Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 17 19:50:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rrp_24665/08_2023/7rrp_24665.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rrp_24665/08_2023/7rrp_24665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rrp_24665/08_2023/7rrp_24665.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rrp_24665/08_2023/7rrp_24665.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rrp_24665/08_2023/7rrp_24665.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rrp_24665/08_2023/7rrp_24665.pdb" } resolution = 1.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 206 6.06 5 S 192 5.16 5 Na 72 4.78 5 C 22248 2.51 5 N 6096 2.21 5 O 9360 1.98 5 H 34080 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 92": "OD1" <-> "OD2" Residue "A ASP 131": "OD1" <-> "OD2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 92": "OD1" <-> "OD2" Residue "B ASP 131": "OD1" <-> "OD2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 92": "OD1" <-> "OD2" Residue "C ASP 131": "OD1" <-> "OD2" Residue "C GLU 140": "OE1" <-> "OE2" Residue "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 92": "OD1" <-> "OD2" Residue "D ASP 131": "OD1" <-> "OD2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "D TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 92": "OD1" <-> "OD2" Residue "E ASP 131": "OD1" <-> "OD2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "E TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 92": "OD1" <-> "OD2" Residue "F ASP 131": "OD1" <-> "OD2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 92": "OD1" <-> "OD2" Residue "G ASP 131": "OD1" <-> "OD2" Residue "G GLU 140": "OE1" <-> "OE2" Residue "G TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 92": "OD1" <-> "OD2" Residue "H ASP 131": "OD1" <-> "OD2" Residue "H GLU 140": "OE1" <-> "OE2" Residue "H TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 92": "OD1" <-> "OD2" Residue "I ASP 131": "OD1" <-> "OD2" Residue "I GLU 140": "OE1" <-> "OE2" Residue "I TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ASP 92": "OD1" <-> "OD2" Residue "J ASP 131": "OD1" <-> "OD2" Residue "J GLU 140": "OE1" <-> "OE2" Residue "J TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 92": "OD1" <-> "OD2" Residue "K ASP 131": "OD1" <-> "OD2" Residue "K GLU 140": "OE1" <-> "OE2" Residue "K TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 92": "OD1" <-> "OD2" Residue "L ASP 131": "OD1" <-> "OD2" Residue "L GLU 140": "OE1" <-> "OE2" Residue "L TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 92": "OD1" <-> "OD2" Residue "M ASP 131": "OD1" <-> "OD2" Residue "M GLU 140": "OE1" <-> "OE2" Residue "M TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 92": "OD1" <-> "OD2" Residue "N ASP 131": "OD1" <-> "OD2" Residue "N GLU 140": "OE1" <-> "OE2" Residue "N TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ASP 92": "OD1" <-> "OD2" Residue "O ASP 131": "OD1" <-> "OD2" Residue "O GLU 140": "OE1" <-> "OE2" Residue "O TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ASP 92": "OD1" <-> "OD2" Residue "P ASP 131": "OD1" <-> "OD2" Residue "P GLU 140": "OE1" <-> "OE2" Residue "P TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ASP 92": "OD1" <-> "OD2" Residue "Q ASP 131": "OD1" <-> "OD2" Residue "Q GLU 140": "OE1" <-> "OE2" Residue "Q TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ASP 92": "OD1" <-> "OD2" Residue "R ASP 131": "OD1" <-> "OD2" Residue "R GLU 140": "OE1" <-> "OE2" Residue "R TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ASP 92": "OD1" <-> "OD2" Residue "S ASP 131": "OD1" <-> "OD2" Residue "S GLU 140": "OE1" <-> "OE2" Residue "S TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T ASP 92": "OD1" <-> "OD2" Residue "T ASP 131": "OD1" <-> "OD2" Residue "T GLU 140": "OE1" <-> "OE2" Residue "T TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U ASP 92": "OD1" <-> "OD2" Residue "U ASP 131": "OD1" <-> "OD2" Residue "U GLU 140": "OE1" <-> "OE2" Residue "U TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V ASP 92": "OD1" <-> "OD2" Residue "V ASP 131": "OD1" <-> "OD2" Residue "V GLU 140": "OE1" <-> "OE2" Residue "V TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W ASP 92": "OD1" <-> "OD2" Residue "W ASP 131": "OD1" <-> "OD2" Residue "W GLU 140": "OE1" <-> "OE2" Residue "W TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X ASP 92": "OD1" <-> "OD2" Residue "X ASP 131": "OD1" <-> "OD2" Residue "X TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 72254 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 2895 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2671 Conformer: "C" Number of residues, atoms: 172, 2661 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 2671 Chain: "B" Number of atoms: 2895 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2671 Conformer: "C" Number of residues, atoms: 172, 2661 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 2671 Chain: "C" Number of atoms: 2895 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2671 Conformer: "C" Number of residues, atoms: 172, 2661 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 2671 Chain: "D" Number of atoms: 2895 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2671 Conformer: "C" Number of residues, atoms: 172, 2661 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 2671 Chain: "E" Number of atoms: 2895 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2671 