Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 24 17:30:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zg7_14705/08_2023/7zg7_14705.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zg7_14705/08_2023/7zg7_14705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zg7_14705/08_2023/7zg7_14705.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zg7_14705/08_2023/7zg7_14705.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zg7_14705/08_2023/7zg7_14705.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zg7_14705/08_2023/7zg7_14705.pdb" } resolution = 1.77 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 270 6.06 5 S 192 5.16 5 Na 112 4.78 5 C 22680 2.51 5 N 6264 2.21 5 O 9568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 39086 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 1501 Number of conformers: 4 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: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "B" Number of atoms: 1501 Number of conformers: 4 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: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "C" Number of atoms: 1501 Number of conformers: 4 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: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "D" Number of atoms: 1501 Number of conformers: 4 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: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "E" Number of atoms: 1501 Number of conformers: 4 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: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "F" Number of atoms: 1501 Number of conformers: 4 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: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "G" Number of atoms: 1501 Number of conformers: 4 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: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "H" Number of atoms: 1501 Number of conformers: 4 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: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "I" Number of atoms: 1501 Number of conformers: 4 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: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "J" Number of atoms: 1501 Number of conformers: 4 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: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "K" Number of atoms: 1501 Number of conformers: 4 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: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "L" Number of atoms: 1501 Number of conformers: 4 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: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "M" Number of atoms: 1501 Number of conformers: 4 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: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "N" Number of atoms: 1501 Number of conformers: 4 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: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "O" Number of atoms: 1501 Number of conformers: 4 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: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "P" Number of atoms: 1501 Number of conformers: 4 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: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "Q" Number of atoms: 1501 Number of conformers: 4 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: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "R" Number of atoms: 1501 Number of conformers: 4 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: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "S" Number of atoms: 1501 Number of conformers: 4 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: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "T" Number of atoms: 1501 Number of conformers: 4 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: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "U" Number of atoms: 1501 Number of conformers: 4 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: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "V" Number of atoms: 1501 Number of conformers: 4 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: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "W" Number of atoms: 1501 Number of conformers: 4 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: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "X" Number of atoms: 1501 Number of conformers: 4 