (tmm) REVERT: H 193 GLU cc_start: 0.5828 (tt0) cc_final: 0.5625 (tp30) REVERT: I 46 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7434 (tm-30) REVERT: I 227 LYS cc_start: 0.4851 (pttm) cc_final: 0.4641 (pttm) REVERT: J 58 TYR cc_start: 0.7587 (m-80) cc_final: 0.7126 (m-80) REVERT: J 94 GLU cc_start: 0.8325 (tp30) cc_final: 0.7890 (tp30) REVERT: J 118 TYR cc_start: 0.7849 (t80) cc_final: 0.7519 (m-10) REVERT: K 66 VAL cc_start: 0.8731 (t) cc_final: 0.8459 (p) REVERT: K 143 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7388 (mm) REVERT: K 150 GLN cc_start: 0.8418 (mm-40) cc_final: 0.7860 (mt0) REVERT: L 39 LYS cc_start: 0.8812 (pttt) cc_final: 0.8303 (ptpt) REVERT: L 137 TYR cc_start: 0.8050 (t80) cc_final: 0.7698 (t80) REVERT: L 142 PRO cc_start: 0.8578 (Cg_exo) cc_final: 0.8274 (Cg_endo) REVERT: L 234 GLU cc_start: 0.7258 (pm20) cc_final: 0.6603 (pm20) REVERT: M 71 ASP cc_start: 0.7912 (t70) cc_final: 0.7329 (m-30) REVERT: M 95 GLU cc_start: 0.7660 (tp30) cc_final: 0.7437 (tp30) REVERT: M 156 MET cc_start: 0.6412 (ttp) cc_final: 0.5885 (tmm) REVERT: N 24 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7948 (tp30) REVERT: N 139 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.7259 (p0) REVERT: N 196 LEU cc_start: 0.8088 (mm) cc_final: 0.7049 (tp) REVERT: O 8 ARG cc_start: 0.7848 (mtt90) cc_final: 0.7431 (mtt90) REVERT: O 17 ARG cc_start: 0.7206 (mtm110) cc_final: 0.6858 (mtp-110) REVERT: O 72 MET cc_start: 0.7979 (ttm) cc_final: 0.6786 (mtp) REVERT: O 89 GLU cc_start: 0.8095 (tp30) cc_final: 0.6756 (tp30) REVERT: O 174 MET cc_start: 0.6948 (mmp) cc_final: 0.6407 (mmm) REVERT: P 117 MET cc_start: 0.8685 (ttm) cc_final: 0.8354 (ttm) REVERT: P 118 GLN cc_start: 0.9138 (tm-30) cc_final: 0.8521 (tm-30) REVERT: P 138 TRP cc_start: 0.8064 (t-100) cc_final: 0.7527 (t-100) REVERT: P 151 SER cc_start: 0.8341 (p) cc_final: 0.7987 (t) REVERT: P 157 TRP cc_start: 0.8937 (m100) cc_final: 0.8728 (m100) REVERT: P 181 LEU cc_start: 0.8101 (tp) cc_final: 0.7723 (pp) REVERT: P 224 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8067 (mp0) REVERT: Q 118 TYR cc_start: 0.7690 (t80) cc_final: 0.7273 (m-10) REVERT: Q 144 ASP cc_start: 0.7710 (m-30) cc_final: 0.7499 (m-30) REVERT: Q 169 ARG cc_start: 0.7287 (ttp80) cc_final: 0.6924 (ttp80) REVERT: R 185 LYS cc_start: 0.8252 (mttt) cc_final: 0.7728 (ttpt) REVERT: S 152 GLN cc_start: 0.7750 (tp-100) cc_final: 0.7373 (tp40) REVERT: S 158 MET cc_start: 0.5763 (mmm) cc_final: 0.5385 (mmt) REVERT: S 172 MET cc_start: 0.7708 (tpt) cc_final: 0.7254 (mmm) REVERT: S 174 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7969 (mm) REVERT: T 3 TYR cc_start: 0.8614 (t80) cc_final: 0.8042 (t80) REVERT: T 52 ASP cc_start: 0.8598 (m-30) cc_final: 0.8324 (m-30) REVERT: T 69 MET cc_start: 0.8042 (mmm) cc_final: 0.7653 (mmt) REVERT: U 33 MET cc_start: 0.9053 (tmm) cc_final: 0.8726 (ttt) REVERT: U 49 TYR cc_start: 0.8881 (m-10) cc_final: 0.8676 (m-10) REVERT: U 97 LYS cc_start: 0.7754 (mttt) cc_final: 0.7525 (mttt) REVERT: U 98 ARG cc_start: 0.8236 (ttt-90) cc_final: 0.7995 (ttt90) REVERT: U 148 MET cc_start: 0.8736 (mmm) cc_final: 0.8502 (mmm) REVERT: V 38 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.7107 (mtt) REVERT: V 52 ASP cc_start: 0.8736 (m-30) cc_final: 0.8317 (m-30) REVERT: V 166 GLU cc_start: 0.8253 (tp30) cc_final: 0.8041 (tp30) REVERT: W 127 MET cc_start: 0.8101 (ptp) cc_final: 0.7804 (ptm) REVERT: W 147 GLN cc_start: 0.7963 (tp40) cc_final: 0.7431 (tp40) REVERT: X 8 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8460 (t0) REVERT: X 158 MET cc_start: 0.6089 (mmm) cc_final: 0.5628 (mmt) REVERT: Y 33 MET cc_start: 0.8937 (tmm) cc_final: 0.8574 (ttt) REVERT: Y 44 MET cc_start: 0.8313 (mtp) cc_final: 0.7970 (mtp) REVERT: Y 76 LYS cc_start: 0.8596 (ttmt) cc_final: 0.8204 (ttpt) REVERT: Y 98 ARG cc_start: 0.8269 (tpt90) cc_final: 0.7942 (tpt-90) REVERT: Y 105 GLU cc_start: 0.9141 (mp0) cc_final: 0.8900 (mp0) REVERT: Y 146 TYR cc_start: 0.8648 (m-80) cc_final: 0.8397 (m-80) REVERT: Y 148 MET cc_start: 0.8817 (mmm) cc_final: 0.8490 (mmm) REVERT: Y 156 ASN cc_start: 0.8238 (OUTLIER) cc_final: 0.8022 (t0) REVERT: Y 193 LYS cc_start: 0.9059 (pttt) cc_final: 0.8777 (pttp) REVERT: Y 197 ARG cc_start: 0.7713 (mtm-85) cc_final: 0.7367 (mtm180) REVERT: Z 72 MET cc_start: 0.7481 (mtp) cc_final: 0.6882 (ttt) REVERT: Z 89 GLU cc_start: 0.7886 (tp30) cc_final: 0.6764 (tp30) REVERT: Z 140 ASP cc_start: 0.8104 (p0) cc_final: 0.7732 (p0) REVERT: a 127 MET cc_start: 0.7985 (ptp) cc_final: 0.7727 (ptm) REVERT: a 147 GLN cc_start: 0.7834 (tp40) cc_final: 0.7430 (tp40) REVERT: b 38 LYS cc_start: 0.8190 (ttpp) cc_final: 0.7935 (ttpt) REVERT: b 117 MET cc_start: 0.8760 (ttm) cc_final: 0.8477 (ttm) REVERT: b 118 GLN cc_start: 0.8946 (tm-30) cc_final: 0.8468 (tm-30) REVERT: b 138 TRP cc_start: 0.8160 (t-100) cc_final: 0.7629 (t-100) REVERT: b 157 TRP cc_start: 0.8984 (m100) cc_final: 0.8656 (m100) REVERT: b 172 PHE cc_start: 0.7305 (t80) cc_final: 0.6985 (t80) REVERT: b 174 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7601 (tm-30) REVERT: b 175 LYS cc_start: 0.8492 (ptpp) cc_final: 0.8071 (ptpt) outliers start: 168 outliers final: 139 residues processed: 1240 average time/residue: 0.5759 time to fit residues: 1179.4502 Evaluate side-chains 1249 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1102 time to evaluate : 5.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 119 TYR Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 217 LYS Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 227 HIS Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 122 ASN Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 143 ASN Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 137 CYS Chi-restraints excluded: chain K residue 143 ILE Chi-restraints excluded: chain L residue 9 ASP Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 178 GLU Chi-restraints excluded: chain M residue 43 SER Chi-restraints excluded: chain M residue 121 LEU Chi-restraints excluded: chain M residue 163 VAL Chi-restraints excluded: chain M residue 206 MET Chi-restraints excluded: chain M residue 209 LYS Chi-restraints excluded: chain M residue 216 GLU Chi-restraints excluded: chain M residue 227 HIS Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 122 ASN Chi-restraints excluded: chain N residue 129 ILE Chi-restraints excluded: chain N residue 139 ASP Chi-restraints excluded: chain N residue 227 LYS Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 78 MET Chi-restraints excluded: chain P residue 119 GLU Chi-restraints excluded: chain P residue 166 TYR Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 207 ILE Chi-restraints excluded: chain P residue 221 THR Chi-restraints excluded: chain P residue 229 LEU Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 81 LEU Chi-restraints excluded: chain Q residue 143 ASN Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 156 VAL Chi-restraints excluded: chain Q residue 226 ILE Chi-restraints excluded: chain R residue 33 ASN Chi-restraints excluded: chain R residue 201 CYS Chi-restraints excluded: chain S residue 48 ASP Chi-restraints excluded: chain S residue 113 LEU Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain T residue 33 ASP Chi-restraints excluded: chain T residue 41 LYS Chi-restraints excluded: chain T residue 191 LEU Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 50 ILE Chi-restraints excluded: chain U residue 84 TYR Chi-restraints excluded: chain V residue 33 ASP Chi-restraints excluded: chain V residue 38 MET Chi-restraints excluded: chain V residue 41 LYS Chi-restraints excluded: chain V residue 151 ILE Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 25 ASP Chi-restraints excluded: chain W residue 84 SER Chi-restraints excluded: chain W residue 96 MET Chi-restraints excluded: chain W residue 189 ILE Chi-restraints excluded: chain W residue 205 THR Chi-restraints excluded: chain X residue 8 ASN Chi-restraints excluded: chain X residue 48 ASP Chi-restraints excluded: chain X residue 78 SER Chi-restraints excluded: chain X residue 181 SER Chi-restraints excluded: chain Y residue 18 CYS Chi-restraints excluded: chain Y residue 36 THR Chi-restraints excluded: chain Y residue 75 LEU Chi-restraints excluded: chain Y residue 84 TYR Chi-restraints excluded: chain Y residue 156 ASN Chi-restraints excluded: chain Z residue 19 TYR Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain a residue 10 SER Chi-restraints excluded: chain a residue 25 ASP Chi-restraints excluded: chain a residue 73 ASP Chi-restraints excluded: chain a residue 189 ILE Chi-restraints excluded: chain a residue 192 VAL Chi-restraints excluded: chain a residue 205 THR Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain b residue 167 VAL Chi-restraints excluded: chain b residue 212 CYS Chi-restraints excluded: chain b residue 229 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 533 optimal weight: 0.4980 chunk 561 optimal weight: 4.9990 chunk 512 optimal weight: 2.9990 chunk 546 optimal weight: 5.9990 chunk 328 optimal weight: 2.9990 chunk 237 optimal weight: 3.9990 chunk 428 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 493 optimal weight: 0.9980 chunk 516 optimal weight: 0.0470 chunk 544 optimal weight: 2.9990 overall best weight: 1.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 ASN D 198 GLN G 175 HIS ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 GLN K 75 ASN ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 109 GLN O 198 ASN ** Q 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 75 ASN R 90 GLN S 8 ASN S 77 HIS S 108 ASN ** S 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 24 ASN ** T 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 48615 Z= 0.228 Angle : 0.651 14.417 65860 Z= 0.331 Chirality : 0.044 0.219 7460 Planarity : 0.004 0.056 8519 Dihedral : 5.418 78.984 6908 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.35 % Favored : 95.61 % Rotamer: Outliers : 3.53 % Allowed : 20.10 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.06 (0.11), residues: 6174 helix: 1.48 (0.11), residues: 2246 sheet: -0.77 (0.14), residues: 1423 loop : -0.93 (0.12), residues: 2505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP J 215 HIS 0.007 0.001 HIS V 132 PHE 0.026 0.002 PHE W 187 TYR 0.027 0.002 TYR D 153 ARG 0.013 0.001 ARG Z 226 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12348 Ramachandran restraints generated. 6174 Oldfield, 0 Emsley, 6174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12348 Ramachandran restraints generated. 6174 Oldfield, 0 Emsley, 6174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1312 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1151 time to evaluate : 5.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.7568 (t0) cc_final: 0.6933 (p0) REVERT: A 42 TYR cc_start: 0.8540 (m-80) cc_final: 0.8264 (m-10) REVERT: A 163 MET cc_start: 0.7757 (ptt) cc_final: 0.7502 (ptt) REVERT: B 51 ASP cc_start: 0.7855 (m-30) cc_final: 0.7397 (m-30) REVERT: B 135 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8276 (mm) REVERT: B 188 THR cc_start: 0.8525 (p) cc_final: 0.8279 (t) REVERT: C 46 SER cc_start: 0.8765 (t) cc_final: 0.8400 (p) REVERT: C 97 MET cc_start: 0.8326 (ttt) cc_final: 0.7983 (ptm) REVERT: C 139 MET cc_start: 0.7202 (mtp) cc_final: 0.6860 (ttm) REVERT: C 141 SER cc_start: 0.8855 (m) cc_final: 0.8469 (t) REVERT: C 179 MET cc_start: 0.7881 (tpp) cc_final: 0.6225 (tpp) REVERT: D 54 TYR cc_start: 0.9025 (t80) cc_final: 0.8779 (t80) REVERT: D 90 TYR cc_start: 0.8337 (m-80) cc_final: 0.7657 (m-10) REVERT: D 115 ASP cc_start: 0.8148 (t70) cc_final: 0.7784 (t70) REVERT: D 141 SER cc_start: 0.8658 (m) cc_final: 0.8248 (t) REVERT: D 146 ASN cc_start: 0.7553 (t0) cc_final: 0.7176 (t0) REVERT: D 154 ASP cc_start: 0.7852 (t0) cc_final: 0.7362 (t0) REVERT: E 131 GLN cc_start: 0.7509 (pm20) cc_final: 0.7078 (pm20) REVERT: F 32 ASP cc_start: 0.7499 (t0) cc_final: 0.6941 (p0) REVERT: G 39 LYS cc_start: 0.8689 (pttt) cc_final: 0.8247 (ptpt) REVERT: G 142 PRO cc_start: 0.8427 (Cg_exo) cc_final: 0.8191 (Cg_endo) REVERT: G 206 THR cc_start: 0.8197 (t) cc_final: 0.7744 (p) REVERT: H 156 MET cc_start: 0.6633 (ttp) cc_final: 0.6143 (tmm) REVERT: H 193 GLU cc_start: 0.5823 (tt0) cc_final: 0.5603 (tp30) REVERT: I 46 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7391 (tm-30) REVERT: I 197 GLU cc_start: 0.6623 (mp0) cc_final: 0.6394 (mp0) REVERT: J 58 TYR cc_start: 0.7575 (m-80) cc_final: 0.7126 (m-80) REVERT: J 94 GLU cc_start: 0.8281 (tp30) cc_final: 0.7760 (tp30) REVERT: J 118 TYR cc_start: 0.7729 (t80) cc_final: 0.7460 (m-10) REVERT: K 66 VAL cc_start: 0.8603 (t) cc_final: 0.8357 (p) REVERT: K 143 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7355 (mm) REVERT: L 31 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7981 (tt0) REVERT: L 39 LYS cc_start: 0.8812 (pttt) cc_final: 0.8291 (ptpt) REVERT: L 137 TYR cc_start: 