Starting phenix.real_space_refine on Fri Mar 15 21:22:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s61_10101/03_2024/6s61_10101.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s61_10101/03_2024/6s61_10101.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s61_10101/03_2024/6s61_10101.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s61_10101/03_2024/6s61_10101.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s61_10101/03_2024/6s61_10101.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s61_10101/03_2024/6s61_10101.pdb" } resolution = 1.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 6 7.16 5 Zn 24 6.06 5 S 192 5.16 5 C 21456 2.51 5 N 6048 2.21 5 O 10430 1.98 5 H 32904 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 91": "OD1" <-> "OD2" Residue "A ASP 171": "OD1" <-> "OD2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 27": "OE1" <-> "OE2" Residue "D ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 27": "OE1" <-> "OE2" Residue "F ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 27": "OE1" <-> "OE2" Residue "G ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 27": "OE1" <-> "OE2" Residue "H ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 27": "OE1" <-> "OE2" Residue "I ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 27": "OE1" <-> "OE2" Residue "J ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 27": "OE1" <-> "OE2" Residue "K ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 27": "OE1" <-> "OE2" Residue "L ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M GLU 27": "OE1" <-> "OE2" Residue "M ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 27": "OE1" <-> "OE2" Residue "N ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O GLU 27": "OE1" <-> "OE2" Residue "O ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P GLU 27": "OE1" <-> "OE2" Residue "P ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q GLU 27": "OE1" <-> "OE2" Residue "Q ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R GLU 27": "OE1" <-> "OE2" Residue "R ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S GLU 27": "OE1" <-> "OE2" Residue "S ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T GLU 27": "OE1" <-> "OE2" Residue "T ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U GLU 27": "OE1" <-> "OE2" Residue "U ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V GLU 27": "OE1" <-> "OE2" Residue "V ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W GLU 27": "OE1" <-> "OE2" Residue "W ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X GLU 27": "OE1" <-> "OE2" Residue "X ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 71060 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "B" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "C" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "D" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "E" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "F" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "G" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "H" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "I" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "J" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "K" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "L" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "M" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "N" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "O" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "P" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "Q" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "R" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "S" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "T" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "U" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "V" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "W" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "X" Number of atoms: 2799 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2759 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2758 Conformer: "C" Number of residues, atoms: 172, 2741 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2758 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "B" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "C" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "D" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "E" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "F" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "G" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "H" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "I" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 162 Classifications: {'water': 162} Link IDs: {None: 161} Chain: "J" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "K" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "L" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "M" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "N" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "O" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "P" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 162 Classifications: {'water': 162} Link IDs: {None: 161} Chain: "Q" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 162 Classifications: {'water': 162} Link IDs: {None: 161} Chain: "R" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "S" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "T" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "U" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "V" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "W" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 