Starting phenix.real_space_refine (version: dev) on Tue May 17 09:33:10 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3w_22658/05_2022/7k3w_22658.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3w_22658/05_2022/7k3w_22658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3w_22658/05_2022/7k3w_22658.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3w_22658/05_2022/7k3w_22658.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3w_22658/05_2022/7k3w_22658.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3w_22658/05_2022/7k3w_22658.pdb" } resolution = 1.36 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.019 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 Convert atoms to be neutral 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 168, 'PCIS': 1} 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: 67.03, per 1000 atoms: 1.71 Number of scatterers: 39086 At special positions: 0 Unit cell: (136.042, 136.042, 136.042, 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: 18.18 Conformation dependent library (CDL) restraints added in 18.6 seconds Dynamic metal coordination Zn2+ tetrahedral 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: 0.89 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: 12.35 Time building geometry restraints manager: 19.07 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: 12072 1.34 - 1.46: 7632 1.46 - 1.58: 16752 1.58 - 1.70: 0 1.70 - 1.82: 288 Bond restraints: 36744 Sorted by residual: bond pdb=" CB PHE L 41 " pdb=" CG PHE L 41 " ideal model delta sigma weight residual 1.502 1.481 0.021 2.30e-02 1.89e+03 8.16e-01 bond pdb=" CB PHE N 41 " pdb=" CG PHE N 41 " ideal model delta sigma weight residual 1.502 1.481 0.021 2.30e-02 1.89e+03 8.16e-01 bond pdb=" CB PHE R 41 " pdb=" CG PHE R 41 " ideal model delta sigma weight residual 1.502 1.481 0.021 2.30e-02 1.89e+03 8.16e-01 bond pdb=" CB PHE F 41 " pdb=" CG PHE F 41 " ideal model delta sigma weight residual 1.502 1.481 0.021 2.30e-02 1.89e+03 8.16e-01 bond pdb=" CB PHE W 41 " pdb=" CG PHE W 41 " ideal model delta sigma weight residual 1.502 1.481 0.021 2.30e-02 1.89e+03 8.16e-01 ... (remaining 36739 not shown) Histogram of bond angle deviations from ideal: 98.98 - 105.96: 360 105.96 - 112.95: 19944 112.95 - 119.93: 13584 119.93 - 126.91: 15168 126.91 - 133.89: 408 Bond angle restraints: 49464 Sorted by residual: angle pdb=" C TRP F 93 " pdb=" N GLU F 94 " pdb=" CA GLU F 94 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.26e+01 angle pdb=" C TRP I 93 " pdb=" N GLU I 94 " pdb=" CA GLU I 94 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.26e+01 angle pdb=" C TRP N 93 " pdb=" N GLU N 94 " pdb=" CA GLU N 94 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.26e+01 angle pdb=" C TRP S 93 " pdb=" N GLU S 94 " pdb=" CA GLU S 94 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.26e+01 angle pdb=" C TRP W 93 " pdb=" N GLU W 94 " pdb=" CA GLU W 94 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.26e+01 ... (remaining 49459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.83: 20616 15.83 - 31.65: 1824 31.65 - 47.48: 432 47.48 - 63.31: 168 63.31 - 79.13: 72 Dihedral angle restraints: 23112 sinusoidal: 10032 harmonic: 13080 Sorted by residual: dihedral pdb=" CA VAL L 46 " pdb=" C VAL L 46 " pdb=" N ALA L 47 " pdb=" CA ALA L 47 " ideal model delta harmonic sigma weight residual 180.00 161.58 18.42 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA VAL P 46 " pdb=" C VAL P 46 " pdb=" N ALA P 47 " pdb=" CA ALA P 47 " ideal model delta harmonic sigma weight residual 180.00 161.58 18.42 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA VAL U 46 " pdb=" C VAL U 46 " pdb=" N ALA U 47 " pdb=" CA ALA U 47 " ideal model delta harmonic sigma weight residual 180.00 161.58 18.42 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 23109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2688 0.026 - 0.052: 1656 0.052 - 0.078: 528 0.078 - 0.104: 216 0.104 - 0.130: 216 Chirality restraints: 5304 Sorted by residual: chirality pdb=" CA TYR V 39 " pdb=" N TYR V 39 " pdb=" C TYR V 39 " pdb=" CB TYR V 39 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA TYR G 39 " pdb=" N TYR G 39 " pdb=" C TYR G 39 " pdb=" CB TYR G 39 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA TYR I 39 " pdb=" N TYR I 39 " pdb=" C TYR I 39 " pdb=" CB TYR I 39 " both_signs ideal model delta sigma weight residual False 2.51 2.38 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 GLU C 94 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C GLU C 94 " 0.033 2.00e-02 2.50e+03 pdb=" O GLU C 94 " -0.012 2.00e-02 2.50e+03 pdb=" N SER C 95 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 94 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C GLU B 94 " 0.033 2.00e-02 2.50e+03 pdb=" O GLU B 94 " -0.012 2.00e-02 2.50e+03 pdb=" N SER B 95 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU S 94 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C GLU S 94 " 0.033 2.00e-02 2.50e+03 pdb=" O GLU S 94 " -0.012 2.00e-02 2.50e+03 pdb=" N SER S 95 " -0.011 2.00e-02 2.50e+03 ... (remaining 6405 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 720 2.53 - 3.12: 32688 3.12 - 3.71: 74220 3.71 - 4.31: 111552 4.31 - 4.90: 166356 Nonbonded interactions: 385536 Sorted by model distance: nonbonded pdb=" OE1 GLN O 112 " pdb="NA NA O 215 " model vdw 1.934 2.470 nonbonded pdb=" OE1 GLN M 112 " pdb="NA NA M 215 " model vdw 1.934 2.470 nonbonded pdb=" OE1 GLN H 112 " pdb="NA NA H 216 " model vdw 1.934 2.470 nonbonded pdb=" OE1 GLN E 112 " pdb="NA NA E 215 " model vdw 1.934 2.470 nonbonded pdb=" OE1 GLN K 112 " pdb="NA NA K 215 " model vdw 1.934 2.470 ... (remaining 385531 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 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. 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: 1.910 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: 0.040 Extract box with map and model: 12.300 Check model and map are aligned: 0.650 Convert atoms to be neutral: 0.360 Process input model: 171.760 Find NCS groups from input model: 3.160 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 202.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 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 : 0.005 0.027 36744 Z= 0.286 Angle : 0.757 6.786 49464 Z= 0.422 Chirality : 0.042 0.130 5304 Planarity : 0.004 0.033 6408 Dihedral : 14.503 79.134 14376 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 3.63 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: 3.35 (0.13), residues: 4080 helix: 2.52 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.09 (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 408 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 4.850 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 1.4664 time to fit residues: 735.0557 Evaluate side-chains 384 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 4.537 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6414 ------------------------------------------------------------------------------- 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: 4.9990 chunk 309 optimal weight: 0.9980 chunk 171 optimal weight: 20.0000 chunk 105 optimal weight: 9.9990 chunk 208 optimal weight: 3.9990 chunk 165 optimal weight: 20.0000 chunk 319 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 194 optimal weight: 3.9990 chunk 238 optimal weight: 9.9990 chunk 370 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS B 60 HIS C 60 HIS D 60 HIS E 60 HIS F 60 HIS G 60 HIS H 60 HIS I 60 HIS J 60 HIS K 60 HIS L 60 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 V 60 HIS W 60 HIS X 60 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.0354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.016 36744 Z= 0.180 Angle : 0.632 6.791 49464 Z= 0.343 Chirality : 0.038 0.139 5304 Planarity : 0.004 0.031 6408 Dihedral : 4.553 17.898 4560 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 3.17 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: 4.06 (0.13), residues: 4080 helix: 3.05 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.12 (0.25), residues: 816 *********************** 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 408 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 4.425 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 1.4159 time to fit residues: 711.4024 Evaluate side-chains 384 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 4.587 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.0029 ------------------------------------------------------------------------------- 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: 20.0000 chunk 114 optimal weight: 0.7980 chunk 308 optimal weight: 5.9990 chunk 252 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 371 optimal weight: 4.9990 chunk 400 optimal weight: 0.8980 chunk 330 optimal weight: 6.9990 chunk 368 optimal weight: 9.9990 chunk 126 optimal weight: 0.9980 chunk 297 optimal weight: 10.0000 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS B 60 HIS C 60 HIS D 60 HIS E 60 HIS F 60 HIS G 60 HIS H 60 HIS I 60 HIS J 60 HIS K 60 HIS L 60 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 V 60 HIS W 60 HIS X 60 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.0475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.014 36744 Z= 0.162 Angle : 0.595 6.663 49464 Z= 0.322 Chirality : 0.037 0.140 5304 Planarity : 0.004 0.029 6408 Dihedral : 4.490 18.342 4560 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.09 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: 4.36 (0.13), residues: 4080 helix: 3.28 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.15 (0.26), residues: 816 *********************** 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 