Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 24 14:03:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vd8_31910/08_2023/7vd8_31910.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vd8_31910/08_2023/7vd8_31910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vd8_31910/08_2023/7vd8_31910.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vd8_31910/08_2023/7vd8_31910.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vd8_31910/08_2023/7vd8_31910.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vd8_31910/08_2023/7vd8_31910.pdb" } resolution = 1.96 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= 0.615 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: 6 Type Number sf(0) Gaussians Zn 254 6.06 5 S 192 5.16 5 Na 75 4.78 5 C 22248 2.51 5 N 6096 2.21 5 O 9336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 42": "OD1" <-> "OD2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "B ASP 42": "OD1" <-> "OD2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "C ASP 42": "OD1" <-> "OD2" Residue "C GLU 140": "OE1" <-> "OE2" Residue "D ASP 42": "OD1" <-> "OD2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "F ASP 42": "OD1" <-> "OD2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G ASP 42": "OD1" <-> "OD2" Residue "G GLU 140": "OE1" <-> "OE2" Residue "H GLU 140": "OE1" <-> "OE2" Residue "I ASP 42": "OD1" <-> "OD2" Residue "I GLU 62": "OE1" <-> "OE2" Residue "I GLU 140": "OE1" <-> "OE2" Residue "J GLU 140": "OE1" <-> "OE2" Residue "K GLU 17": "OE1" <-> "OE2" Residue "K ASP 42": "OD1" <-> "OD2" Residue "L ASP 42": "OD1" <-> "OD2" Residue "L GLU 140": "OE1" <-> "OE2" Residue "M ASP 42": "OD1" <-> "OD2" Residue "M GLU 62": "OE1" <-> "OE2" Residue "M GLU 140": "OE1" <-> "OE2" Residue "N ASP 91": "OD1" <-> "OD2" Residue "N GLU 101": "OE1" <-> "OE2" Residue "O GLU 62": "OE1" <-> "OE2" Residue "O GLU 140": "OE1" <-> "OE2" Residue "P GLU 140": "OE1" <-> "OE2" Residue "Q ASP 42": "OD1" <-> "OD2" Residue "Q GLU 140": "OE1" <-> "OE2" Residue "R GLU 140": "OE1" <-> "OE2" Residue "S GLU 17": "OE1" <-> "OE2" Residue "S ASP 42": "OD1" <-> "OD2" Residue "S GLU 140": "OE1" <-> "OE2" Residue "T GLU 140": "OE1" <-> "OE2" Residue "U GLU 17": "OE1" <-> "OE2" Residue "U ASP 42": "OD1" <-> "OD2" Residue "U GLU 140": "OE1" <-> "OE2" Residue "V GLU 62": "OE1" <-> "OE2" Residue "V GLU 140": "OE1" <-> "OE2" Residue "W ASP 42": "OD1" <-> "OD2" Residue "W GLU 62": "OE1" <-> "OE2" Residue "W GLU 134": "OE1" <-> "OE2" Residue "W GLU 140": "OE1" <-> "OE2" Residue "X GLU 140": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 38201 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "B" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "C" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "D" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "E" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "F" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "G" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "H" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "I" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "J" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "K" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "L" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "M" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "N" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "O" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "P" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "Q" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "R" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "S" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "T" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "U" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "V" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "W" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "X" Number of atoms: 1475 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1389 Conformer: "C" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 1389 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Unusual residues: {' NA': 3, ' ZN': 13} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Unusual residues: {' NA': 3, ' ZN': 13} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Unusual residues: {' NA': 3, ' ZN': 13} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Unusual residues: {' NA': 3, ' ZN': 12} Classifications: {'undetermined': 15} Link IDs: {None: 14} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Unusual residues: {' NA': 4, ' ZN': 11} Classifications: {'undetermined': 15} Link IDs: {None: 14} Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 3, ' ZN': 11} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 4, ' ZN': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 3, ' ZN': 11} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Unusual residues: {' NA': 4, ' ZN': 12} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 3, ' ZN': 11} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "K" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Unusual residues: {' NA': 4, ' ZN': 11} Classifications: {'undetermined': 15} Link IDs: {None: 14} Chain: "L" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Unusual residues: {' NA': 4, ' ZN': 11} Classifications: {'undetermined': 15} Link IDs: {None: 14} Chain: "M" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 4, ' ZN': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "N" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' NA': 3, ' ZN': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "O" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Unusual residues: {' NA': 4, ' ZN': 11} Classifications: {'undetermined': 15} Link IDs: {None: 14} Chain: "P" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Unusual residues: {' NA': 3, ' ZN': 9} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "Q" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Unusual residues: {' NA': 3, ' ZN': 9} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "R" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' NA': 3, ' ZN': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "S" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' NA': 2, ' ZN': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "T" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' NA': 3, ' ZN': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "U" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' NA': 2, ' ZN': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "V" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Unusual residues: {' NA': 3, ' ZN': 9} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "W" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' NA': 2, ' ZN': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "X" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Unusual residues: {' NA': 2, ' ZN': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "B" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Chain: "C" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 105 Classifications: {'water': 105} Link IDs: {None: 104} Chain: "D" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "E" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "F" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Chain: "G" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "H" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 104 Classifications: {'water': 104} Link IDs: {None: 103} Chain: "I" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "J" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "K" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "L" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 105 Classifications: {'water': 105} Link IDs: {None: 104} Chain: "M" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 107 Classifications: {'water': 107} Link IDs: {None: 106} Chain: "N" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "O" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Chain: "P" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 101 Classifications: {'water': 101} Link IDs: {None: 100} Chain: "Q" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 98 Classifications: {'water': 98} Link IDs: {None: 97} Chain: "R" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 105 Classifications: {'water': 105} Link IDs: {None: 104} Chain: "S" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 104 Classifications: {'water': 104} Link IDs: {None: 103} Chain: "T" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 97 Classifications: {'water': 97} Link IDs: {None: 96} Chain: "U" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "V" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "W" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "X" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 99 Classifications: {'water': 99} Link IDs: {None: 98} Time building chain proxies: 48.06, per 1000 atoms: 1.26 Number of scatterers: 38201 At special positions: 0 Unit cell: (137.004, 137.004, 137.004, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 254 29.99 S 192 16.00 Na 75 11.00 O 9336 8.00 N 6096 7.00 C 22248 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.74 Conformation dependent library (CDL) restraints added in 13.