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: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Unusual residues: {' NA': 5, ' ZN': 13} Classifications: {'undetermined': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Unusual residues: {' NA': 5, ' ZN': 13} Classifications: {'undetermined': 18} Link IDs: {None: 17} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Unusual residues: {' NA': 5, ' ZN': 13} Classifications: {'undetermined': 18} Link IDs: {None: 17} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Unusual residues: {' NA': 5, ' ZN': 13} Classifications: {'undetermined': 18} Link IDs: {None: 17} Chain: "E" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Unusual residues: {' NA': 5, ' ZN': 12} Classifications: {'undetermined': 17} Link IDs: {None: 16} Chain: "F" 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: "G" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Unusual residues: {' NA': 5, ' ZN': 11} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "H" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Unusual residues: {' NA': 5, ' ZN': 13} Classifications: {'undetermined': 18} Link IDs: {None: 17} Chain: "I" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Unusual residues: {' NA': 5, ' ZN': 12} Classifications: {'undetermined': 17} Link IDs: {None: 16} Chain: "J" 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: "K" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Unusual residues: {' NA': 5, ' ZN': 11} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "L" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Unusual residues: {' NA': 5, ' ZN': 12} Classifications: {'undetermined': 17} Link IDs: {None: 16} Chain: "M" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Unusual residues: {' NA': 5, ' ZN': 11} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "N" 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: "O" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Unusual residues: {' NA': 5, ' ZN': 11} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "P" 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: "Q" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Unusual residues: {' NA': 5, ' ZN': 11} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Unusual residues: {' NA': 5, ' ZN': 11} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "S" 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: "T" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Unusual residues: {' NA': 5, ' ZN': 11} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "U" 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: "V" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Unusual residues: {' NA': 5, ' ZN': 11} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "W" 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: "X" 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: "A" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "B" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "C" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "D" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "E" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "F" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "G" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "H" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "I" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "J" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} 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: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "M" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "N" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "O" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "P" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "Q" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "R" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "S" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "T" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "U" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "V" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "W" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "X" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Time building chain proxies: 61.64, per 1000 atoms: 1.58 Number of scatterers: 39086 At special positions: 0 Unit cell: (135.297, 136.202, 135.297, 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 270 29.99 S 192 16.00 Na 112 11.00 O 9568 8.00 N 6264 7.00 C 22680 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: 18.61 Conformation dependent library (CDL) restraints added in 18.