432 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 432 time to evaluate : 4.172 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 1.5311 time to fit residues: 807.9806 Evaluate side-chains 384 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 4.482 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5707 ------------------------------------------------------------------------------- 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: 2.9990 chunk 279 optimal weight: 9.9990 chunk 192 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 177 optimal weight: 20.0000 chunk 249 optimal weight: 30.0000 chunk 372 optimal weight: 6.9990 chunk 394 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 353 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS B 60 HIS B 112 GLN C 60 HIS C 112 GLN D 60 HIS D 112 GLN E 60 HIS E 112 GLN F 60 HIS F 112 GLN G 60 HIS G 112 GLN H 60 HIS H 112 GLN I 60 HIS I 112 GLN J 60 HIS J 112 GLN K 60 HIS K 112 GLN L 60 HIS L 112 GLN M 60 HIS M 112 GLN N 60 HIS N 112 GLN O 60 HIS O 112 GLN P 60 HIS P 112 GLN Q 60 HIS Q 112 GLN R 60 HIS R 112 GLN S 60 HIS S 112 GLN T 60 HIS T 112 GLN U 60 HIS U 112 GLN V 60 HIS V 112 GLN W 60 HIS W 112 GLN X 60 HIS X 112 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.0379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 36744 Z= 0.221 Angle : 0.667 6.888 49464 Z= 0.364 Chirality : 0.039 0.146 5304 Planarity : 0.005 0.033 6408 Dihedral : 4.565 17.844 4560 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 3.03 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: 4.00 (0.13), residues: 4080 helix: 2.99 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.20 (0.26), residues: 816 *********************** 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 408 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 4.511 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 1.5085 time to fit residues: 761.2703 Evaluate side-chains 384 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 4.686 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.8586 ------------------------------------------------------------------------------- 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: 8.9990 chunk 223 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 293 optimal weight: 4.9990 chunk 162 optimal weight: 10.0000 chunk 336 optimal weight: 3.9990 chunk 272 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 201 optimal weight: 1.9990 chunk 353 optimal weight: 0.1980 chunk 99 optimal weight: 0.5980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 112 GLN B 60 HIS B 112 GLN C 60 HIS C 112 GLN D 60 HIS D 112 GLN E 60 HIS E 112 GLN F 60 HIS F 112 GLN G 60 HIS G 112 GLN H 60 HIS H 112 GLN I 60 HIS I 112 GLN J 60 HIS J 112 GLN K 60 HIS K 112 GLN L 60 HIS L 112 GLN M 60 HIS M 112 GLN N 60 HIS N 112 GLN O 60 HIS O 112 GLN P 60 HIS P 112 GLN Q 60 HIS Q 112 GLN R 60 HIS R 112 GLN S 60 HIS S 112 GLN T 60 HIS T 112 GLN U 60 HIS U 112 GLN V 60 HIS V 112 GLN W 60 HIS W 112 GLN X 60 HIS X 112 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.0541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.014 36744 Z= 0.152 Angle : 0.576 6.591 49464 Z= 0.311 Chirality : 0.036 0.141 5304 Planarity : 0.004 0.029 6408 Dihedral : 4.483 18.570 4560 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 2.73 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: 4.51 (0.13), residues: 4080 helix: 3.37 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.27 (0.26), residues: 816 *********************** 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 408 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 4.671 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 1.5089 time to fit residues: 760.2830 Evaluate side-chains 384 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 4.585 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3865 ------------------------------------------------------------------------------- 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: 3.9990 chunk 355 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 231 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 394 optimal weight: 0.1980 chunk 327 optimal weight: 6.9990 chunk 182 optimal weight: 0.7980 chunk 32 optimal weight: 20.0000 chunk 130 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 112 GLN B 60 HIS B 112 GLN C 60 HIS C 112 GLN D 60 HIS D 112 GLN E 60 HIS E 112 GLN F 60 HIS G 60 HIS G 112 GLN H 60 HIS H 112 GLN I 60 HIS I 112 GLN J 60 HIS J 112 GLN K 60 HIS K 112 GLN L 60 HIS L 112 GLN M 60 HIS M 112 GLN N 60 HIS O 60 HIS O 112 GLN P 60 HIS P 112 GLN Q 60 HIS Q 112 GLN R 60 HIS R 112 GLN S 60 HIS S 112 GLN T 60 HIS T 112 GLN U 60 HIS U 112 GLN V 60 HIS V 112 GLN W 60 HIS W 112 GLN X 60 HIS X 112 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.0491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.016 