Conformer: "C" Number of residues, atoms: 172, 2661 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 2671 Chain: "F" Number of atoms: 2895 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2671 Conformer: "C" Number of residues, atoms: 172, 2661 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 2671 Chain: "G" Number of atoms: 2895 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2671 Conformer: "C" Number of residues, atoms: 172, 2661 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 2671 Chain: "H" Number of atoms: 2895 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2671 Conformer: "C" Number of residues, atoms: 172, 2661 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 2671 Chain: "I" Number of atoms: 2895 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2671 Conformer: "C" Number of residues, atoms: 172, 2661 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 2671 Chain: "J" Number of atoms: 2895 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2671 Conformer: "C" Number of residues, atoms: 172, 2661 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 2671 Chain: "K" Number of atoms: 2895 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2671 Conformer: "C" Number of residues, atoms: 172, 2661 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 2671 Chain: "L" Number of atoms: 2895 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2671 Conformer: "C" Number of residues, atoms: 172, 2661 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 2671 Chain: "M" Number of atoms: 2895 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2671 Conformer: "C" Number of residues, atoms: 172, 2661 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 2671 Chain: "N" Number of atoms: 2895 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2671 Conformer: "C" Number of residues, atoms: 172, 2661 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 2671 Chain: "O" Number of atoms: 2895 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2671 Conformer: "C" Number of residues, atoms: 172, 2661 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 2671 Chain: "P" Number of atoms: 2895 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2671 Conformer: "C" Number of residues, atoms: 172, 2661 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 2671 Chain: "Q" Number of atoms: 2895 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2671 Conformer: "C" Number of residues, atoms: 172, 2661 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 2671 Chain: "R" Number of atoms: 2895 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2671 Conformer: "C" Number of residues, atoms: 172, 2661 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 2671 Chain: "S" Number of atoms: 2895 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2671 Conformer: "C" Number of residues, atoms: 172, 2661 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 2671 Chain: "T" Number of atoms: 2895 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2671 Conformer: "C" Number of residues, atoms: 172, 2661 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 2671 Chain: "U" Number of atoms: 2895 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2671 Conformer: "C" Number of residues, atoms: 172, 2661 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 2671 Chain: "V" Number of atoms: 2895 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2671 Conformer: "C" Number of residues, atoms: 172, 2661 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 2671 Chain: "W" Number of atoms: 2895 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2671 Conformer: "C" Number of residues, atoms: 172, 2661 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 2671 Chain: "X" Number of atoms: 2895 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 2760 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 2671 Conformer: "C" Number of residues, atoms: 172, 2661 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 2671 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' NA': 3, ' ZN': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' NA': 3, ' ZN': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' NA': 3, ' ZN': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' NA': 3, ' ZN': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Unusual residues: {' NA': 3, ' ZN': 9} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Unusual residues: {' NA': 3, ' ZN': 9} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "G" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' NA': 3, ' ZN': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "H" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' NA': 3, ' ZN': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Unusual residues: {' NA': 3, ' ZN': 9} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "J" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' NA': 3, ' ZN': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "K" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' NA': 3, ' ZN': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "L" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Unusual residues: {' NA': 3, ' ZN': 9} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "M" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' NA': 3, ' ZN': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "N" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' NA': 