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 203 " pdb="ZN ZN A 203 " - pdb=" ND1 HIS A 65 " pdb=" ZN B 203 " pdb="ZN ZN B 203 " - pdb=" ND1 HIS B 65 " pdb=" ZN C 203 " pdb="ZN ZN C 203 " - pdb=" ND1 HIS C 65 " pdb=" ZN D 203 " pdb="ZN ZN D 203 " - pdb=" ND1 HIS D 65 " pdb=" ZN E 202 " pdb="ZN ZN E 202 " - pdb=" ND1 HIS E 65 " pdb=" ZN F 208 " pdb="ZN ZN F 208 " - pdb=" ND1 HIS F 65 " pdb=" ZN G 206 " pdb="ZN ZN G 206 " - pdb=" ND1 HIS G 65 " pdb=" ZN H 203 " pdb="ZN ZN H 203 " - pdb=" ND1 HIS H 65 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" ND1 HIS I 65 " pdb=" ZN J 207 " pdb="ZN ZN J 207 " - pdb=" ND1 HIS J 65 " pdb=" ZN K 206 " pdb="ZN ZN K 206 " - pdb=" ND1 HIS K 65 " pdb=" ZN L 202 " pdb="ZN ZN L 202 " - pdb=" ND1 HIS L 65 " pdb=" ZN M 206 " pdb="ZN ZN M 206 " - pdb=" ND1 HIS M 65 " pdb=" ZN N 207 " pdb="ZN ZN N 207 " - pdb=" ND1 HIS N 65 " pdb=" ZN O 206 " pdb="ZN ZN O 206 " - pdb=" ND1 HIS O 65 " pdb=" ZN P 207 " pdb="ZN ZN P 207 " - pdb=" ND1 HIS P 65 " pdb=" ZN Q 211 " pdb="ZN ZN Q 211 " - pdb=" ND1 HIS Q 65 " pdb=" ZN R 211 " pdb="ZN ZN R 211 " - pdb=" ND1 HIS R 65 " pdb=" ZN S 209 " pdb="ZN ZN S 209 " - pdb=" ND1 HIS S 65 " pdb=" ZN T 211 " pdb="ZN ZN T 211 " - pdb=" ND1 HIS T 65 " pdb=" ZN U 209 " pdb="ZN ZN U 209 " - pdb=" ND1 HIS U 65 " pdb=" ZN V 211 " pdb="ZN ZN V 211 " - pdb=" ND1 HIS V 65 " pdb=" ZN W 209 " pdb="ZN ZN W 209 " - pdb=" ND1 HIS W 65 " pdb=" ZN X 209 " pdb="ZN ZN X 209 " - pdb=" ND1 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: 8736 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: 2.73 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: 11.83 Time building geometry restraints manager: 19.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12090 1.34 - 1.46: 5053 1.46 - 1.57: 19313 1.57 - 1.69: 0 1.69 - 1.81: 288 Bond restraints: 36744 Sorted by residual: bond pdb=" C SER A 163 " pdb=" O SER A 163 " ideal model delta sigma weight residual 1.235 1.248 -0.012 1.23e-02 6.61e+03 1.03e+00 bond pdb=" C SER R 163 " pdb=" O SER R 163 " ideal model delta sigma weight residual 1.235 1.248 -0.012 1.23e-02 6.61e+03 9.86e-01 bond pdb=" C SER H 163 " pdb=" O SER H 163 " ideal model delta sigma weight residual 1.235 1.248 -0.012 1.23e-02 6.61e+03 9.86e-01 bond pdb=" C SER B 163 " pdb=" O SER B 163 " ideal model delta sigma weight residual 1.235 1.248 -0.012 1.23e-02 6.61e+03 9.86e-01 bond pdb=" C SER F 163 " pdb=" O SER F 163 " ideal model delta sigma weight residual 1.235 1.248 -0.012 1.23e-02 6.61e+03 9.86e-01 ... (remaining 36739 not shown) Histogram of bond angle deviations from ideal: 99.71 - 106.55: 648 106.55 - 113.39: 20526 113.39 - 120.23: 13872 120.23 - 127.07: 14034 127.07 - 133.91: 384 Bond angle restraints: 49464 Sorted by residual: angle pdb=" C TRP V 93 " pdb=" N GLU V 94 " pdb=" CA GLU V 94 " ideal model delta sigma weight residual 121.54 128.14 -6.60 1.91e+00 2.74e-01 1.19e+01 angle pdb=" C TRP B 93 " pdb=" N GLU B 94 " pdb=" CA GLU B 94 " ideal model delta sigma weight residual 121.54 128.14 -6.60 1.91e+00 2.74e-01 1.19e+01 angle pdb=" C TRP N 93 " pdb=" N GLU N 94 " pdb=" CA GLU N 94 " ideal model delta sigma weight residual 121.54 128.11 -6.57 1.91e+00 2.74e-01 1.18e+01 angle pdb=" C TRP K 93 " pdb=" N GLU K 94 " pdb=" CA GLU K 94 " ideal model delta sigma weight residual 121.54 128.11 -6.57 1.91e+00 2.74e-01 1.18e+01 angle pdb=" C TRP W 93 " pdb=" N GLU W 94 " pdb=" CA GLU W 94 " ideal model delta sigma weight residual 121.54 128.11 -6.57 1.91e+00 2.74e-01 1.18e+01 ... (remaining 49459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.80: 20588 15.80 - 31.59: 1852 31.59 - 47.39: 432 47.39 - 63.18: 168 63.18 - 78.98: 72 Dihedral angle restraints: 23112 sinusoidal: 10032 harmonic: 13080 Sorted by residual: dihedral pdb=" CA VAL W 46 " pdb=" C VAL W 46 " pdb=" N ALA W 47 " pdb=" CA ALA W 47 " ideal model delta harmonic sigma weight residual 180.00 161.69 18.31 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA VAL T 46 " pdb=" C VAL T 46 " pdb=" N ALA T 47 " pdb=" CA ALA T 47 " ideal model delta harmonic sigma weight residual 180.00 161.71 18.29 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA VAL C 46 " pdb=" C VAL C 46 " pdb=" N ALA C 47 " pdb=" CA ALA C 47 " ideal model delta harmonic sigma weight residual 180.00 161.74 18.26 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 23109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2951 0.026 - 0.053: 1496 0.053 - 0.079: 457 0.079 - 0.105: 