0.8003 (t80) cc_final: 0.7682 (t80) REVERT: L 142 PRO cc_start: 0.8503 (Cg_exo) cc_final: 0.8208 (Cg_endo) REVERT: L 234 GLU cc_start: 0.7259 (pm20) cc_final: 0.6612 (pm20) REVERT: M 71 ASP cc_start: 0.7888 (t70) cc_final: 0.7303 (m-30) REVERT: M 78 MET cc_start: 0.6089 (ptp) cc_final: 0.5710 (ptp) REVERT: M 156 MET cc_start: 0.6408 (ttp) cc_final: 0.5940 (tmm) REVERT: N 5 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7543 (mtp180) REVERT: N 24 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7946 (tp30) REVERT: N 197 GLU cc_start: 0.6482 (mp0) cc_final: 0.5931 (mt-10) REVERT: O 8 ARG cc_start: 0.7810 (mtt90) cc_final: 0.7277 (mtt90) REVERT: O 17 ARG cc_start: 0.7139 (mtm110) cc_final: 0.6869 (mtp-110) REVERT: O 49 ARG cc_start: 0.4655 (mtm-85) cc_final: 0.4090 (mtm-85) REVERT: O 72 MET cc_start: 0.7849 (ttm) cc_final: 0.6810 (mtm) REVERT: O 174 MET cc_start: 0.6885 (mmp) cc_final: 0.6410 (mmm) REVERT: P 117 MET cc_start: 0.8641 (ttm) cc_final: 0.8348 (ttm) REVERT: P 118 GLN cc_start: 0.9119 (tm-30) cc_final: 0.8500 (tm-30) REVERT: P 138 TRP cc_start: 0.8051 (t-100) cc_final: 0.7639 (t-100) REVERT: P 157 TRP cc_start: 0.8905 (m100) cc_final: 0.8705 (m100) REVERT: P 162 MET cc_start: 0.7173 (pmm) cc_final: 0.6816 (pmm) REVERT: P 181 LEU cc_start: 0.8099 (tp) cc_final: 0.7746 (pp) REVERT: P 224 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8077 (mp0) REVERT: Q 169 ARG cc_start: 0.7287 (ttp80) cc_final: 0.6975 (ttp80) REVERT: R 185 LYS cc_start: 0.8218 (mttt) cc_final: 0.7721 (ttpt) REVERT: S 152 GLN cc_start: 0.7697 (tp-100) cc_final: 0.7226 (tp40) REVERT: S 158 MET cc_start: 0.5442 (mmm) cc_final: 0.4995 (mmt) REVERT: S 172 MET cc_start: 0.7686 (tpt) cc_final: 0.7230 (mmm) REVERT: T 1 MET cc_start: 0.8017 (tmm) cc_final: 0.7229 (tmm) REVERT: T 3 TYR cc_start: 0.8655 (t80) cc_final: 0.8005 (t80) REVERT: T 25 ILE cc_start: 0.8237 (mm) cc_final: 0.7756 (mp) REVERT: T 52 ASP cc_start: 0.8590 (m-30) cc_final: 0.8299 (m-30) REVERT: T 69 MET cc_start: 0.8029 (mmm) cc_final: 0.7599 (mmt) REVERT: U 33 MET cc_start: 0.9023 (tmm) cc_final: 0.8571 (ttt) REVERT: U 36 THR cc_start: 0.8889 (OUTLIER) cc_final: 0.8666 (m) REVERT: U 98 ARG cc_start: 0.8215 (ttt-90) cc_final: 0.7902 (ttt90) REVERT: U 148 MET cc_start: 0.8734 (mmm) cc_final: 0.8485 (mmm) REVERT: V 38 MET cc_start: 0.7459 (OUTLIER) cc_final: 0.7098 (mtt) REVERT: V 52 ASP cc_start: 0.8738 (m-30) cc_final: 0.8359 (m-30) REVERT: V 58 GLU cc_start: 0.8333 (tt0) cc_final: 0.7901 (mt-10) REVERT: V 74 GLU cc_start: 0.8302 (pm20) cc_final: 0.8061 (pm20) REVERT: V 166 GLU cc_start: 0.8423 (tp30) cc_final: 0.8206 (tp30) REVERT: W 16 PHE cc_start: 0.9140 (p90) cc_final: 0.8584 (p90) REVERT: W 75 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7093 (tm-30) REVERT: W 127 MET cc_start: 0.8129 (ptp) cc_final: 0.7847 (ptm) REVERT: W 147 GLN cc_start: 0.7931 (tp40) cc_final: 0.7588 (tp40) REVERT: X 8 ASN cc_start: 0.8667 (OUTLIER) cc_final: 0.8397 (t0) REVERT: Y 33 MET cc_start: 0.8926 (tmm) cc_final: 0.8612 (ttt) REVERT: Y 44 MET cc_start: 0.8292 (mtp) cc_final: 0.8081 (mtp) REVERT: Y 76 LYS cc_start: 0.8584 (ttmt) cc_final: 0.8305 (ttpt) REVERT: Y 98 ARG cc_start: 0.8239 (tpt90) cc_final: 0.7986 (ttt90) REVERT: Y 146 TYR cc_start: 0.8614 (m-80) cc_final: 0.8413 (m-80) REVERT: Y 148 MET cc_start: 0.8830 (mmm) cc_final: 0.8540 (mmm) REVERT: Y 156 ASN cc_start: 0.8290 (OUTLIER) cc_final: 0.8049 (t0) REVERT: Y 157 MET cc_start: 0.8063 (mtt) cc_final: 0.7709 (mtt) REVERT: Y 193 LYS cc_start: 0.9062 (pttt) cc_final: 0.8777 (pttp) REVERT: Y 197 ARG cc_start: 0.7676 (mtm-85) cc_final: 0.7376 (mtm180) REVERT: Z 72 MET cc_start: 0.7493 (mtp) cc_final: 0.7032 (ttt) REVERT: a 79 ASP cc_start: 0.5865 (p0) cc_final: 0.5386 (m-30) REVERT: a 147 GLN cc_start: 0.7837 (tp40) cc_final: 0.7347 (tp40) REVERT: b 38 LYS cc_start: 0.8197 (ttpp) cc_final: 0.7944 (ttpt) REVERT: b 51 GLN cc_start: 0.5961 (tp-100) cc_final: 0.5723 (tp40) REVERT: b 117 MET cc_start: 0.8675 (ttm) cc_final: 0.8331 (ttm) REVERT: b 118 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8436 (tm-30) REVERT: b 138 TRP cc_start: 0.8097 (t-100) cc_final: 0.7581 (t-100) REVERT: b 157 TRP cc_start: 0.8968 (m100) cc_final: 0.8681 (m100) REVERT: b 172 PHE cc_start: 0.7274 (t80) cc_final: 0.6942 (t80) REVERT: b 174 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7635 (tm-30) REVERT: b 175 LYS cc_start: 0.8442 (ptpp) cc_final: 0.8076 (ptpt) outliers start: 161 outliers final: 134 residues processed: 1233 average time/residue: 0.5921 time to fit residues: 1211.4668 Evaluate side-chains 1251 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1109 time to evaluate : 4.