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 201 " pdb="ZN ZN A 201 " - pdb=" NE2 HIS A 65 " pdb=" ZN A 214 " pdb="ZN ZN A 214 " - pdb=" NE2 HIS A 65 " pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" ND1 HIS B 65 " pdb=" ZN B 214 " pdb="ZN ZN B 214 " - pdb=" NE2 HIS B 65 " pdb=" ZN C 201 " pdb="ZN ZN C 201 " - pdb=" ND1 HIS C 65 " pdb=" ZN C 214 " pdb="ZN ZN C 214 " - pdb=" NE2 HIS C 65 " pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" NE2 HIS D 65 " pdb=" ZN D 214 " pdb="ZN ZN D 214 " - pdb=" NE2 HIS D 65 " pdb=" ZN E 202 " pdb="ZN ZN E 202 " - pdb=" ND1 HIS E 65 " pdb=" ZN E 214 " pdb="ZN ZN E 214 " - pdb=" NE2 HIS E 65 " pdb=" ZN F 207 " pdb="ZN ZN F 207 " - pdb=" ND1 HIS F 65 " pdb=" ZN F 213 " pdb="ZN ZN F 213 " - pdb=" NE2 HIS F 65 " pdb=" ZN G 203 " pdb="ZN ZN G 203 " - pdb=" ND1 HIS G 65 " pdb=" ZN G 214 " pdb="ZN ZN G 214 " - pdb=" NE2 HIS G 65 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" ND1 HIS H 65 " pdb=" ZN H 213 " pdb="ZN ZN H 213 " - pdb=" NE2 HIS H 65 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" ND1 HIS I 65 " pdb=" ZN I 214 " pdb="ZN ZN I 214 " - pdb=" NE2 HIS I 65 " pdb=" ZN J 208 " pdb="ZN ZN J 208 " - pdb=" NE2 HIS J 65 " pdb=" ZN J 213 " pdb="ZN ZN J 213 " - pdb=" NE2 HIS J 65 " pdb=" ZN K 203 " pdb="ZN ZN K 203 " - pdb=" NE2 HIS K 65 " pdb=" ZN K 214 " pdb="ZN ZN K 214 " - pdb=" NE2 HIS K 65 " pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" ND1 HIS L 65 " pdb=" ZN L 214 " pdb="ZN ZN L 214 " - pdb=" NE2 HIS L 65 " pdb=" ZN M 204 " pdb="ZN ZN M 204 " - pdb=" ND1 HIS M 65 " pdb=" ZN M 213 " pdb="ZN ZN M 213 " - pdb=" NE2 HIS M 65 " pdb=" ZN N 207 " pdb="ZN ZN N 207 " - pdb=" ND1 HIS N 65 " pdb=" ZN N 212 " pdb="ZN ZN N 212 " - pdb=" NE2 HIS N 65 " pdb=" ZN O 204 " pdb="ZN ZN O 204 " - pdb=" ND1 HIS O 65 " pdb=" ZN O 214 " pdb="ZN ZN O 214 " - pdb=" NE2 HIS O 65 " pdb=" ZN P 207 " pdb="ZN ZN P 207 " - pdb=" ND1 HIS P 65 " pdb=" ZN P 211 " pdb="ZN ZN P 211 " - pdb=" NE2 HIS P 65 " pdb=" ZN Q 208 " pdb="ZN ZN Q 208 " - pdb=" ND1 HIS Q 65 " pdb=" ZN Q 212 " pdb="ZN ZN Q 212 " - pdb=" NE2 HIS Q 65 " pdb=" ZN R 209 " pdb="ZN ZN R 209 " - pdb=" ND1 HIS R 65 " pdb=" ZN R 213 " pdb="ZN ZN R 213 " - pdb=" NE2 HIS R 65 " pdb=" ZN S 207 " pdb="ZN ZN S 207 " - pdb=" ND1 HIS S 65 " pdb=" ZN S 211 " pdb="ZN ZN S 211 " - pdb=" NE2 HIS S 65 " pdb=" ZN T 208 " pdb="ZN ZN T 208 " - pdb=" ND1 HIS T 65 " pdb=" ZN T 213 " pdb="ZN ZN T 213 " - pdb=" NE2 HIS T 65 " pdb=" ZN U 207 " pdb="ZN ZN U 207 " - pdb=" ND1 HIS U 65 " pdb=" ZN U 211 " pdb="ZN ZN U 211 " - pdb=" NE2 HIS U 65 " pdb=" ZN V 208 " pdb="ZN ZN V 208 " - pdb=" ND1 HIS V 65 " pdb=" ZN V 212 " pdb="ZN ZN V 212 " - pdb=" NE2 HIS V 65 " pdb=" ZN W 207 " pdb="ZN ZN W 207 " - pdb=" ND1 HIS W 65 " pdb=" ZN W 211 " pdb="ZN ZN W 211 " - pdb=" NE2 HIS W 65 " pdb=" ZN X 207 " pdb="ZN ZN X 207 " - pdb=" ND1 HIS X 65 " pdb=" ZN X 212 " pdb="ZN ZN X 212 " - pdb=" NE2 HIS X 65 " 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8496 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 79.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.34 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 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 163 through 174 2688 hydrogen bonds defined for protein. 8064 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: 13.27 Time building geometry restraints manager: 18.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11952 1.34 - 1.46: 5887 1.46 - 1.58: 17993 1.58 - 1.69: 0 1.69 - 1.81: 288 Bond restraints: 36120 Sorted by residual: bond pdb=" CB LYS E 86 " pdb=" CG LYS E 86 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.51e+00 bond pdb=" CB LYS N 86 " pdb=" CG LYS N 86 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.48e+00 bond pdb=" CB LYS S 86 " pdb=" CG LYS S 86 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.44e+00 bond pdb=" CB LYS U 86 " pdb=" CG LYS U 86 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.43e+00 bond pdb=" CB LYS A 86 " pdb=" CG LYS A 86 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.42e+00 ... (remaining 36115 not shown) Histogram of bond angle deviations from ideal: 100.62 - 107.29: 933 107.29 - 113.96: 20111 113.96 - 120.63: 15630 120.63 - 127.30: 11638 127.30 - 133.97: 360 Bond angle restraints: 48672 Sorted by residual: angle pdb=" C TRP C 93 " pdb=" N GLU C 94 " pdb=" CA GLU C 94 " ideal model delta sigma weight residual 121.54 127.21 -5.67 1.91e+00 2.74e-01 8.80e+00 angle pdb=" C TRP J 93 " pdb=" N GLU J 94 " pdb=" CA GLU J 94 " ideal model delta sigma weight residual 121.54 127.20 -5.66 1.91e+00 2.74e-01 8.77e+00 angle pdb=" C TRP L 93 " pdb=" N GLU L 94 " pdb=" CA GLU L 94 " ideal model delta sigma weight residual 121.54 127.19 -5.65 1.91e+00 2.74e-01 8.75e+00 angle pdb=" C TRP W 93 " pdb=" N GLU W 94 " pdb=" CA GLU W 94 " ideal model delta sigma weight residual 121.54 127.18 -5.64 1.91e+00 2.74e-01 8.72e+00 angle pdb=" C TRP T 93 " pdb=" N GLU T 94 " pdb=" CA GLU T 94 " ideal model delta sigma weight residual 121.54 127.16 -5.62 1.91e+00 2.74e-01 8.66e+00 ... (remaining 48667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 19766 17.54 - 35.08: 1910 35.08 - 52.63: 501 52.63 - 70.17: 182 70.17 - 87.71: 57 Dihedral angle restraints: 22416 sinusoidal: 9576 harmonic: 12840 Sorted by residual: dihedral pdb=" CA TRP I 93 " pdb=" C TRP I 93 " pdb=" N GLU I 94 " pdb=" CA GLU I 94 " ideal model delta harmonic sigma weight residual 180.00 