308 0.105 - 0.132: 92 Chirality restraints: 5304 Sorted by residual: chirality pdb=" CA ILE V 80 " pdb=" N ILE V 80 " pdb=" C ILE V 80 " pdb=" CB ILE V 80 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA ILE N 80 " pdb=" N ILE N 80 " pdb=" C ILE N 80 " pdb=" CB ILE N 80 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA ILE W 80 " pdb=" N ILE W 80 " pdb=" C ILE W 80 " pdb=" CB ILE W 80 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 5301 not shown) Planarity restraints: 6408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER J 163 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.68e+00 pdb=" C SER J 163 " -0.033 2.00e-02 2.50e+03 pdb=" O SER J 163 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY J 164 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 163 " -0.010 2.00e-02 2.50e+03 1.92e-02 3.68e+00 pdb=" C SER B 163 " 0.033 2.00e-02 2.50e+03 pdb=" O SER B 163 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY B 164 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER V 163 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" C SER V 163 " -0.033 2.00e-02 2.50e+03 pdb=" O SER V 163 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY V 164 " 0.011 2.00e-02 2.50e+03 ... (remaining 6405 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 1054 2.54 - 3.13: 33170 3.13 - 3.72: 74240 3.72 - 4.31: 109338 4.31 - 4.90: 168897 Nonbonded interactions: 386699 Sorted by model distance: nonbonded pdb=" OE1 GLU E 62 " pdb="ZN ZN E 202 " model vdw 1.952 2.230 nonbonded pdb=" OE1 GLU P 62 " pdb="ZN ZN P 207 " model vdw 1.952 2.230 nonbonded pdb=" OE1 GLU K 62 " pdb="ZN ZN K 206 " model vdw 1.952 2.230 nonbonded pdb=" OE1 GLU R 62 " pdb="ZN ZN R 211 " model vdw 1.952 2.230 nonbonded pdb=" OE1 GLU C 62 " pdb="ZN ZN C 203 " model vdw 1.952 2.230 ... (remaining 386694 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 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) 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 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) 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 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) 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 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) 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 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) 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 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) 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 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) 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 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) 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 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) 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 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) 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 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) 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 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) 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 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) 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 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) 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 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) 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 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) 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 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) 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 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) 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 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) 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 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) 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 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) 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 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) 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 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) 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 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 max=1.00 mean=0.95 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: 0.990 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: 9.270 Check model and map are aligned: 0.570 Set scattering table: 0.330 Process input model: 166.520 Find NCS groups from input model: 3.140 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 193.