162 Classifications: {'water': 162} Link IDs: {None: 161} Chain: "X" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Residues with excluded nonbonded symmetry interactions: 56 residue: pdb=" N ASER A 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER A 113 " occ=0.30 residue: pdb=" N ASER B 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER B 113 " occ=0.30 residue: pdb=" N ASER C 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER C 113 " occ=0.30 residue: pdb=" N ASER D 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER D 113 " occ=0.30 residue: pdb=" N ASER E 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER E 113 " occ=0.30 residue: pdb=" N ASER F 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER F 113 " occ=0.30 residue: pdb=" N ASER G 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER G 113 " occ=0.30 residue: pdb=" N ASER H 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER H 113 " occ=0.30 residue: pdb=" N ASER I 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER I 113 " occ=0.30 residue: pdb=" N ASER J 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER J 113 " occ=0.30 residue: pdb=" N ASER K 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER K 113 " occ=0.30 residue: pdb=" N ASER L 113 " occ=0.55 ... (31 atoms not shown) pdb=" HG CSER L 113 " occ=0.30 ... (remaining 44 not shown) Time building chain proxies: 58.82, per 1000 atoms: 0.83 Number of scatterers: 71060 At special positions: 0 Unit cell: (134.48, 134.48, 134.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 24 29.99 Fe 6 26.01 S 192 16.00 O 10430 8.00 N 6048 7.00 C 21456 6.00 H 32904 1.00 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: 48.19 Conformation dependent library (CDL) restraints added in 13.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 202 " pdb="ZN ZN A 202 " - pdb=" ND1 HIS A 65 " pdb=" ZN B 202 " pdb="ZN ZN B 202 " - pdb=" ND1 HIS B 65 " pdb=" ZN C 202 " pdb="ZN ZN C 202 " - pdb=" ND1 HIS C 65 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" ND1 HIS D 65 " pdb=" ZN E 201 " pdb="ZN ZN E 201 " - pdb=" ND1 HIS E 65 " pdb=" ZN F 201 " pdb="ZN ZN F 201 " - pdb=" ND1 HIS F 65 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" ND1 HIS G 65 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" ND1 HIS H 65 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" ND1 HIS I 65 " pdb=" ZN J 201 " pdb="ZN ZN J 201 " - pdb=" ND1 HIS J 65 " pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" ND1 HIS K 65 " pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" ND1 HIS L 65 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" ND1 HIS M 65 " pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" ND1 HIS N 65 " pdb=" ZN O 201 " pdb="ZN ZN O 201 " - pdb=" ND1 HIS O 65 " pdb=" ZN P 201 " pdb="ZN ZN P 201 " - pdb=" ND1 HIS P 65 " pdb=" ZN Q 202 " pdb="ZN ZN Q 202 " - pdb=" ND1 HIS Q 65 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 65 " pdb=" ZN S 201 " pdb="ZN ZN S 201 " - pdb=" ND1 HIS S 65 " pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" ND1 HIS T 65 " pdb=" ZN U 201 " pdb="ZN ZN U 201 " - pdb=" ND1 HIS U 65 " pdb=" ZN V 201 " pdb="ZN ZN V 201 " - pdb=" ND1 HIS V 65 " pdb=" ZN W 201 " pdb="ZN ZN W 201 " - pdb=" ND1 HIS W 65 " pdb=" ZN X 201 " pdb="ZN ZN X 201 " - pdb=" ND1 HIS X 65 " 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8064 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 78.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.22 Creating SS restraints... Processing helix chain 'A' and resid 13 through 42 Processing helix chain 'A' and resid 48 through 76 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 42 Processing helix chain 'B' and resid 48 through 76 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 42 Processing helix chain 'C' and resid 48 through 76 Processing helix chain 'C' and resid 95 through 124 Processing helix chain 'C' and resid 126 through 137 Processing helix chain 'C' and resid 137 through 159 Processing helix chain 'C' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 42 Processing helix chain 'D' and resid 48 through 76 Processing helix chain 'D' and resid 95 through 124 Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 137 through 159 Processing helix chain 'D' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR D 168 " --> pdb=" O GLY D 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 42 Processing helix chain 'E' and resid 48 through 76 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR E 168 " --> pdb=" O GLY E 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 42 Processing helix chain 'F' and resid 48 through 76 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR F 168 " --> pdb=" O GLY F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 42 Processing helix chain 'G' and resid 48 through 76 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 137 through 159 Processing helix chain 'G' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR G 168 " --> pdb=" O GLY G 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 42 Processing helix chain 'H' and resid 48 through 76 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 137 through 159 Processing helix chain 'H' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR H 168 " --> pdb=" O GLY H 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 42 Processing helix chain 'I' and resid 48 through 76 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 Processing helix chain 'I' and resid 137 through 159 Processing helix chain 'I' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR I 168 " --> pdb=" O