159.26 20.74 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA TRP M 93 " pdb=" C TRP M 93 " pdb=" N GLU M 94 " pdb=" CA GLU M 94 " ideal model delta harmonic sigma weight residual 180.00 159.27 20.73 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA TRP Q 93 " pdb=" C TRP Q 93 " pdb=" N GLU Q 94 " pdb=" CA GLU Q 94 " ideal model delta harmonic sigma weight residual 180.00 159.29 20.71 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 22413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 3582 0.028 - 0.056: 977 0.056 - 0.084: 408 0.084 - 0.112: 169 0.112 - 0.140: 48 Chirality restraints: 5184 Sorted by residual: chirality pdb=" CA TYR L 39 " pdb=" N TYR L 39 " pdb=" C TYR L 39 " pdb=" CB TYR L 39 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA TYR R 39 " pdb=" N TYR R 39 " pdb=" C TYR R 39 " pdb=" CB TYR R 39 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA TYR P 39 " pdb=" N TYR P 39 " pdb=" C TYR P 39 " pdb=" CB TYR P 39 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 5181 not shown) Planarity restraints: 6360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG P 63 " -0.116 9.50e-02 1.11e+02 5.25e-02 2.32e+00 pdb=" NE ARG P 63 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG P 63 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG P 63 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG P 63 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG U 63 " -0.114 9.50e-02 1.11e+02 5.16e-02 2.22e+00 pdb=" NE ARG U 63 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG U 63 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG U 63 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG U 63 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Q 63 " 0.113 9.50e-02 1.11e+02 5.11e-02 2.14e+00 pdb=" NE ARG Q 63 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG Q 63 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG Q 63 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG Q 63 " -0.000 2.00e-02 2.50e+03 ... (remaining 6357 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 1689 2.59 - 3.17: 33253 3.17 - 3.75: 76200 3.75 - 4.32: 99860 4.32 - 4.90: 157022 Nonbonded interactions: 368024 Sorted by model distance: nonbonded pdb=" OD1 ASP G 91 " pdb="ZN ZN G 206 " model vdw 2.013 2.230 nonbonded pdb=" OD1 ASP P 91 " pdb="ZN ZN P 202 " model vdw 2.013 2.230 nonbonded pdb=" OD1 ASP N 91 " pdb="ZN ZN N 203 " model vdw 2.013 2.230 nonbonded pdb=" OD1 ASP E 91 " pdb="ZN ZN E 204 " model vdw 2.022 2.230 nonbonded pdb=" OD1 ASP R 91 " pdb="ZN ZN R 205 " model vdw 2.022 2.230 ... (remaining 368019 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 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'B' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'C' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'D' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'E' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'F' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'G' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'H' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'I' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'J' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'K' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'L' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'M' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'N' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'O' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'P' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'Q' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'R' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'S' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'T' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'U' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'V' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'W' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) selection = (chain 'X' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 211)) } 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=0.33 max=1.00 mean=0.96 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: 4.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 25.600 Check model and map are aligned: 0.560 Set scattering table: 0.310 Process input model: 143.340 Find NCS groups from input model: 3.120 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:13.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 190.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 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 : 0.002 0.037 36120 Z= 0.153 Angle : 0.537 6.649 48672 Z= 0.288 Chirality : 0.035 0.140 5184 Planarity : 0.004 0.053 6360 Dihedral : 16.174 87.708 13920 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 0.03 % 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: 5.39 (0.13), residues: 4080 helix: 4.13 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.76 (0.22), residues: 792 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1022 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1021 time to evaluate : 4.