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 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 : 0.004 0.027 36744 Z= 0.246 Angle : 0.740 6.596 49464 Z= 0.409 Chirality : 0.040 0.132 5304 Planarity : 0.005 0.030 6408 Dihedral : 14.441 78.980 14376 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % 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: 3.49 (0.13), residues: 4080 helix: 2.61 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.12 (0.25), residues: 816 *********************** 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 557 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 557 time to evaluate : 4.301 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 557 average time/residue: 2.0689 time to fit residues: 1339.3147 Evaluate side-chains 487 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 487 time to evaluate : 4.860 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.9399 ------------------------------------------------------------------------------- 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: 10.0000 chunk 309 optimal weight: 10.0000 chunk 171 optimal weight: 30.0000 chunk 105 optimal weight: 7.9990 chunk 208 optimal weight: 20.0000 chunk 165 optimal weight: 7.9990 chunk 319 optimal weight: 20.0000 chunk 123 optimal weight: 0.4980 chunk 194 optimal weight: 10.0000 chunk 238 optimal weight: 6.9990 chunk 370 optimal weight: 20.0000 overall best weight: 6.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.0609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 36744 Z= 0.192 Angle : 0.642 6.497 49464 Z= 0.349 Chirality : 0.038 0.141 5304 Planarity : 0.005 0.038 6408 Dihedral : 4.445 18.169 4560 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 0.37 % 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: 4.65 (0.13), residues: 4080 helix: 3.47 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.24 (0.27), 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 527 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 512 time to evaluate : 4.740 Fit side-chains outliers start: 15 outliers final: 0 residues processed: 527 average time/residue: 1.9753 time to fit residues: 1221.3902 Evaluate side-chains 486 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 486 time to evaluate : 4.215 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3412 ------------------------------------------------------------------------------- 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: 40.0000 chunk 114 optimal weight: 5.9990 chunk 308 optimal weight: 50.0000 chunk 252 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 371 optimal weight: 9.9990 chunk 400 optimal weight: 40.0000 chunk 330 optimal weight: 7.9990 chunk 368 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 297 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 136 HIS B 60 HIS B 136 HIS C 60 HIS C 136 HIS D 60 HIS D 136 HIS E 60 HIS E 136 HIS F 60 HIS F 136 HIS G 60 HIS G 136 HIS H 60 HIS H 136 HIS I 60 HIS I 136 HIS J 60 HIS J 136 HIS K 60 HIS K 136 HIS L 60 HIS L 136 HIS M 60 HIS M 136 HIS N 60 HIS N 136 HIS O 60 HIS O 136 HIS P 60 HIS P 136 HIS Q 60 HIS Q 136 HIS R 60 HIS R 136 HIS S 60 HIS S 136 HIS T 60 HIS T 136 HIS U 60 HIS U 136 HIS V 60 HIS V 136 HIS W 60 HIS W 136 HIS X 60 HIS X 136 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.0785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 36744 Z= 0.183 Angle : 0.624 6.776 49464 Z= 0.338 Chirality : 0.037 0.147 5304 Planarity : 0.004 0.025 6408 Dihedral : 4.402 18.297 4560 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 0.37 % 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: 4.96 (0.13), residues: 4080 helix: 3.73 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.14 (0.28), 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 519 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 504 time to evaluate : 3.995 Fit side-chains outliers start: 15 outliers final: 0 residues processed: 519 average time/residue: 1.9179 time to fit residues: 1169.5513 Evaluate side-chains 456 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 456 time to evaluate : 4.208 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4413 ------------------------------------------------------------------------------- 