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 119 TYR Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 227 HIS Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 122 ASN Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 143 ASN Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 137 CYS Chi-restraints excluded: chain K residue 143 ILE Chi-restraints excluded: chain K residue 176 THR Chi-restraints excluded: chain L residue 9 ASP Chi-restraints excluded: chain L residue 31 GLN Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 178 GLU Chi-restraints excluded: chain M residue 43 SER Chi-restraints excluded: chain M residue 121 LEU Chi-restraints excluded: chain M residue 163 VAL Chi-restraints excluded: chain M residue 206 MET Chi-restraints excluded: chain M residue 209 LYS Chi-restraints excluded: chain M residue 216 GLU Chi-restraints excluded: chain M residue 227 HIS Chi-restraints excluded: chain N residue 5 ARG Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 227 LYS Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 78 MET Chi-restraints excluded: chain P residue 166 TYR Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 207 ILE Chi-restraints excluded: chain P residue 221 THR Chi-restraints excluded: chain P residue 229 LEU Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 81 LEU Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 156 VAL Chi-restraints excluded: chain Q residue 226 ILE Chi-restraints excluded: chain R residue 201 CYS Chi-restraints excluded: chain S residue 8 ASN Chi-restraints excluded: chain S residue 48 ASP Chi-restraints excluded: chain S residue 113 LEU Chi-restraints excluded: chain S residue 206 GLU Chi-restraints excluded: chain T residue 33 ASP Chi-restraints excluded: chain T residue 41 LYS Chi-restraints excluded: chain T residue 191 LEU Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 84 TYR Chi-restraints excluded: chain V residue 33 ASP Chi-restraints excluded: chain V residue 38 MET Chi-restraints excluded: chain V residue 151 ILE Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 25 ASP Chi-restraints excluded: chain W residue 84 SER Chi-restraints excluded: chain W residue 96 MET Chi-restraints excluded: chain W residue 189 ILE Chi-restraints excluded: chain W residue 205 THR Chi-restraints excluded: chain X residue 8 ASN Chi-restraints excluded: chain X residue 48 ASP Chi-restraints excluded: chain X residue 78 SER Chi-restraints excluded: chain X residue 181 SER Chi-restraints excluded: chain Y residue 18 CYS Chi-restraints excluded: chain Y residue 75 LEU Chi-restraints excluded: chain Y residue 84 TYR Chi-restraints excluded: chain Y residue 156 ASN Chi-restraints excluded: chain Z residue 19 TYR Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain a residue 10 SER Chi-restraints excluded: chain a residue 25 ASP Chi-restraints excluded: chain a residue 73 ASP Chi-restraints excluded: chain a residue 189 ILE Chi-restraints excluded: chain a residue 192 VAL Chi-restraints excluded: chain a residue 205 THR Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 167 VAL Chi-restraints excluded: chain b residue 212 CYS Chi-restraints excluded: chain b residue 229 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 358 optimal weight: 6.9990 chunk 577 optimal weight: 1.9990 chunk 352 optimal weight: 0.0870 chunk 273 optimal weight: 0.7980 chunk 401 optimal weight: 0.9990 chunk 605 optimal weight: 6.9990 chunk 557 optimal weight: 10.0000 chunk 482 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 372 optimal weight: 0.6980 chunk 295 optimal weight: 6.