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 1021 average time/residue: 1.9854 time to fit residues: 2355.5354 Evaluate side-chains 975 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 975 time to evaluate : 4.140 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4190 ------------------------------------------------------------------------------- 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: 0.6980 chunk 309 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 208 optimal weight: 0.5980 chunk 165 optimal weight: 1.9990 chunk 319 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 370 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 60 HIS ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN B 13 HIS B 60 HIS B 141 GLN C 13 HIS C 60 HIS D 60 HIS ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 GLN E 13 HIS E 60 HIS E 141 GLN F 60 HIS F 141 GLN G 60 HIS G 105 HIS G 141 GLN H 60 HIS H 105 HIS I 13 HIS I 60 HIS I 141 GLN J 13 HIS J 60 HIS K 13 HIS K 60 HIS K 141 GLN L 13 HIS L 60 HIS L 141 GLN M 60 HIS M 105 HIS M 139 ASN N 13 HIS N 60 HIS N 141 GLN O 60 HIS O 141 GLN P 13 HIS P 105 HIS P 141 GLN Q 13 HIS Q 60 HIS Q 141 GLN R 13 HIS R 60 HIS R 141 GLN S 13 HIS S 60 HIS S 141 GLN T 13 HIS T 141 GLN U 13 HIS U 60 HIS ** U 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 141 GLN V 60 HIS V 141 GLN W 13 HIS ** W 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 141 GLN X 13 HIS X 141 GLN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.0654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 36120 Z= 0.200 Angle : 0.586 6.402 48672 Z= 0.317 Chirality : 0.037 0.142 5184 Planarity : 0.004 0.027 6360 Dihedral : 4.430 21.270 4536 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.63 % 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: 5.18 (0.13), residues: 4080 helix: 3.97 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.74 (0.22), residues: 792 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 983 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 958 time to evaluate : 4.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 21 residues processed: 958 average time/residue: 1.9288 time to fit residues: 2157.7937 Evaluate side-chains 945 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 924 time to evaluate : 4.051 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.4129 time to fit residues: 20.6092 ------------------------------------------------------------------------------- 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: 2.9990 chunk 114 optimal weight: 9.9990 chunk 308 optimal weight: 7.9990 chunk 252 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 371 optimal weight: 2.9990 chunk 400 optimal weight: 4.9990 chunk 330 optimal weight: 0.6980 chunk 368 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 297 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 60 HIS ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 HIS B 60 HIS ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 GLN C 13 HIS C 60 HIS D 60 HIS ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 HIS E 60 HIS E 141 GLN G 60 HIS ** G 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 HIS H 139 ASN H 141 GLN I 13 HIS I 60 HIS I 141 GLN J 13 HIS J 139 ASN J 141 GLN K 13 HIS K 60 HIS K 139 ASN L 13 HIS L 139 ASN M 60 HIS N 13 HIS N 60 HIS N 105 HIS ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 141 GLN O 60 HIS O 139 ASN O 141 GLN P 13 HIS ** P 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 13 HIS Q 141 GLN R 13 HIS R 139 ASN R 141 GLN S 13 HIS S 139 ASN T 13 HIS T 139 ASN T 141 GLN U 13 HIS W 13 HIS W 139 ASN X 13 HIS X 139 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 36120 Z= 0.248 Angle : 0.637 6.944 48672 Z= 0.347 Chirality : 0.039 0.148 5184 Planarity : 0.005 0.037 6360 Dihedral : 4.506 21.080 4536 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.28 % 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: 4.89 (0.13), residues: 4080 helix: 3.77 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.65 (0.22), residues: 792 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 943 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 932 time to evaluate : 4.