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: 30.0000 chunk 279 optimal weight: 6.9990 chunk 192 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 177 optimal weight: 20.0000 chunk 249 optimal weight: 30.0000 chunk 372 optimal weight: 20.0000 chunk 394 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 353 optimal weight: 10.0000 chunk 106 optimal weight: 20.0000 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 136 HIS B 60 HIS B 136 HIS C 60 HIS D 60 HIS E 60 HIS F 60 HIS G 60 HIS H 60 HIS I 60 HIS I 136 HIS J 60 HIS J 136 HIS K 60 HIS L 60 HIS L 136 HIS M 60 HIS N 60 HIS O 60 HIS P 60 HIS Q 60 HIS R 60 HIS S 60 HIS T 60 HIS U 60 HIS U 136 HIS V 60 HIS V 136 HIS W 60 HIS X 60 HIS X 136 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.0806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 36744 Z= 0.182 Angle : 0.622 6.700 49464 Z= 0.337 Chirality : 0.037 0.149 5304 Planarity : 0.004 0.025 6408 Dihedral : 4.381 18.396 4560 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 0.37 % 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: 3.75 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.18 (0.28), 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 495 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 480 time to evaluate : 4.356 Fit side-chains outliers start: 15 outliers final: 15 residues processed: 495 average time/residue: 1.9337 time to fit residues: 1128.9330 Evaluate side-chains 471 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 456 time to evaluate : 4.464 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 15 residues processed: 0 time to fit residues: 5.9128 ------------------------------------------------------------------------------- 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: 6.9990 chunk 223 optimal weight: 50.0000 chunk 5 optimal weight: 1.9990 chunk 293 optimal weight: 10.0000 chunk 162 optimal weight: 30.0000 chunk 336 optimal weight: 10.0000 chunk 272 optimal weight: 30.0000 chunk 0 optimal weight: 50.0000 chunk 201 optimal weight: 5.9990 chunk 353 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 overall best weight: 5.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 136 HIS B 60 HIS B 136 HIS C 60 HIS C 136 HIS D 60 HIS D 136 HIS E 60 HIS E 136 HIS F 60 HIS F 136 HIS G 60 HIS G 136 HIS H 60 HIS H 136 HIS I 60 HIS I 136 HIS J 60 HIS J 136 HIS K 60 HIS K 136 HIS L 60 HIS L 136 HIS M 60 HIS M 136 HIS N 60 HIS N 136 HIS O 60 HIS O 136 HIS P 60 HIS P 136 HIS Q 60 HIS Q 136 HIS R 60 HIS R 136 HIS S 60 HIS S 136 HIS T 60 HIS T 136 HIS U 60 HIS U 136 HIS V 60 HIS V 136 HIS W 60 HIS W 136 HIS X 60 HIS X 136 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 36744 Z= 0.179 Angle : 0.617 6.718 49464 Z= 0.334 Chirality : 0.037 0.149 5304 Planarity : 0.004 0.023 6408 Dihedral : 4.382 18.396 4560 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 0.37 % 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: 5.04 (0.13), residues: 4080 helix: 3.78 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.17 (0.28), 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 495 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 480 time to evaluate : 4.406 Fit side-chains outliers start: 15 outliers final: 15 residues processed: 495 average time/residue: 1.9158 time to fit residues: 1118.6915 Evaluate side-chains 471 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 456 time to evaluate : 4.257 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 15 residues processed: 0 time to fit residues: 5.3045 ------------------------------------------------------------------------------- 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: 20.0000 chunk 355 optimal weight: 20.0000 chunk 77 optimal weight: 30.0000 chunk 231 optimal weight: 40.0000 chunk 97 optimal weight: 5.9990 chunk 394 optimal weight: 3.9990 chunk 327 optimal weight: 8.9990 chunk 182 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 136 HIS B 60 HIS B 136 HIS C 60 HIS C 136 HIS D 60 HIS D 136 HIS E 60 HIS E 136 HIS F 60 HIS F 136 HIS G 60 HIS G 136 HIS H 60 HIS H 136 HIS I 60 HIS I 136 HIS J 60 HIS J 136 HIS K 60 HIS K 136 HIS L 60 HIS L 136 HIS M 60 HIS M 136 HIS N 60 HIS N 136 HIS O 60 HIS O 136 HIS P 60 HIS P 136 HIS Q 60 HIS Q 136 HIS R 60 HIS R 136 HIS S 60 HIS S 136 HIS T 60 HIS T 136 HIS U 60 HIS U 136 HIS V 60 HIS V 136 HIS W 60 HIS W 136 HIS X 60 HIS X 136 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 36744 Z= 0.198 Angle : 0.644 