GLY I 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 42 Processing helix chain 'J' and resid 48 through 76 Processing helix chain 'J' and resid 95 through 124 Processing helix chain 'J' and resid 126 through 137 Processing helix chain 'J' and resid 137 through 159 Processing helix chain 'J' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR J 168 " --> pdb=" O GLY J 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 42 Processing helix chain 'K' and resid 48 through 76 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 137 through 159 Processing helix chain 'K' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR K 168 " --> pdb=" O GLY K 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 42 Processing helix chain 'L' and resid 48 through 76 Processing helix chain 'L' and resid 95 through 124 Processing helix chain 'L' and resid 126 through 137 Processing helix chain 'L' and resid 137 through 159 Processing helix chain 'L' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR L 168 " --> pdb=" O GLY L 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 42 Processing helix chain 'M' and resid 48 through 76 Processing helix chain 'M' and resid 95 through 124 Processing helix chain 'M' and resid 126 through 137 Processing helix chain 'M' and resid 137 through 159 Processing helix chain 'M' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR M 168 " --> pdb=" O GLY M 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 42 Processing helix chain 'N' and resid 48 through 76 Processing helix chain 'N' and resid 95 through 124 Processing helix chain 'N' and resid 126 through 137 Processing helix chain 'N' and resid 137 through 159 Processing helix chain 'N' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR N 168 " --> pdb=" O GLY N 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 42 Processing helix chain 'O' and resid 48 through 76 Processing helix chain 'O' and resid 95 through 124 Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 137 through 159 Processing helix chain 'O' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR O 168 " --> pdb=" O GLY O 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 42 Processing helix chain 'P' and resid 48 through 76 Processing helix chain 'P' and resid 95 through 124 Processing helix chain 'P' and resid 126 through 137 Processing helix chain 'P' and resid 137 through 159 Processing helix chain 'P' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR P 168 " --> pdb=" O GLY P 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 42 Processing helix chain 'Q' and resid 48 through 76 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 Processing helix chain 'Q' and resid 137 through 159 Processing helix chain 'Q' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR Q 168 " --> pdb=" O GLY Q 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 42 Processing helix chain 'R' and resid 48 through 76 Processing helix chain 'R' and resid 95 through 124 Processing helix chain 'R' and resid 126 through 137 Processing helix chain 'R' and resid 137 through 159 Processing helix chain 'R' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR R 168 " --> pdb=" O GLY R 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 42 Processing helix chain 'S' and resid 48 through 76 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 Processing helix chain 'S' and resid 137 through 159 Processing helix chain 'S' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR S 168 " --> pdb=" O GLY S 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 42 Processing helix chain 'T' and resid 48 through 76 Processing helix chain 'T' and resid 95 through 124 Processing helix chain 'T' and resid 126 through 137 Processing helix chain 'T' and resid 137 through 159 Processing helix chain 'T' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR T 168 " --> pdb=" O GLY T 164 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 42 Processing helix chain 'U' and resid 48 through 76 Processing helix chain 'U' and resid 95 through 124 Processing helix chain 'U' and resid 126 through 137 Processing helix chain 'U' and resid 137 through 159 Processing helix chain 'U' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR U 168 " --> pdb=" O GLY U 164 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 42 Processing helix chain 'V' and resid 48 through 76 Processing helix chain 'V' and resid 95 through 124 Processing helix chain 'V' and resid 126 through 137 Processing helix chain 'V' and resid 137 through 159 Processing helix chain 'V' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR V 168 " --> pdb=" O GLY V 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 42 Processing helix chain 'W' and resid 48 through 76 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 Processing helix chain 'W' and resid 137 through 159 Processing helix chain 'W' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR W 168 " --> pdb=" O GLY W 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 42 Processing helix chain 'X' and resid 48 through 76 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 Processing helix chain 'X' and resid 137 through 159 Processing helix chain 'X' and resid 164 through 174 removed outlier: 4.399A pdb=" N TYR X 168 " --> pdb=" O GLY X 164 " (cutoff:3.500A) 2664 hydrogen bonds defined for protein. 8040 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: 21.66 Time building geometry restraints manager: 50.