36744 Z= 0.168 Angle : 0.600 6.718 49464 Z= 0.325 Chirality : 0.037 0.142 5304 Planarity : 0.004 0.030 6408 Dihedral : 4.493 18.452 4560 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 3.02 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: 4.41 (0.13), residues: 4080 helix: 3.29 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.31 (0.26), residues: 816 *********************** 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 444 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 444 time to evaluate : 4.378 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 444 average time/residue: 1.4736 time to fit residues: 803.3215 Evaluate side-chains 408 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 4.661 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.7790 ------------------------------------------------------------------------------- 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: 20.0000 chunk 44 optimal weight: 20.0000 chunk 224 optimal weight: 4.9990 chunk 288 optimal weight: 0.4980 chunk 223 optimal weight: 9.9990 chunk 332 optimal weight: 9.9990 chunk 220 optimal weight: 0.6980 chunk 393 optimal weight: 8.9990 chunk 246 optimal weight: 0.5980 chunk 239 optimal weight: 20.0000 chunk 181 optimal weight: 30.0000 overall best weight: 3.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 112 GLN B 60 HIS B 112 GLN C 60 HIS C 112 GLN D 60 HIS D 112 GLN E 60 HIS E 112 GLN F 60 HIS F 112 GLN G 60 HIS G 112 GLN H 60 HIS H 112 GLN I 60 HIS I 112 GLN J 60 HIS J 112 GLN K 60 HIS K 112 GLN L 60 HIS L 112 GLN M 60 HIS M 112 GLN N 60 HIS N 112 GLN O 60 HIS O 112 GLN P 60 HIS P 112 GLN Q 60 HIS Q 112 GLN R 60 HIS R 112 GLN S 60 HIS S 112 GLN T 60 HIS T 112 GLN U 60 HIS U 112 GLN V 60 HIS V 112 GLN W 60 HIS W 112 GLN X 60 HIS X 112 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.0486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.017 36744 Z= 0.172 Angle : 0.602 6.721 49464 Z= 0.327 Chirality : 0.037 0.142 5304 Planarity : 0.004 0.029 6408 Dihedral : 4.497 18.423 4560 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 3.05 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: 4.36 (0.13), residues: 4080 helix: 3.26 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.29 (0.26), residues: 816 *********************** 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 444 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 444 time to evaluate : 4.789 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 444 average time/residue: 1.4852 time to fit residues: 811.0980 Evaluate side-chains 408 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 4.022 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.7416 ------------------------------------------------------------------------------- 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: 4.9990 chunk 157 optimal weight: 20.0000 chunk 234 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 250 optimal weight: 40.0000 chunk 267 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 309 optimal weight: 0.5980 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 112 GLN B 60 HIS B 112 GLN C 60 HIS C 112 GLN D 60 HIS D 112 GLN E 60 HIS E 112 GLN F 60 HIS F 112 GLN G 60 HIS G 112 GLN H 60 HIS H 112 GLN I 60 HIS I 112 GLN J 60 HIS J 112 GLN K 60 HIS K 112 GLN L 60 HIS L 112 GLN M 60 HIS M 112 GLN N 60 HIS N 112 GLN O 60 HIS O 112 GLN P 60 HIS P 112 GLN Q 60 HIS Q 112 GLN R 60 HIS R 112 GLN S 60 HIS S 112 GLN T 60 HIS T 112 GLN U 60 HIS U 112 GLN V 60 HIS V 112 GLN W 60 HIS W 112 GLN X 60 HIS X 112 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.0446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.019 36744 Z= 0.187 Angle : 0.625 6.803 49464 Z= 0.340 Chirality : 0.038 0.143 5304 Planarity : 0.004 0.030 6408 Dihedral : 4.517 18.225 4560 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 2.77 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: 4.25 (0.13), residues: 4080 helix: 3.17 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.28 (0.26), residues: 816 *********************** 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 412 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 412 time to evaluate : 4.428 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 1.4717 time to fit residues: 749.1902 Evaluate side-chains 388 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 388 time to evaluate : 4.346 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5877 ------------------------------------------------------------------------------- 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: 7.9990 chunk 376 optimal weight: 10.0000 chunk 343 optimal weight: 0.9980 chunk 366 optimal weight: 9.9990 chunk 220 optimal weight: 6.9990 chunk 159 optimal weight: 30.0000 chunk 287 optimal weight: 6.9990 chunk 112 optimal weight: 20.0000 chunk 331 optimal weight: 9.9990 chunk 346 optimal weight: 30.0000 chunk 365 optimal weight: 5.