6.777 49464 Z= 0.348 Chirality : 0.038 0.150 5304 Planarity : 0.004 0.024 6408 Dihedral : 4.403 18.230 4560 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 0.37 % 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: 4.96 (0.13), residues: 4080 helix: 3.72 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.17 (0.28), 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 495 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 480 time to evaluate : 4.256 Fit side-chains outliers start: 15 outliers final: 15 residues processed: 495 average time/residue: 1.9090 time to fit residues: 1114.7493 Evaluate side-chains 471 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 456 time to evaluate : 4.335 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 15 residues processed: 0 time to fit residues: 5.5327 ------------------------------------------------------------------------------- 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: 9.9990 chunk 44 optimal weight: 20.0000 chunk 224 optimal weight: 9.9990 chunk 288 optimal weight: 7.9990 chunk 223 optimal weight: 20.0000 chunk 332 optimal weight: 20.0000 chunk 220 optimal weight: 7.9990 chunk 393 optimal weight: 50.0000 chunk 246 optimal weight: 7.9990 chunk 239 optimal weight: 40.0000 chunk 181 optimal weight: 20.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 136 HIS B 60 HIS B 136 HIS C 60 HIS C 136 HIS D 60 HIS D 136 HIS E 60 HIS E 136 HIS F 60 HIS F 136 HIS G 60 HIS G 136 HIS H 60 HIS H 136 HIS I 60 HIS I 136 HIS J 60 HIS J 136 HIS K 60 HIS K 136 HIS L 60 HIS L 136 HIS M 60 HIS M 136 HIS N 60 HIS N 136 HIS O 60 HIS O 136 HIS P 60 HIS P 136 HIS Q 60 HIS Q 136 HIS R 60 HIS R 136 HIS S 60 HIS S 136 HIS T 60 HIS T 136 HIS U 60 HIS U 136 HIS V 60 HIS V 136 HIS W 60 HIS W 136 HIS X 60 HIS X 136 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 36744 Z= 0.222 Angle : 0.675 6.973 49464 Z= 0.366 Chirality : 0.039 0.152 5304 Planarity : 0.005 0.025 6408 Dihedral : 4.424 17.867 4560 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 0.37 % 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: 4.84 (0.13), residues: 4080 helix: 3.63 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.16 (0.28), 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 495 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 480 time to evaluate : 4.434 Fit side-chains outliers start: 15 outliers final: 15 residues processed: 495 average time/residue: 1.9516 time to fit residues: 1142.0130 Evaluate side-chains 471 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 456 time to evaluate : 4.256 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 15 residues processed: 0 time to fit residues: 5.4186 ------------------------------------------------------------------------------- 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: 0.7980 chunk 157 optimal weight: 5.9990 chunk 234 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 76 optimal weight: 8.9990 chunk 250 optimal weight: 5.9990 chunk 267 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 309 optimal weight: 10.0000 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 136 HIS B 60 HIS B 136 HIS C 60 HIS C 136 HIS D 60 HIS D 136 HIS E 60 HIS E 136 HIS F 60 HIS F 136 HIS G 60 HIS G 136 HIS H 60 HIS H 136 HIS I 60 HIS I 136 HIS J 60 HIS J 136 HIS K 60 HIS K 136 HIS L 60 HIS L 136 HIS M 60 HIS M 136 HIS N 60 HIS N 136 HIS O 60 HIS O 136 HIS P 60 HIS P 136 HIS Q 60 HIS Q 136 HIS R 60 HIS R 136 HIS S 60 HIS S 136 HIS T 60 HIS T 136 HIS U 60 HIS U 136 HIS V 60 HIS V 136 HIS W 60 HIS W 136 HIS X 60 HIS X 136 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 36744 Z= 0.181 Angle : 0.627 7.009 49464 Z= 0.338 Chirality : 0.037 0.151 5304 Planarity : 0.004 0.019 6408 Dihedral : 4.392 17.962 4560 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 0.37 % 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: 5.03 (0.13), residues: 4080 helix: 3.78 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.15 (0.28), 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 495 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 480 time to evaluate : 4.471 Fit side-chains outliers start: 15 outliers final: 15 residues processed: 495 average time/residue: 1.9086 time to fit residues: 1114.1110 Evaluate side-chains 471 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 456 time to evaluate : 4.198 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 15 residues processed: 0 time to fit residues: 5.4298 ------------------------------------------------------------------------------- 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: 30.0000 chunk 376 optimal weight: 50.0000 chunk 343 optimal weight: 7.9990 chunk 366 optimal weight: 20.0000 chunk 220 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 chunk 287 optimal weight: 20.0000 chunk 112 optimal weight: 40.0000 chunk 331 optimal weight: 5.9990 chunk 346 optimal weight: 10.0000 chunk 365 optimal weight: 7.9990 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 136 HIS B 60 HIS B 136 HIS C 60 HIS D 60 HIS D 136 HIS E 60 HIS F 60 HIS G 60 HIS G 136 HIS H 60 HIS I 60 HIS I 136 HIS J 60 HIS J 136 HIS K 60 HIS L 60 HIS L 136 HIS M 60 HIS N 60 HIS N 136 HIS O 60 HIS P 60 HIS Q 60 HIS R 60 HIS S 60 HIS T 60 HIS U 60 HIS U 136 HIS V 60 HIS V 136 HIS W 60 HIS W 136 HIS X 60 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 36744 Z= 0.206 Angle : 0.661 7.078 49464 Z= 0.357 Chirality : 0.038 0.151 5304 Planarity : 0.004 0.023 6408 Dihedral : 4.413 17.937 4560 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 0.37 % 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: 3.67 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.16 (0.28), 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 495 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 480 time to evaluate : 4.184 Fit side-chains outliers start: 15 outliers final: 15 residues processed: 495 average time/residue: 1.9859 time to fit residues: 1158.5685 Evaluate side-chains 471 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 456 time to evaluate : 4.378 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 15 residues processed: 0 time to fit residues: 6.4219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.9102 > 50: distance: 56 - 76: 17.954 distance: 61 - 84: 21.187 distance: 66 - 92: 12.278 distance: 71 - 76: 19.538 distance: 72 - 110: 25.470 distance: 76 - 77: 4.904 distance: 77 - 78: 16.449 distance: 77 - 80: 22.470 distance: 78 - 79: 23.610 distance: 78 - 84: 8.233 distance: 79 - 119: 26.357 distance: 80 - 81: 40.733 distance: 81 - 82: 21.807 distance: 81 - 83: 21.110 distance: 84 - 85: 12.547 distance: 85 - 86: 42.172 distance: 85 - 88: 33.519 distance: 86 - 87: 13.332 distance: 86 - 92: 17.062 distance: 87 - 127: 17.232 distance: 88 - 89: 18.238 distance: 89 - 90: 30.344 distance: 89 - 91: 23.186 distance: 92 - 93: 20.456 distance: 93 - 94: 25.282 distance: 93 - 96: 26.272 distance: 93 - 103: 13.333 distance: 94 - 95: 26.561 distance: 94 - 110: 38.375 distance: 96 - 97: 13.778 distance: 97 - 98: 10.016 distance: 98 - 99: 15.931 distance: 99 - 100: 10.271 distance: 100 - 101: 26.215 distance: 100 - 102: 25.879 distance: 103 - 104: 12.499 distance: 104 - 105: 11.925 distance: 105 - 106: 18.117 distance: 106 - 107: 12.757 distance: 107 - 108: 15.227 distance: 107 - 109: 28.731 distance: 110 - 111: 27.467 distance: 111 - 112: 30.738 distance: 111 - 114: 31.942 distance: 112 - 113: 27.777 distance: 112 - 119: 21.047 distance: 114 - 115: 46.320 distance: 115 - 116: 23.744 distance: 116 - 117: 16.693 distance: 117 - 118: 45.494 distance: 119 - 120: 29.322 distance: 120 - 121: 18.939 distance: 120 - 123: 33.118 distance: 121 - 122: 9.040 distance: 121 - 127: 17.912 distance: 123 - 124: 33.538 distance: 124 - 125: 15.492 distance: 125 - 126: 40.166 distance: 127 - 128: 31.665 distance: 128 - 129: 8.081 distance: 129 - 130: 38.841 distance: 129 - 131: 18.002 distance: 131 - 132: 32.696 distance: 132 - 133: 25.421 distance: 132 - 135: 30.763 distance: 133 - 134: 22.623 distance: 133 - 136: 42.291 distance: 136 - 137: 19.497 distance: 136 - 142: 30.626 distance: 137 - 138: 36.176 distance: 137 - 140: 12.035 distance: 138 - 139: 8.966 distance: 138 - 143: 30.471 distance: 140 - 141: 10.573 distance: 141 - 142: 41.194 distance: 143 - 144: 31.800 distance: 144 - 145: 5.733 distance: 144 - 147: 33.153 distance: 144 - 152: 34.680 distance: 144 - 157: 7.526 distance: 145 - 146: 28.453 distance: 145 - 162: 34.940 distance: 147 - 148: 13.989 distance: 148 - 149: 6.594 distance: 149 - 150: 17.121 distance: 149 - 151: 32.424 distance: 152 - 153: 30.500 distance: 153 - 154: 20.779 distance: 154 - 155: 30.747 distance: 154 - 156: 12.994 distance: 157 - 158: 44.386 distance: 158 - 159: 27.422 distance: 159 - 160: 30.428 distance: 159 - 161: 19.319 distance: 162 - 163: 35.153 distance: 163 - 164: 10.871 distance: 163 - 166: 18.940 distance: 164 - 165: 23.875 distance: 164 - 168: 28.799 distance: 165 - 183: 16.935 distance: 166 - 167: 37.100