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 32808 1.03 - 1.23: 2040 1.23 - 1.42: 13296 1.42 - 1.62: 19464 1.62 - 1.81: 312 Bond restraints: 67920 Sorted by residual: bond pdb=" CA ARG U 63 " pdb=" HA ARG U 63 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" CA ARG G 63 " pdb=" HA ARG G 63 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" CA ARG L 63 " pdb=" HA ARG L 63 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" CA ARG E 63 " pdb=" HA ARG E 63 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" CA ARG F 63 " pdb=" HA ARG F 63 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.58e+01 ... (remaining 67915 not shown) Histogram of bond angle deviations from ideal: 97.31 - 104.63: 528 104.63 - 111.94: 74376 111.94 - 119.26: 18312 119.26 - 126.57: 28512 126.57 - 133.88: 480 Bond angle restraints: 122208 Sorted by residual: angle pdb=" N ARG I 63 " pdb=" CA ARG I 63 " pdb=" C ARG I 63 " ideal model delta sigma weight residual 111.07 102.68 8.39 1.07e+00 8.73e-01 6.16e+01 angle pdb=" N ARG J 63 " pdb=" CA ARG J 63 " pdb=" C ARG J 63 " ideal model delta sigma weight residual 111.07 102.68 8.39 1.07e+00 8.73e-01 6.16e+01 angle pdb=" N ARG M 63 " pdb=" CA ARG M 63 " pdb=" C ARG M 63 " ideal model delta sigma weight residual 111.07 102.68 8.39 1.07e+00 8.73e-01 6.16e+01 angle pdb=" N ARG X 63 " pdb=" CA ARG X 63 " pdb=" C ARG X 63 " ideal model delta sigma weight residual 111.07 102.68 8.39 1.07e+00 8.73e-01 6.16e+01 angle pdb=" N ARG R 63 " pdb=" CA ARG R 63 " pdb=" C ARG R 63 " ideal model delta sigma weight residual 111.07 102.68 8.39 1.07e+00 8.73e-01 6.16e+01 ... (remaining 122203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 29808 17.50 - 34.99: 1440 34.99 - 52.48: 480 52.48 - 69.98: 360 69.98 - 87.47: 24 Dihedral angle restraints: 32112 sinusoidal: 17232 harmonic: 14880 Sorted by residual: dihedral pdb=" CA VAL Q 46 " pdb=" C VAL Q 46 " pdb=" N ALA Q 47 " pdb=" CA ALA Q 47 " ideal model delta harmonic sigma weight residual 180.00 162.90 17.10 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA VAL K 46 " pdb=" C VAL K 46 " pdb=" N ALA K 47 " pdb=" CA ALA K 47 " ideal model delta harmonic sigma weight residual 180.00 162.90 17.10 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA VAL P 46 " pdb=" C VAL P 46 " pdb=" N ALA P 47 " pdb=" CA ALA P 47 " ideal model delta harmonic sigma weight residual 180.00 162.90 17.10 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 32109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3168 0.047 - 0.093: 1128 0.093 - 0.140: 408 0.140 - 0.186: 120 0.186 - 0.232: 96 Chirality restraints: 4920 Sorted by residual: chirality pdb=" CA ASN P 50 " pdb=" N ASN P 50 " pdb=" C ASN P 50 " pdb=" CB ASN P 50 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ASN H 50 " pdb=" N ASN H 50 " pdb=" C ASN H 50 " pdb=" CB ASN H 50 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ASN B 50 " pdb=" N ASN B 50 " pdb=" C ASN B 50 " pdb=" CB ASN B 50 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 4917 not shown) Planarity restraints: 10344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN S 75 " 0.244 2.00e-02 2.50e+03 3.19e-01 1.53e+03 pdb=" CD GLN S 75 " 0.001 2.00e-02 2.50e+03 pdb=" OE1 GLN S 75 " -0.250 2.00e-02 2.50e+03 pdb=" NE2 GLN S 75 " 0.004 2.00e-02 2.50e+03 pdb="HE21 GLN S 75 " -0.495 2.00e-02 2.50e+03 pdb="HE22 GLN S 75 " 0.495 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN V 75 " -0.244 2.00e-02 2.50e+03 3.19e-01 1.53e+03 pdb=" CD GLN V 75 " -0.001 2.00e-02 2.50e+03 pdb=" OE1 GLN V 75 " 0.250 2.00e-02 2.50e+03 pdb=" NE2 GLN V 75 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN V 75 " 0.495 2.00e-02 2.50e+03 pdb="HE22 GLN V 75 " -0.495 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN F 75 " 0.244 2.00e-02 2.50e+03 3.19e-01 1.53e+03 pdb=" CD GLN F 75 " 0.001 2.00e-02 2.50e+03 pdb=" OE1 GLN F 75 " -0.250 2.00e-02 2.50e+03 pdb=" NE2 GLN F 75 " 0.004 2.00e-02 2.50e+03 pdb="HE21 GLN F 75 " -0.495 2.00e-02 2.50e+03 pdb="HE22 GLN F 75 " 0.495 2.00e-02 2.50e+03 ... (remaining 10341 not shown) Histogram of nonbonded interaction distances: 0.31 - 1.17: 168 1.17 - 2.03: 1776 2.03 - 2.88: 180624 2.88 - 3.74: 350652 3.74 - 4.60: 593820 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1127040 Sorted by model distance: nonbonded pdb=" NH2BARG O 63 " pdb=" NH2BARG V 63 " model vdw 0.312 3.100 nonbonded pdb=" NH2BARG E 63 " pdb=" NH2BARG U 63 " model vdw 0.312 3.100 nonbonded pdb=" NH2BARG H 63 " pdb=" NH2BARG S 63 " model vdw 0.312 3.100 nonbonded pdb=" NH2BARG F 63 " pdb=" NH2BARG Q 63 " model vdw 0.312 3.100 nonbonded pdb=" NH2BARG G 63 " pdb=" NH2BARG X 63 " model vdw 0.312 3.100 ... (remaining 1127035 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'B' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'C' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'D' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'E' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'F' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'G' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'H' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'I' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'J' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'K' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'L' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'M' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'N' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'O' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'P' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'Q' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'R' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'S' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'T' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'U' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'V' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'W' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) selection = (chain 'X' and (resid 5 through 62 or resid 64 through 112 or resid 114 through \ 176)) } 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=0.15 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.240 Extract box with map and model: 8.580 Check model and map are aligned: 0.770 Set scattering table: 0.500 Process input model: 234.600 Find NCS groups from input model: 2.990 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 258.