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 ASN G 175 HIS ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 ASN ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 198 ASN ** Q 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 75 ASN S 8 ASN S 157 ASN ** T 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.335 48615 Z= 0.328 Angle : 0.736 59.199 65860 Z= 0.391 Chirality : 0.044 0.352 7460 Planarity : 0.004 0.062 8519 Dihedral : 5.404 79.010 6905 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.48 % Favored : 95.48 % Rotamer: Outliers : 3.47 % Allowed : 20.38 % Favored : 76.15 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.11), residues: 6174 helix: 1.50 (0.11), residues: 2244 sheet: -0.76 (0.14), residues: 1423 loop : -0.93 (0.12), residues: 2507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.003 TRP C 184 HIS 0.007 0.001 HIS V 132 PHE 0.026 0.002 PHE W 187 TYR 0.049 0.002 TYR U 102 ARG 0.014 0.001 ARG Z 17 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12348 Ramachandran restraints generated. 6174 Oldfield, 0 Emsley, 6174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12348 Ramachandran restraints generated. 6174 Oldfield, 0 Emsley, 6174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1265 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1107 time to evaluate : 5.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.7561 (t0) cc_final: 0.6934 (p0) REVERT: A 42 TYR cc_start: 0.8539 (m-80) cc_final: 0.8260 (m-10) REVERT: A 163 MET cc_start: 0.7755 (ptt) cc_final: 0.7494 (ptt) REVERT: B 51 ASP cc_start: 0.7850 (m-30) cc_final: 0.7373 (m-30) REVERT: B 135 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8275 (mm) REVERT: B 188 THR cc_start: 0.8535 (p) cc_final: 0.8283 (t) REVERT: C 46 SER cc_start: 0.8761 (t) cc_final: 0.8382 (p) REVERT: C 90 TYR cc_start: 0.8125 (m-80) cc_final: 0.7011 (m-80) REVERT: C 97 MET cc_start: 0.8304 (ttt) cc_final: 0.7696 (ptm) REVERT: C 139 MET cc_start: 0.7204 (mtp) cc_final: 0.6849 (ttm) REVERT: C 141 SER cc_start: 0.8880 (m) cc_final: 0.8462 (t) REVERT: C 179 MET cc_start: 0.7863 (tpp) cc_final: 0.6220 (tpp) REVERT: D 54 TYR cc_start: 0.9029 (t80) cc_final: 0.8733 (t80) REVERT: D 90 TYR cc_start: 0.8331 (m-80) cc_final: 0.7657 (m-10) REVERT: D 115 ASP cc_start: 0.8108 (t70) cc_final: 0.7798 (t70) REVERT: D 141 SER cc_start: 0.8643 (m) cc_final: 0.8244 (t) REVERT: D 146 ASN cc_start: 0.7551 (t0) cc_final: 0.7173 (t0) REVERT: D 154 ASP cc_start: 0.7861 (t0) cc_final: 0.7332 (t0) REVERT: E 131 GLN cc_start: 0.7513 (pm20) cc_final: 0.7001 (pm20) REVERT: F 32 ASP cc_start: 0.7493 (t0) cc_final: 0.6938 (p0) REVERT: G 39 LYS cc_start: 0.8679 (pttt) cc_final: 0.8247 (ptpt) REVERT: G 142 PRO cc_start: 0.8395 (Cg_exo) cc_final: 0.8189 (Cg_endo) REVERT: G 206 THR cc_start: 0.8201 (t) cc_final: 0.7735 (p) REVERT: H 156 MET cc_start: 0.6623 (ttp) cc_final: 0.6137 (tmm) REVERT: H 193 GLU cc_start: 0.5810 (tt0) cc_final: 0.5601 (tp30) REVERT: I 46 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7391 (tm-30) REVERT: I 197 GLU cc_start: 0.6639 (mp0) cc_final: 0.6398 (mp0) REVERT: J 58 TYR cc_start: 0.7575 (m-80) cc_final: 0.7125 (m-80) REVERT: J 94 GLU cc_start: 0.8277 (tp30) cc_final: 0.7751 (tp30) REVERT: J 118 TYR cc_start: 0.7728 (t80) cc_final: 0.7457 (m-10) REVERT: K 66 VAL cc_start: 0.8603 (t) cc_final: 0.8352 (p) REVERT: K 143 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7451 (mm) REVERT: L 39 LYS cc_start: 0.8803 (pttt) cc_final: 0.8290 (ptpt) REVERT: L 137 TYR cc_start: 0.8001 (t80) cc_final: 0.7687 (t80) REVERT: L 142 PRO cc_start: 0.8507 (Cg_exo) cc_final: 0.8199 (Cg_endo) REVERT: L 234 GLU cc_start: 0.7262 (pm20) cc_final: 0.6608 (pm20) REVERT: M 71 ASP cc_start: 0.7876 (t70) cc_final: 0.7295 (m-30) REVERT: M 78 MET cc_start: 0.6075 (ptp) cc_final: 0.5729 (ptp) REVERT: M 156 MET cc_start: 0.6401 (ttp) cc_final: 0.5932 (tmm) REVERT: N 5 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7543 (mtp180) REVERT: N 24 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7943 (tp30) REVERT: N 197 GLU cc_start: 0.6484 (mp0) cc_final: 0.5934 (mt-10) REVERT: O 8 ARG cc_start: 0.7805 (mtt90) cc_final: 0.7278 (mtt90) REVERT: O 17 ARG cc_start: 0.7133 (mtm110) cc_final: 0.6862 (mtp-110) REVERT: O 49 ARG cc_start: 0.4638 (mtm-85) cc_final: 0.4080 (mtm-85) REVERT: O 72 MET cc_start: 0.7845 (ttm) cc_final: 0.6801 (mtm) REVERT: O 174 MET cc_start: 0.6891 (mmp) cc_final: 0.6405 (mmm) REVERT: P 117 MET cc_start: 0.8643 (ttm) cc_final: 0.8340 (ttm) REVERT: P 118 GLN cc_start: 0.9121 (tm-30) cc_final: 0.8498 (tm-30) REVERT: P 138 TRP cc_start: 0.8048 (t-100) cc_final: 0.7635 (t-100) REVERT: P 157 TRP