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 932 average time/residue: 1.9257 time to fit residues: 2095.8257 Evaluate side-chains 927 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 917 time to evaluate : 4.073 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3438 time to fit residues: 11.9610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 4.9990 chunk 279 optimal weight: 1.9990 chunk 192 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 177 optimal weight: 0.5980 chunk 249 optimal weight: 1.9990 chunk 372 optimal weight: 0.9990 chunk 394 optimal weight: 5.9990 chunk 194 optimal weight: 0.8980 chunk 353 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 60 HIS A 141 GLN B 13 HIS B 60 HIS B 141 GLN C 13 HIS C 60 HIS C 141 GLN D 60 HIS ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 GLN E 13 HIS E 60 HIS E 105 HIS ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 GLN F 141 GLN G 60 HIS ** G 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 141 GLN H 60 HIS H 141 GLN I 13 HIS I 60 HIS I 141 GLN J 13 HIS J 141 GLN K 13 HIS K 60 HIS K 141 GLN L 13 HIS L 141 GLN M 60 HIS M 141 GLN N 13 HIS N 60 HIS N 105 HIS N 141 GLN O 60 HIS O 141 GLN P 13 HIS ** P 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 141 GLN Q 13 HIS Q 141 GLN R 13 HIS R 141 GLN S 13 HIS T 13 HIS T 141 GLN U 13 HIS U 141 GLN V 141 GLN W 13 HIS W 141 GLN X 13 HIS X 141 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.0610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 36120 Z= 0.175 Angle : 0.560 6.855 48672 Z= 0.301 Chirality : 0.036 0.142 5184 Planarity : 0.003 0.024 6360 Dihedral : 4.388 20.938 4536 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.33 % 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: 5.25 (0.13), residues: 4080 helix: 4.03 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.71 (0.22), residues: 792 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 939 time to evaluate : 4.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 939 average time/residue: 1.9456 time to fit residues: 2137.5749 Evaluate side-chains 920 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 909 time to evaluate : 3.770 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3296 time to fit residues: 11.9048 ------------------------------------------------------------------------------- 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: 1.9990 chunk 223 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 293 optimal weight: 0.5980 chunk 162 optimal weight: 9.9990 chunk 336 optimal weight: 0.5980 chunk 272 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 0.9980 chunk 353 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 60 HIS A 139 ASN A 141 GLN B 13 HIS B 60 HIS ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 GLN C 13 HIS C 60 HIS C 141 GLN D 60 HIS D 139 ASN D 141 GLN E 13 HIS E 60 HIS E 141 GLN F 141 GLN G 60 HIS ** G 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 141 GLN H 60 HIS H 141 GLN I 13 HIS I 60 HIS I 141 GLN J 13 HIS J 141 GLN K 13 HIS K 60 HIS K 141 GLN L 13 HIS L 141 GLN M 60 HIS M 105 HIS M 141 GLN N 13 HIS N 60 HIS ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 141 GLN O 60 HIS O 141 GLN P 13 HIS ** P 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 141 GLN Q 13 HIS Q 141 GLN R 13 HIS R 141 GLN S 13 HIS S 141 GLN T 13 HIS T 141 GLN U 13 HIS U 141 GLN W 13 HIS W 141 GLN X 13 HIS X 141 GLN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.0786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 36120 Z= 0.220 Angle : 0.610 6.583 48672 Z= 0.331 Chirality : 0.038 0.147 5184 Planarity : 0.004 0.032 6360 Dihedral : 4.477 21.058 4536 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.25 % 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: 5.01 (0.13), residues: 4080 helix: 3.85 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.69 (0.22), residues: 792 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 921 time to evaluate : 4.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 921 average time/residue: 1.9512 time to fit residues: 2113.6908 Evaluate side-chains 909 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 900 time to evaluate : 4.011 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3609 time to fit residues: 11.8056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 1.9990 chunk 355 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 231 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 394 optimal weight: 5.9990 chunk 327 optimal weight: 0.5980 chunk 182 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 60 HIS A 141 GLN B 13 HIS B 60 HIS ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 GLN C 13 HIS C 60 HIS C 141 GLN D 60 HIS D 141 GLN E 13 HIS E 60 HIS E 141 GLN F 141 GLN G 60 HIS ** G 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 141 GLN H 60 HIS H 105 HIS H 141 GLN I 13 HIS I 60 HIS I 141 GLN J 13 HIS J 141 GLN K 13 HIS K 60 HIS K 141 GLN L 13 HIS L 141 GLN M 60 HIS M 105 HIS M 141 GLN N 13 HIS N 60 HIS N 105 HIS ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 141 GLN O 60 HIS O 141 GLN P 13 HIS P 141 GLN Q 13 HIS Q 141 GLN R 13 HIS R 141 GLN S 13 HIS S 141 GLN T 13 HIS T 141 GLN U 13 HIS U 141 GLN V 141 GLN W 13 HIS W 141 GLN X 13 HIS X 141 GLN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.0632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 36120 Z= 0.173 Angle : 0.559 6.709 48672 Z= 0.301 Chirality : 0.036 0.141 5184 Planarity : 0.003 0.025 6360 Dihedral : 4.382 20.911 4536 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.10 % 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: 5.27 (0.13), residues: 4080 helix: 4.05 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.72 (0.22), residues: 792 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 920 time to evaluate : 4.