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.088 35016 Z= 0.731 Angle : 1.356 8.395 47160 Z= 0.990 Chirality : 0.063 0.232 4920 Planarity : 0.010 0.046 6216 Dihedral : 12.210 87.470 13344 Min Nonbonded Distance : 0.312 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.29 % Allowed : 2.58 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.69 (0.12), residues: 4224 helix: 2.89 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.60 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.005 TRP F 93 HIS 0.013 0.005 HIS U 151 PHE 0.032 0.007 PHE R 41 TYR 0.080 0.007 TYR A 32 ARG 0.010 0.001 ARG P 9 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 984 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 936 time to evaluate : 4.367 Fit side-chains REVERT: A 100 MET cc_start: 0.9067 (mmt) cc_final: 0.8735 (mmt) REVERT: B 100 MET cc_start: 0.9067 (mmt) cc_final: 0.8735 (mmt) REVERT: C 100 MET cc_start: 0.9071 (mmt) cc_final: 0.8737 (mmt) REVERT: D 100 MET cc_start: 0.9067 (mmt) cc_final: 0.8741 (mmt) REVERT: E 100 MET cc_start: 0.9071 (mmt) cc_final: 0.8732 (mmt) REVERT: F 100 MET cc_start: 0.9073 (mmt) cc_final: 0.8735 (mmt) REVERT: G 100 MET cc_start: 0.9073 (mmt) cc_final: 0.8743 (mmt) REVERT: H 100 MET cc_start: 0.9067 (mmt) cc_final: 0.8735 (mmt) REVERT: I 100 MET cc_start: 0.9068 (mmt) cc_final: 0.8742 (mmt) REVERT: J 100 MET cc_start: 0.9073 (mmt) cc_final: 0.8736 (mmt) REVERT: K 100 MET cc_start: 0.9068 (mmt) cc_final: 0.8742 (mmt) REVERT: L 100 MET cc_start: 0.9073 (mmt) cc_final: 0.8743 (mmt) REVERT: M 100 MET cc_start: 0.9073 (mmt) cc_final: 0.8742 (mmt) REVERT: N 100 MET cc_start: 0.9071 (mmt) cc_final: 0.8737 (mmt) REVERT: O 100 MET cc_start: 0.9071 (mmt) cc_final: 0.8732 (mmt) REVERT: P 100 MET cc_start: 0.9064 (mmt) cc_final: 0.8738 (mmt) REVERT: Q 100 MET cc_start: 0.9064 (mmt) cc_final: 0.8738 (mmt) REVERT: R 100 MET cc_start: 0.9071 (mmt) cc_final: 0.8737 (mmt) REVERT: S 100 MET cc_start: 0.9071 (mmt) cc_final: 0.8732 (mmt) REVERT: T 100 MET cc_start: 0.9073 (mmt) cc_final: 0.8736 (mmt) REVERT: U 100 MET cc_start: 0.9067 (mmt) cc_final: 0.8735 (mmt) REVERT: V 100 MET cc_start: 0.9067 (mmt) cc_final: 0.8735 (mmt) REVERT: W 100 MET cc_start: 0.9064 (mmt) cc_final: 0.8738 (mmt) REVERT: X 100 MET cc_start: 0.9067 (mmt) cc_final: 0.8735 (mmt) outliers start: 48 outliers final: 0 residues processed: 984 average time/residue: 3.5351 time to fit residues: 4038.9630 Evaluate side-chains 744 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 744 time to evaluate : 4.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 0.9990 chunk 309 optimal weight: 0.7980 chunk 171 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 208 optimal weight: 0.9990 chunk 165 optimal weight: 7.9990 chunk 319 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 194 optimal weight: 0.9980 chunk 238 optimal weight: 0.8980 chunk 370 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN A 141 GLN B 83 GLN B 141 GLN C 83 GLN C 141 GLN D 83 GLN D 141 GLN E 83 GLN E 141 GLN F 83 GLN F 141 GLN G 83 GLN G 141 GLN H 83 GLN H 141 GLN I 83 GLN I 141 GLN J 83 GLN J 141 GLN K 83 GLN K 125 ASN K 141 GLN L 83 GLN L 141 GLN M 83 GLN M 141 GLN N 83 GLN N 141 GLN O 83 GLN O 141 GLN P 83 GLN P 141 GLN Q 83 GLN Q 141 GLN R 83 GLN R 141 GLN S 83 GLN S 141 GLN T 83 GLN T 141 GLN U 83 GLN U 141 GLN V 83 GLN V 125 ASN V 141 GLN W 83 GLN W 141 GLN X 83 GLN X 141 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 35016 Z= 0.153 Angle : 0.513 4.165 47160 Z= 0.281 Chirality : 0.032 0.125 4920 Planarity : 0.003 0.015 6216 Dihedral : 3.991 19.970 4632 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.22 (0.13), residues: 4224 helix: 4.05 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.69 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP F 93 HIS 0.005 0.001 HIS Q 128 PHE 0.007 0.001 PHE F 41 TYR 0.033 0.003 TYR F 32 ARG 0.002 0.000 ARG N 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 790 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 790 time to evaluate : 4.507 Fit side-chains REVERT: A 100 MET cc_start: 0.9114 (mmt) cc_final: 0.8897 (mmt) REVERT: B 100 MET cc_start: 0.9114 (mmt) cc_final: 0.8897 (mmt) REVERT: C 100 MET cc_start: 0.9119 (mmt) cc_final: 0.8900 (mmt) REVERT: D 100 MET cc_start: 0.9115 (mmt) cc_final: 0.8899 (mmt) REVERT: E 100 MET cc_start: 0.9119 (mmt) cc_final: 0.8895 (mmt) REVERT: F 100 MET cc_start: 0.9124 (mmt) cc_final: 0.8900 (mmt) REVERT: G 100 MET cc_start: 0.9119 (mmt) cc_final: 0.8898 (mmt) REVERT: H 100 MET cc_start: 0.9116 (mmt) cc_final: 0.8895 (mmt) REVERT: I 100 MET cc_start: 0.9115 (mmt) cc_final: 0.8900 (mmt) REVERT: J 100 MET cc_start: 0.9124 (mmt) cc_final: 0.8901 (mmt) REVERT: K 100 MET cc_start: 0.9115 (mmt) cc_final: 0.8901 (mmt) REVERT: L 100 MET cc_start: 0.9119 (mmt) cc_final: 0.8898 (mmt) REVERT: M 100 MET cc_start: 0.9119 (mmt) cc_final: 0.8898 (mmt) REVERT: N 100 MET cc_start: 0.9119 (mmt) cc_final: 0.8900 (mmt) REVERT: O 100 MET cc_start: 0.9119 (mmt) cc_final: 0.8895 (mmt) REVERT: P 100 MET cc_start: 0.9111 (mmt) cc_final: 0.8896 (mmt) REVERT: Q 100 MET cc_start: 0.9111 (mmt) cc_final: 0.8896 (mmt) REVERT: R 100 MET cc_start: 0.9119 (mmt) cc_final: 0.8899 (mmt) REVERT: S 100 MET cc_start: 0.9119 (mmt) cc_final: 0.8896 (mmt) REVERT: T 100 MET cc_start: 0.9124 (mmt) cc_final: 0.8901 (mmt) REVERT: U 100 MET cc_start: 0.9116 (mmt) cc_final: 0.8895 (mmt) REVERT: V 100 MET cc_start: 0.9116 (mmt) cc_final: 0.8895 (mmt) REVERT: W 100 MET cc_start: 0.9111 (mmt) cc_final: 0.8896 (mmt) REVERT: X 100 MET cc_start: 0.9114 (mmt) cc_final: 0.8897 (mmt) outliers start: 0 outliers final: 0 residues processed: 790 average time/residue: 4.0411 time to fit residues: 3642.0631 Evaluate side-chains 692 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 692 time to evaluate : 4.