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS B 60 HIS C 60 HIS D 60 HIS E 60 HIS F 60 HIS G 60 HIS H 60 HIS I 60 HIS J 60 HIS K 60 HIS L 60 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 V 60 HIS W 60 HIS X 60 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.0404 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= 0.242 Angle : 0.688 6.945 49464 Z= 0.377 Chirality : 0.040 0.145 5304 Planarity : 0.005 0.037 6408 Dihedral : 4.579 17.811 4560 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 3.01 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: 3.91 (0.13), residues: 4080 helix: 2.92 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.22 (0.26), residues: 816 *********************** 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 408 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 4.554 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 1.5020 time to fit residues: 756.2756 Evaluate side-chains 384 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 4.421 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 3.9990 chunk 387 optimal weight: 2.9990 chunk 236 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 chunk 269 optimal weight: 0.9980 chunk 406 optimal weight: 20.0000 chunk 374 optimal weight: 6.9990 chunk 323 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 250 optimal weight: 0.9990 chunk 198 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS B 60 HIS C 60 HIS D 60 HIS E 60 HIS F 60 HIS G 60 HIS H 60 HIS I 60 HIS J 60 HIS K 60 HIS L 60 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 V 60 HIS W 60 HIS X 60 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.0623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.015 36744 Z= 0.139 Angle : 0.552 6.472 49464 Z= 0.297 Chirality : 0.036 0.140 5304 Planarity : 0.003 0.028 6408 Dihedral : 4.476 18.464 4560 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 3.27 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: 4.67 (0.13), residues: 4080 helix: 3.49 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.31 (0.27), residues: 816 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 4.672 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 1.4978 time to fit residues: 754.4127 Evaluate side-chains 384 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 4.369 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 7.9990 chunk 344 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 298 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 chunk 324 optimal weight: 20.0000 chunk 135 optimal weight: 0.7980 chunk 332 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS B 60 HIS C 60 HIS D 60 HIS E 60 HIS F 60 HIS G 60 HIS H 60 HIS I 60 HIS J 60 HIS K 60 HIS L 60 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 V 60 HIS W 60 HIS X 60 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.213829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.147137 restraints weight = 49310.843| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 0.67 r_work: 0.3615 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 1.91 restraints_weight: 0.2500 r_work: 0.3384 rms_B_bonded: 2.89 restraints_weight: 0.1250 r_work: 0.3325 rms_B_bonded: 4.92 restraints_weight: 0.0625 r_work: 0.3283 rms_B_bonded: 4.63 restraints_weight: 0.0312 r_work: 0.3272 rms_B_bonded: 4.58 restraints_weight: 0.0156 r_work: 0.3249 rms_B_bonded: 4.61 restraints_weight: 0.0078 r_work: 0.3240 rms_B_bonded: 4.71 restraints_weight: 0.0039 r_work: 0.3238 rms_B_bonded: 4.82 restraints_weight: 0.0020 r_work: 0.3232 rms_B_bonded: 4.86 restraints_weight: 0.0010 r_work: 0.3230 rms_B_bonded: 4.96 restraints_weight: 0.0005 r_work: 0.3226 rms_B_bonded: 4.99 restraints_weight: 0.0002 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4436 r_free = 0.4436 target_work(ls_wunit_k1) = 0.214 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4432 r_free = 0.4432 target_work(ls_wunit_k1) = 0.213 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 168 | |-----------------------------------------------------------------------------| r_final: 0.4432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.0448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 36744 Z= 0.208 Angle : 0.646 6.860 49464 Z= 0.352 Chirality : 0.039 0.143 5304 Planarity : 0.004 0.031 6408 Dihedral : 4.539 18.015 4560 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 2.97 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: 4.21 (0.13), residues: 4080 helix: 3.13 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.31 (0.26), residues: 816 =============================================================================== Job complete usr+sys time: 16295.98 seconds wall clock time: 291 minutes 40.52 seconds (17500.52 seconds total)