cc_start: 0.8907 (m100) cc_final: 0.8697 (m100) REVERT: P 162 MET cc_start: 0.7166 (pmm) cc_final: 0.6791 (pmm) REVERT: P 181 LEU cc_start: 0.8094 (tp) cc_final: 0.7747 (pp) REVERT: P 224 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8065 (mp0) REVERT: Q 169 ARG cc_start: 0.7290 (ttp80) cc_final: 0.6971 (ttp80) REVERT: R 185 LYS cc_start: 0.8218 (mttt) cc_final: 0.7718 (ttpt) REVERT: S 152 GLN cc_start: 0.7500 (tp-100) cc_final: 0.7236 (tp40) REVERT: S 158 MET cc_start: 0.5433 (mmm) cc_final: 0.4993 (mmt) REVERT: S 172 MET cc_start: 0.7687 (tpt) cc_final: 0.7227 (mmm) REVERT: T 1 MET cc_start: 0.8004 (tmm) cc_final: 0.7267 (tmm) REVERT: T 3 TYR cc_start: 0.8649 (t80) cc_final: 0.8015 (t80) REVERT: T 25 ILE cc_start: 0.8194 (mm) cc_final: 0.7747 (mp) REVERT: T 52 ASP cc_start: 0.8617 (m-30) cc_final: 0.8300 (m-30) REVERT: T 69 MET cc_start: 0.8029 (mmm) cc_final: 0.7595 (mmt) REVERT: U 33 MET cc_start: 0.9016 (tmm) cc_final: 0.8578 (ttt) REVERT: U 36 THR cc_start: 0.8879 (OUTLIER) cc_final: 0.8667 (m) REVERT: U 98 ARG cc_start: 0.8215 (ttt-90) cc_final: 0.7893 (ttt90) REVERT: U 148 MET cc_start: 0.8727 (mmm) cc_final: 0.8475 (mmm) REVERT: V 38 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.7094 (mtt) REVERT: V 52 ASP cc_start: 0.8744 (m-30) cc_final: 0.8349 (m-30) REVERT: V 58 GLU cc_start: 0.8323 (tt0) cc_final: 0.7895 (mt-10) REVERT: V 74 GLU cc_start: 0.8309 (pm20) cc_final: 0.8065 (pm20) REVERT: W 16 PHE cc_start: 0.9122 (p90) cc_final: 0.8594 (p90) REVERT: W 147 GLN cc_start: 0.8065 (tp40) cc_final: 0.7578 (tp40) REVERT: X 8 ASN cc_start: 0.8659 (OUTLIER) cc_final: 0.8397 (t0) REVERT: Y 33 MET cc_start: 0.8973 (tmm) cc_final: 0.8641 (ttt) REVERT: Y 76 LYS cc_start: 0.8543 (ttmt) cc_final: 0.8290 (ttpt) REVERT: Y 98 ARG cc_start: 0.8227 (tpt90) cc_final: 0.7976 (ttt90) REVERT: Y 148 MET cc_start: 0.8835 (mmm) cc_final: 0.8533 (mmm) REVERT: Y 156 ASN cc_start: 0.8288 (OUTLIER) cc_final: 0.8050 (t0) REVERT: Y 157 MET cc_start: 0.8052 (mtt) cc_final: 0.7701 (mtt) REVERT: Y 193 LYS cc_start: 0.9060 (pttt) cc_final: 0.8763 (pttp) REVERT: Y 197 ARG cc_start: 0.7672 (mtm-85) cc_final: 0.7380 (mtm180) REVERT: Z 72 MET cc_start: 0.7482 (mtp) cc_final: 0.7008 (ttt) REVERT: a 79 ASP cc_start: 0.5859 (p0) cc_final: 0.5383 (m-30) REVERT: a 147 GLN cc_start: 0.7845 (tp40) cc_final: 0.7327 (tp40) REVERT: b 38 LYS cc_start: 0.8194 (ttpp) cc_final: 0.7943 (ttpt) REVERT: b 51 GLN cc_start: 0.5955 (tp-100) cc_final: 0.5723 (tp40) REVERT: b 117 MET cc_start: 0.8671 (ttm) cc_final: 0.8317 (ttm) REVERT: b 118 GLN cc_start: 0.8915 (tm-30) cc_final: 0.8432 (tm-30) REVERT: b 138 TRP cc_start: 0.8098 (t-100) cc_final: 0.7579 (t-100) REVERT: b 157 TRP cc_start: 0.8962 (m100) cc_final: 0.8675 (m100) REVERT: b 172 PHE cc_start: 0.7292 (t80) cc_final: 0.6934 (t80) REVERT: b 174 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7633 (tm-30) REVERT: b 175 LYS cc_start: 0.8444 (ptpp) cc_final: 0.8076 (ptpt) outliers start: 158 outliers final: 141 residues processed: 1187 average time/residue: 0.5918 time to fit residues: 1169.4839 Evaluate side-chains 1253 residues out of total 5101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1105 time to evaluate : 5.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 119 TYR Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 227 HIS Chi-restraints excluded: chain I residue 15 HIS Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 91 CYS Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 122 ASN Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 143 ASN Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 137 CYS Chi-restraints excluded: chain K residue 143 ILE Chi-restraints excluded: chain L residue 9 ASP Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 178 GLU Chi-restraints excluded: chain L residue 226 ASP Chi-restraints excluded: chain M residue 121 LEU Chi-restraints excluded: chain M residue 163 VAL Chi-restraints excluded: chain M residue 206 MET Chi-restraints excluded: chain M residue 209 LYS Chi-restraints excluded: chain M residue 216 GLU Chi-restraints excluded: chain M residue 227 HIS Chi-restraints excluded: chain N residue 5 ARG Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 122 ASN Chi-restraints excluded: chain N residue 227 LYS Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 