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 chunk 308 optimal weight: 9.9990 chunk 252 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 371 optimal weight: 9.9990 chunk 400 optimal weight: 10.0000 chunk 330 optimal weight: 9.9990 chunk 368 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 297 optimal weight: 9.9990 overall best weight: 7.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 141 GLN B 105 HIS B 141 GLN C 105 HIS C 141 GLN D 105 HIS D 141 GLN E 105 HIS E 141 GLN F 105 HIS F 141 GLN G 105 HIS G 141 GLN H 105 HIS H 141 GLN I 105 HIS I 141 GLN J 105 HIS J 141 GLN K 105 HIS K 141 GLN L 105 HIS L 141 GLN M 105 HIS M 141 GLN N 105 HIS N 141 GLN O 105 HIS O 141 GLN P 105 HIS P 141 GLN Q 105 HIS Q 141 GLN R 105 HIS R 141 GLN S 105 HIS S 141 GLN T 105 HIS T 141 GLN U 105 HIS U 141 GLN V 105 HIS V 141 GLN W 105 HIS W 141 GLN X 105 HIS X 141 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 35016 Z= 0.304 Angle : 0.659 5.269 47160 Z= 0.374 Chirality : 0.038 0.129 4920 Planarity : 0.005 0.032 6216 Dihedral : 4.155 18.819 4632 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.65 % Allowed : 9.01 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.25 (0.13), residues: 4224 helix: 3.28 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.77 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.004 TRP D 93 HIS 0.008 0.003 HIS L 57 PHE 0.025 0.004 PHE D 41 TYR 0.052 0.005 TYR J 32 ARG 0.002 0.001 ARG L 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 672 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 648 time to evaluate : 4.483 Fit side-chains REVERT: A 100 MET cc_start: 0.9134 (mmt) cc_final: 0.8718 (mmt) REVERT: B 100 MET cc_start: 0.9135 (mmt) cc_final: 0.8718 (mmt) REVERT: C 100 MET cc_start: 0.9139 (mmt) cc_final: 0.8721 (mmt) REVERT: D 100 MET cc_start: 0.9136 (mmt) cc_final: 0.8727 (mmt) REVERT: E 100 MET cc_start: 0.9138 (mmt) cc_final: 0.8715 (mmt) REVERT: F 100 MET cc_start: 0.9141 (mmt) cc_final: 0.8720 (mmt) REVERT: G 100 MET cc_start: 0.9141 (mmt) cc_final: 0.8726 (mmt) REVERT: H 100 MET cc_start: 0.9135 (mmt) cc_final: 0.8720 (mmt) REVERT: I 100 MET cc_start: 0.9138 (mmt) cc_final: 0.8728 (mmt) REVERT: J 100 MET cc_start: 0.9141 (mmt) cc_final: 0.8721 (mmt) REVERT: K 100 MET cc_start: 0.9137 (mmt) cc_final: 0.8728 (mmt) REVERT: L 100 MET cc_start: 0.9141 (mmt) cc_final: 0.8728 (mmt) REVERT: M 100 MET cc_start: 0.9141 (mmt) cc_final: 0.8728 (mmt) REVERT: N 100 MET cc_start: 0.9138 (mmt) cc_final: 0.8722 (mmt) REVERT: O 100 MET cc_start: 0.9138 (mmt) cc_final: 0.8714 (mmt) REVERT: P 100 MET cc_start: 0.9131 (mmt) cc_final: 0.8722 (mmt) REVERT: Q 100 MET cc_start: 0.9130 (mmt) cc_final: 0.8719 (mmt) REVERT: R 100 MET cc_start: 0.9138 (mmt) cc_final: 0.8721 (mmt) REVERT: S 100 MET cc_start: 0.9138 (mmt) cc_final: 0.8714 (mmt) REVERT: T 100 MET cc_start: 0.9141 (mmt) cc_final: 0.8720 (mmt) REVERT: U 100 MET cc_start: 0.9135 (mmt) cc_final: 0.8720 (mmt) REVERT: V 100 MET cc_start: 0.9135 (mmt) cc_final: 0.8720 (mmt) REVERT: W 100 MET cc_start: 0.9129 (mmt) cc_final: 0.8720 (mmt) REVERT: X 100 MET cc_start: 0.9135 (mmt) cc_final: 0.8718 (mmt) outliers start: 24 outliers final: 24 residues processed: 672 average time/residue: 3.8838 time to fit residues: 3033.8705 Evaluate side-chains 671 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 647 time to evaluate : 4.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain X residue 139 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 7.9990 chunk 279 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 chunk 249 optimal weight: 10.0000 chunk 372 optimal weight: 7.9990 chunk 394 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 353 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 125 ASN B 14 GLN B 125 ASN C 14 GLN C 125 ASN D 14 GLN D 125 ASN E 14 GLN E 125 ASN F 14 GLN F 125 ASN G 14 GLN G 125 ASN H 14 GLN H 125 ASN I 14 GLN I 125 ASN J 14 GLN J 125 ASN K 14 GLN K 125 ASN L 14 GLN L 125 ASN M 14 GLN M 125 ASN N 14 GLN N 125 ASN O 14 GLN O 125 ASN P 14 GLN P 125 ASN Q 14 GLN Q 125 ASN R 14 GLN R 125 ASN S 14 GLN S 125 ASN T 14 GLN T 125 ASN U 14 GLN U 125 ASN V 14 GLN V 125 ASN W 14 GLN W 125 ASN X 14 GLN X 125 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 35016 Z= 0.291 Angle : 0.649 5.298 47160 Z= 0.366 Chirality : 0.037 0.126 4920 Planarity : 0.004 0.030 6216 Dihedral : 4.145 18.850 4632 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.03 % Allowed : 9.65 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.03 (0.12), residues: 4224 helix: 3.15 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.61 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.004 TRP C 93 HIS 0.008 0.003 HIS H 57 PHE 0.025 0.004 PHE E 41 TYR 0.046 0.004 TYR C 32 ARG 0.002 0.001 ARG L 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 628 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 627 time to evaluate : 4.434 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 627 average time/residue: 3.8144 time to fit residues: 2750.5325 Evaluate side-chains 631 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 631 time to evaluate : 4.