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 920 average time/residue: 1.9175 time to fit residues: 2068.2799 Evaluate side-chains 913 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 910 time to evaluate : 4.262 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.9235 time to fit residues: 9.7482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 224 optimal weight: 0.9990 chunk 288 optimal weight: 5.9990 chunk 223 optimal weight: 0.5980 chunk 332 optimal weight: 10.0000 chunk 220 optimal weight: 4.9990 chunk 393 optimal weight: 7.9990 chunk 246 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 60 HIS A 141 GLN B 13 HIS B 60 HIS ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 HIS C 60 HIS C 139 ASN D 60 HIS E 13 HIS E 60 HIS E 105 HIS ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 GLN F 141 GLN G 60 HIS ** G 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 HIS H 105 HIS H 141 GLN I 13 HIS I 60 HIS I 141 GLN J 13 HIS J 141 GLN K 13 HIS K 60 HIS L 13 HIS L 141 GLN M 60 HIS M 105 HIS N 13 HIS N 60 HIS ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 60 HIS O 141 GLN P 13 HIS ** P 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 13 HIS R 13 HIS S 13 HIS T 13 HIS U 13 HIS U 139 ASN U 141 GLN W 13 HIS X 13 HIS X 141 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 36120 Z= 0.229 Angle : 0.621 6.672 48672 Z= 0.337 Chirality : 0.038 0.147 5184 Planarity : 0.004 0.034 6360 Dihedral : 4.492 21.048 4536 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.18 % 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: 4.97 (0.12), residues: 4080 helix: 3.82 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.69 (0.22), residues: 792 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 904 time to evaluate : 3.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 904 average time/residue: 1.9323 time to fit residues: 2049.8404 Evaluate side-chains 898 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 891 time to evaluate : 4.376 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3691 time to fit residues: 10.6837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 234 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 250 optimal weight: 0.5980 chunk 267 optimal weight: 8.9990 chunk 194 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 309 optimal weight: 9.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 60 HIS A 141 GLN B 13 HIS B 60 HIS ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 HIS C 60 HIS D 60 HIS E 13 HIS E 60 HIS ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 GLN G 60 HIS ** G 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 HIS H 105 HIS H 141 GLN I 13 HIS I 60 HIS I 141 GLN J 13 HIS J 141 GLN K 13 HIS K 60 HIS L 13 HIS M 60 HIS M 105 HIS N 13 HIS N 60 HIS ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 60 HIS O 141 GLN P 13 HIS ** P 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 13 HIS R 13 HIS S 13 HIS T 13 HIS U 13 HIS U 141 GLN W 13 HIS X 13 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 36120 Z= 0.258 Angle : 0.654 7.184 48672 Z= 0.356 Chirality : 0.039 0.150 5184 Planarity : 0.005 0.040 6360 Dihedral : 4.529 20.940 4536 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.15 % 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: 4.78 (0.12), residues: 4080 helix: 3.69 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.62 (0.22), residues: 792 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 889 time to evaluate : 4.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 889 average time/residue: 1.9548 time to fit residues: 2041.2288 Evaluate side-chains 893 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 888 time to evaluate : 4.122 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3579 time to fit residues: 8.8341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 3.9990 chunk 376 optimal weight: 6.9990 chunk 343 optimal weight: 8.9990 chunk 366 optimal weight: 3.9990 chunk 220 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 287 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 331 optimal weight: 7.9990 chunk 346 optimal weight: 0.5980 chunk 365 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 60 HIS B 13 HIS B 60 HIS ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 HIS C 60 HIS C 141 GLN D 60 HIS E 13 HIS E 60 HIS ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 GLN G 60 HIS ** G 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 