78 MET Chi-restraints excluded: chain P residue 166 TYR Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 207 ILE Chi-restraints excluded: chain P residue 221 THR Chi-restraints excluded: chain P residue 229 LEU Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 81 LEU Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 156 VAL Chi-restraints excluded: chain Q residue 226 ILE Chi-restraints excluded: chain R residue 201 CYS Chi-restraints excluded: chain S residue 7 PHE Chi-restraints excluded: chain S residue 48 ASP Chi-restraints excluded: chain S residue 113 LEU Chi-restraints excluded: chain S residue 206 GLU Chi-restraints excluded: chain T residue 33 ASP Chi-restraints excluded: chain T residue 41 LYS Chi-restraints excluded: chain T residue 191 LEU Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 50 ILE Chi-restraints excluded: chain U residue 84 TYR Chi-restraints excluded: chain V residue 33 ASP Chi-restraints excluded: chain V residue 38 MET Chi-restraints excluded: chain V residue 41 LYS Chi-restraints excluded: chain V residue 151 ILE Chi-restraints excluded: chain W residue 25 ASP Chi-restraints excluded: chain W residue 84 SER Chi-restraints excluded: chain W residue 96 MET Chi-restraints excluded: chain W residue 189 ILE Chi-restraints excluded: chain W residue 205 THR Chi-restraints excluded: chain X residue 8 ASN Chi-restraints excluded: chain X residue 48 ASP Chi-restraints excluded: chain X residue 78 SER Chi-restraints excluded: chain X residue 174 LEU Chi-restraints excluded: chain X residue 181 SER Chi-restraints excluded: chain Y residue 18 CYS Chi-restraints excluded: chain Y residue 36 THR Chi-restraints excluded: chain Y residue 75 LEU Chi-restraints excluded: chain Y residue 84 TYR Chi-restraints excluded: chain Y residue 156 ASN Chi-restraints excluded: chain Z residue 19 TYR Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain a residue 10 SER Chi-restraints excluded: chain a residue 25 ASP Chi-restraints excluded: chain a residue 73 ASP Chi-restraints excluded: chain a residue 189 ILE Chi-restraints excluded: chain a residue 192 VAL Chi-restraints excluded: chain a residue 205 THR Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 167 VAL Chi-restraints excluded: chain b residue 192 LEU Chi-restraints excluded: chain b residue 212 CYS Chi-restraints excluded: chain b residue 229 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 383 optimal weight: 6.9990 chunk 513 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 444 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 483 optimal weight: 0.9980 chunk 202 optimal weight: 1.9990 chunk 496 optimal weight: 0.0970 chunk 61 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 HIS ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 ASN ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 198 ASN ** Q 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 75 ASN ** S 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 157 ASN ** T 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.167324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.144241 restraints weight = 164780.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.149157 restraints weight = 126993.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.153045 restraints weight = 63794.864| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3646 r_free = 0.3646 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3645 r_free = 0.3645 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.335 48615 Z= 0.328 Angle : 0.736 59.199 65860 Z= 0.391 Chirality : 0.044 0.352 7460 Planarity : 0.004 0.062 8519 Dihedral : 5.404 79.010 6905 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.48 % Favored : 95.48 % Rotamer: Outliers : 3.27 % Allowed : 20.70 % Favored : 76.03 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.11), residues: 6174 helix: 1.50 (0.11), residues: 2244 sheet: -0.76 (0.14), residues: 1423 loop : -0.93 (0.12), residues: 2507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.003 TRP C 184 HIS 0.007 0.001 HIS V 132 PHE 0.026 0.002 PHE W 187 TYR 0.049 0.002 TYR U 102 ARG 0.014 0.001 ARG Z 17 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17626.86 seconds wall clock time: 315 minutes 3.71 seconds (18903.71 seconds total)