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 9.9990 chunk 223 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 293 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 chunk 336 optimal weight: 10.0000 chunk 272 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 0.9980 chunk 353 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 35016 Z= 0.217 Angle : 0.571 5.114 47160 Z= 0.321 Chirality : 0.034 0.123 4920 Planarity : 0.003 0.025 6216 Dihedral : 4.093 19.660 4632 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.65 % Allowed : 9.03 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.44 (0.13), residues: 4224 helix: 3.47 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.61 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP H 93 HIS 0.005 0.002 HIS F 60 PHE 0.017 0.003 PHE F 41 TYR 0.031 0.003 TYR W 32 ARG 0.001 0.000 ARG W 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 649 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 625 time to evaluate : 4.414 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 649 average time/residue: 3.6954 time to fit residues: 2770.5865 Evaluate side-chains 649 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 625 time to evaluate : 4.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain X residue 139 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 2.9990 chunk 355 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 231 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 394 optimal weight: 9.9990 chunk 327 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN B 125 ASN C 125 ASN D 125 ASN E 125 ASN G 125 ASN I 125 ASN J 125 ASN L 125 ASN M 125 ASN N 125 ASN O 125 ASN Q 125 ASN R 125 ASN T 125 ASN U 125 ASN W 125 ASN X 125 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 35016 Z= 0.264 Angle : 0.624 5.174 47160 Z= 0.350 Chirality : 0.036 0.123 4920 Planarity : 0.004 0.029 6216 Dihedral : 4.112 19.074 4632 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.65 % Allowed : 9.03 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.15 (0.13), residues: 4224 helix: 3.25 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.57 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.004 TRP F 93 HIS 0.007 0.002 HIS L 57 PHE 0.025 0.003 PHE U 41 TYR 0.033 0.004 TYR C 32 ARG 0.002 0.001 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 649 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 625 time to evaluate : 4.336 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 649 average time/residue: 3.6673 time to fit residues: 2750.5953 Evaluate side-chains 649 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 625 time to evaluate : 4.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain X residue 139 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 224 optimal weight: 8.9990 chunk 288 optimal weight: 7.9990 chunk 223 optimal weight: 4.9990 chunk 332 optimal weight: 7.9990 chunk 220 optimal weight: 10.0000 chunk 393 optimal weight: 8.9990 chunk 246 optimal weight: 7.9990 chunk 239 optimal weight: 9.9990 chunk 181 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN B 125 ASN C 125 ASN D 125 ASN E 125 ASN F 125 ASN G 125 ASN H 125 ASN I 125 ASN J 125 ASN K 125 ASN L 125 ASN M 125 ASN N 125 ASN O 125 ASN P 125 ASN Q 125 ASN R 125 ASN S 125 ASN T 125 ASN U 125 ASN V 125 ASN W 125 ASN X 125 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 35016 Z= 0.276 Angle : 0.624 5.214 47160 Z= 0.352 Chirality : 0.036 0.125 4920 Planarity : 0.004 0.030 6216 Dihedral : 4.119 18.931 4632 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.65 % Allowed : 9.03 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.12 (0.13), residues: 4224 helix: 3.23 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.56 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.004 TRP U 93 HIS 0.007 0.002 HIS L 57 PHE 0.022 0.003 PHE C 41 TYR 0.030 0.004 TYR C 32 ARG 0.002 0.001 ARG G 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 649 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 625 time to evaluate : 4.393 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 649 average time/residue: 3.6640 time to fit residues: 2748.5554 Evaluate side-chains 649 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 625 time to evaluate : 4.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain X residue 139 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 8.9990 chunk 157 optimal weight: 2.9990 chunk 234 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 250 optimal weight: 6.9990 chunk 267 optimal weight: 9.9990 chunk 194 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 309 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN B 125 ASN C 125 ASN D 125 ASN E 125 ASN F 125 ASN G 125 ASN H 125 ASN I 125 ASN J 125 ASN K 125 ASN L 125 ASN M 125 ASN N 125 ASN O 125 ASN P 125 ASN Q 125 ASN R 125 ASN S 125 ASN T 125 ASN U 125 ASN V 125 ASN W 125 ASN X 125 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 35016 Z= 0.239 Angle : 0.588 5.017 47160 Z= 0.331 Chirality : 0.035 0.123 4920 Planarity : 0.004 0.028 6216 Dihedral : 4.116 19.362 4632 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.65 % Allowed : 9.03 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.33 (0.13), residues: 4224 helix: 3.39 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.56 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.004 TRP C 93 HIS 0.005 0.002 HIS L 57 PHE 0.020 0.003 PHE R 41 TYR 0.025 0.003 TYR C 32 ARG 0.003 0.001 ARG N 22 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 650 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 626 time to evaluate : 4.458 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 650 average time/residue: 3.6692 time to fit residues: 2757.2014 Evaluate side-chains 649 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 625 time to evaluate : 4.