HIS H 105 HIS I 13 HIS I 60 HIS I 141 GLN J 13 HIS K 13 HIS K 60 HIS L 13 HIS M 60 HIS M 105 HIS N 13 HIS N 60 HIS ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 141 GLN O 60 HIS P 13 HIS ** P 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 13 HIS Q 141 GLN R 13 HIS S 13 HIS T 13 HIS U 13 HIS U 141 GLN W 13 HIS X 13 HIS Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 36120 Z= 0.225 Angle : 0.621 7.115 48672 Z= 0.337 Chirality : 0.038 0.146 5184 Planarity : 0.004 0.030 6360 Dihedral : 4.493 20.883 4536 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.03 % 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: 4.95 (0.12), residues: 4080 helix: 3.81 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.68 (0.22), residues: 792 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 893 time to evaluate : 4.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 893 average time/residue: 1.9271 time to fit residues: 2023.0099 Evaluate side-chains 893 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 892 time to evaluate : 4.297 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3499 time to fit residues: 6.2804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 4.9990 chunk 387 optimal weight: 1.9990 chunk 236 optimal weight: 9.9990 chunk 183 optimal weight: 0.9980 chunk 269 optimal weight: 4.9990 chunk 406 optimal weight: 0.5980 chunk 374 optimal weight: 3.9990 chunk 323 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 250 optimal weight: 0.5980 chunk 198 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 60 HIS B 13 HIS B 60 HIS ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 HIS C 60 HIS C 141 GLN D 60 HIS E 13 HIS E 60 HIS ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 GLN G 60 HIS ** G 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 HIS H 105 HIS I 13 HIS I 60 HIS I 141 GLN J 13 HIS K 13 HIS K 60 HIS L 13 HIS M 60 HIS M 105 HIS N 13 HIS N 60 HIS ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 141 GLN O 60 HIS P 13 HIS Q 13 HIS Q 141 GLN R 13 HIS S 13 HIS S 141 GLN T 13 HIS U 13 HIS U 141 GLN W 13 HIS X 13 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.0763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 36120 Z= 0.200 Angle : 0.600 9.774 48672 Z= 0.324 Chirality : 0.037 0.144 5184 Planarity : 0.004 0.026 6360 Dihedral : 4.453 20.801 4536 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.08 % 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: 5.08 (0.13), residues: 4080 helix: 3.90 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.70 (0.22), residues: 792 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 896 time to evaluate : 4.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 896 average time/residue: 1.9351 time to fit residues: 2035.9034 Evaluate side-chains 897 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 894 time to evaluate : 3.944 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3497 time to fit residues: 7.1383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 6.9990 chunk 344 optimal weight: 0.5980 chunk 99 optimal weight: 4.9990 chunk 298 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 89 optimal weight: 0.1980 chunk 324 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 332 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 59 optimal weight: 0.1980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 60 HIS A 141 GLN B 13 HIS B 60 HIS ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 HIS C 60 HIS C 141 GLN D 60 HIS D 141 GLN E 13 HIS E 60 HIS E 141 GLN F 141 GLN G 60 HIS G 141 GLN H 60 HIS H 105 HIS H 141 GLN I 13 HIS I 60 HIS I 141 GLN J 13 HIS K 13 HIS K 60 HIS L 13 HIS M 60 HIS M 105 HIS M 141 GLN N 13 HIS N 60 HIS N 105 HIS ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 141 GLN O 60 HIS O 141 GLN P 13 HIS ** P 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 13 HIS Q 141 GLN R 13 HIS R 141 GLN S 13 HIS S 141 GLN T 13 HIS U 13 HIS U 141 GLN W 13 HIS W 141 GLN X 13 HIS X 141 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.189432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.150696 restraints weight = 685420.157| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 6.10 r_work: 0.2804 rms_B_bonded: 5.08 restraints_weight: 2.0000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.0553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 36120 Z= 0.149 Angle : 0.537 7.063 48672 Z= 0.285 Chirality : 0.035 0.141 5184 Planarity : 0.003 0.027 6360 Dihedral : 4.290 20.496 4536 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer Outliers : 0.00 % 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: 5.47 (0.13), residues: 4080 helix: 4.19 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.75 (0.22), residues: 792 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27089.27 seconds wall clock time: 478 minutes 20.69 seconds (28700.69 seconds total)