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain X residue 139 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 10.0000 chunk 376 optimal weight: 9.9990 chunk 343 optimal weight: 10.0000 chunk 366 optimal weight: 7.9990 chunk 220 optimal weight: 7.9990 chunk 159 optimal weight: 10.0000 chunk 287 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 331 optimal weight: 0.9980 chunk 346 optimal weight: 6.9990 chunk 365 optimal weight: 0.7980 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN B 125 ASN C 125 ASN D 125 ASN E 125 ASN F 125 ASN G 125 ASN H 125 ASN I 125 ASN J 125 ASN K 125 ASN L 125 ASN M 125 ASN N 125 ASN O 125 ASN P 125 ASN Q 125 ASN R 125 ASN S 125 ASN T 125 ASN U 125 ASN V 125 ASN W 125 ASN X 125 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 35016 Z= 0.219 Angle : 0.570 4.999 47160 Z= 0.320 Chirality : 0.034 0.122 4920 Planarity : 0.003 0.026 6216 Dihedral : 4.090 19.742 4632 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.65 % Allowed : 9.03 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.50 (0.13), residues: 4224 helix: 3.52 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.59 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP P 93 HIS 0.005 0.002 HIS D 60 PHE 0.017 0.002 PHE V 41 TYR 0.023 0.003 TYR C 32 ARG 0.002 0.000 ARG G 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 648 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 624 time to evaluate : 4.473 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 648 average time/residue: 3.6581 time to fit residues: 2743.7138 Evaluate side-chains 647 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 623 time to evaluate : 4.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain X residue 139 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 9.9990 chunk 387 optimal weight: 2.9990 chunk 236 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 269 optimal weight: 10.0000 chunk 406 optimal weight: 2.9990 chunk 374 optimal weight: 10.0000 chunk 323 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 250 optimal weight: 4.9990 chunk 198 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN C 125 ASN K 125 ASN N 125 ASN R 125 ASN V 125 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 35016 Z= 0.200 Angle : 0.552 4.903 47160 Z= 0.309 Chirality : 0.034 0.122 4920 Planarity : 0.003 0.025 6216 Dihedral : 4.068 19.983 4632 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.65 % Allowed : 9.03 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.63 (0.13), residues: 4224 helix: 3.63 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.56 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP C 93 HIS 0.004 0.002 HIS K 60 PHE 0.016 0.002 PHE F 41 TYR 0.022 0.003 TYR X 32 ARG 0.002 0.000 ARG N 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Evaluate side-chains 645 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 621 time to evaluate : 5.407 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 645 average time/residue: 3.7390 time to fit residues: 2813.6643 Evaluate side-chains 645 residues out of total 3600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 621 time to evaluate : 4.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain U residue 139 SER Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain X residue 139 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 9.9990 chunk 344 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 298 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 324 optimal weight: 9.9990 chunk 135 optimal weight: 8.9990 chunk 332 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN B 125 ASN C 125 ASN D 125 ASN E 125 ASN F 125 ASN G 125 ASN H 125 ASN I 125 ASN J 125 ASN L 125 ASN M 125 ASN N 125 ASN O 125 ASN P 125 ASN Q 125 ASN R 125 ASN S 125 ASN T 125 ASN U 125 ASN W 125 ASN X 125 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.138314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.115000 restraints weight = 129816.197| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 0.62 r_work: 0.2945 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 1.98 restraints_weight: 0.2500 r_work: 0.2443 rms_B_bonded: 4.38 restraints_weight: 0.1250 r_work (final): 0.2443 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2401 r_free = 0.2401 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2400 r_free = 0.2400 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2400 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 35016 Z= 0.230 Angle : 0.586 5.133 47160 Z= 0.328 Chirality : 0.035 0.123 4920 Planarity : 0.004 0.025 6216 Dihedral : 4.075 19.482 4632 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.65 % Allowed : 9.03 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.46 (0.13), residues: 4224 helix: 3.48 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : 0.60 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP U 93 HIS 0.005 0.002 HIS T 57 PHE 0.020 0.003 PHE A 41 TYR 0.024 0.003 TYR A 32 ARG 0.002 0.000 ARG L 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 37765.97 seconds wall clock time: 647 minutes 15.33 seconds (38835.33 seconds total)