3, ' ZN': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "O" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' NA': 3, ' ZN': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "P" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' NA': 3, ' ZN': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "Q" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' NA': 3, ' ZN': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "R" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' NA': 3, ' ZN': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "S" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' NA': 3, ' ZN': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "T" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' NA': 3, ' ZN': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "U" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' NA': 3, ' ZN': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "V" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' NA': 3, ' ZN': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "W" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' NA': 3, ' ZN': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "X" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' NA': 3, ' ZN': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "B" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "C" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "D" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "E" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "F" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "G" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "H" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "I" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "J" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "K" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "L" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "M" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "N" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "O" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "P" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "Q" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "R" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "S" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "T" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "U" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "V" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "W" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "X" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Time building chain proxies: 55.97, per 1000 atoms: 0.77 Number of scatterers: 72254 At special positions: 0 Unit cell: (137.046, 137.046, 137.046, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 206 29.99 S 192 16.00 Na 72 11.00 O 9360 8.00 N 6096 7.00 C 22248 6.00 H 34080 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 55.24 Conformation dependent library (CDL) restraints added in 10.7 seconds 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8496 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 79.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.02 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: 23.96 Time building geometry restraints manager: 57.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 33984 1.03 - 1.23: 301 1.23 - 1.42: 15467 1.42 - 1.62: 20160 1.62 - 1.81: 288 Bond restraints: 70200 Sorted by residual: bond pdb=" CA ASP P 42 " pdb=" C ASP P 42 " ideal model delta sigma weight residual 1.522 1.534 -0.012 1.37e-02 5.33e+03 7.70e-01 bond pdb=" CA ASP L 42 " pdb=" C ASP L 42 " ideal model delta sigma weight residual 1.522 1.534 -0.012 1.37e-02 5.33e+03 7.63e-01 bond pdb=" CA ASP J 42 " pdb=" C ASP J 42 " ideal model delta sigma weight residual 1.522 1.534 -0.012 1.37e-02 5.33e+03 7.63e-01 bond pdb=" CA ASP A 42 " pdb=" C ASP A 42 " ideal model delta sigma weight residual 1.522 1.534 -0.012 1.37e-02 5.33e+03 7.63e-01 bond pdb=" CA ASP U 42 " pdb=" C ASP U 42 " ideal model delta sigma weight residual 1.522 1.534 -0.012 1.37e-02 5.33e+03 7.63e-01 ... (remaining 70195 not shown) Histogram of bond angle deviations from ideal: 100.00 - 106.80: 855 106.80 - 113.59: 82430 113.59 - 120.38: 24626 120.38 - 127.18: 18497 127.18 - 133.97: 360 Bond angle restraints: 126768 Sorted by residual: angle pdb=" C TRP N 93 " pdb=" N GLU N 94 " pdb=" CA GLU N 94 " ideal model delta sigma weight residual 121.54 126.88 -5.34 1.91e+00 2.74e-01 7.81e+00 angle pdb=" C TRP V 93 " pdb=" N GLU V 94 " pdb=" CA GLU V 94 " ideal model delta sigma weight residual 121.54 126.88 -5.34 1.91e+00 2.74e-01 7.81e+00 angle pdb=" C TRP E 93 " pdb=" N GLU E 94 " pdb=" CA GLU E 94 " ideal model delta sigma weight residual 121.54 126.88 -5.34 1.91e+00 2.74e-01 7.81e+00 angle pdb=" C TRP S 93 " pdb=" N GLU S 94 " pdb=" CA GLU S 94 " ideal model delta sigma weight residual 121.54 126.85 -5.31 1.91e+00 2.74e-01 7.73e+00 angle pdb=" C TRP B 93 " pdb=" N GLU B 94 " pdb=" CA GLU B 94 " ideal model delta sigma weight residual 121.54 126.85 -5.31 1.91e+00 2.74e-01 7.73e+00 ... (remaining 126763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.83: 25599 14.83 - 29.67: 2348 29.67 - 44.50: 589 44.50 - 59.33: 192 59.33 - 74.17: 72 Dihedral angle restraints: 28800 sinusoidal: 13656 harmonic: 15144 Sorted by residual: dihedral pdb=" CA TRP N 93 " pdb=" C TRP N 93 " pdb=" N GLU N 94 " pdb=" CA GLU N 94 " ideal model delta harmonic sigma weight residual 180.00 162.00 18.00 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA TRP V 93 " pdb=" C TRP V 93 " pdb=" N GLU V 94 " pdb=" CA GLU V 94 " ideal model delta harmonic sigma weight residual 180.00 162.00 18.00 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA TRP E 93 " pdb=" C TRP E 93 " pdb=" N GLU E 94 " pdb=" CA GLU E 94 " ideal model delta harmonic sigma weight residual 180.00 162.00 18.00 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 28797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3401 0.027 - 0.055: 1206 0.055 - 0.082: 361 0.082 - 0.109: 121 0.109 - 0.137: 95 Chirality restraints: 5184 Sorted by residual: chirality pdb=" CA TYR Q 39 " pdb=" N TYR Q 39 " pdb=" C TYR Q 39 " pdb=" CB TYR Q 39 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA TYR R 39 " pdb=" N TYR R 39 " pdb=" C TYR R 39 " pdb=" CB TYR R 39 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA TYR U 39 " pdb=" N TYR U 39 " pdb=" C TYR U 39 " pdb=" CB TYR U 39 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 5181 not shown) Planarity restraints: 10392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 63 " -0.158 9.50e-02 1.11e+02 5.30e-02 3.13e+00 pdb=" NE ARG R 63 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG R 63 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG R 63 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG R 63 " -0.002 2.00e-02 2.50e+03 pdb="HH11 ARG R 63 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG R 63 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG R 63 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG R 63 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 39 " -0.020 2.00e-02 2.50e+03 9.15e-03 2.51e+00 pdb=" CG TYR D 39 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR D 39 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR D 39 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 39 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 39 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 39 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 39 " -0.005 2.00e-02 2.50e+03 pdb=" HD1 TYR D 39 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR D 39 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR D 39 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR D 39 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR V 39 " 0.020 2.00e-02 2.50e+03 9.14e-03 2.51e+00 pdb=" CG TYR V 39 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR V 39 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR V 39 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR V 39 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR V 39 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR V 39 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR V 39 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 TYR V 39 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR V 39 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR V 39 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR V 39 " 0.001 2.00e-02 2.50e+03 ... (remaining 10389 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 9646 2.27 - 2.85: 171178 2.85 - 3.43: 217346 3.43 - 4.02: 305843 4.02 - 4.60: 456158 Nonbonded interactions: 1160171 Sorted by model distance: nonbonded pdb=" HE1 HIS E 105 " pdb="HD22 ASN E 109 " model vdw 1.686 2.100 nonbonded pdb=" HH TYR X 12 " pdb=" OE1 GLN X 73 " model vdw 1.698 1.850 nonbonded pdb=" HH TYR F 12 " pdb=" OE1 GLN F 73 " model vdw 1.698 1.850 nonbonded pdb=" HH TYR I 12 " pdb=" OE1 GLN I 73 " model vdw 1.698 1.850 nonbonded pdb=" HH TYR D 12 " pdb=" OE1 GLN D 73 " model vdw 1.698 1.850 ... (remaining 1160166 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 201 through 206)) selection = (chain 'B' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 201 through 206)) selection = (chain 'C' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 201 through 206)) selection = (chain 'D' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 201 through 206)) selection = (chain 'E' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 201 through 206)) selection = (chain 'F' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 201 through 206)) selection = (chain 'G' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 201 through 206)) selection = (chain 'H' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 201 through 206)) selection = (chain 'I' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 201 through 206)) selection = (chain 'J' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 201 through 206)) selection = (chain 'K' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 201 through 206)) selection = (chain 'L' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 201 through 206)) selection = (chain 'M' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 201 through 206)) selection = (chain 'N' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 201 through 206)) selection = (chain 'O' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 201 through 206)) selection = (chain 'P' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 201 through 206)) selection = (chain 'Q' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 201 through 206)) selection = (chain 'R' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 201 through 206)) selection = (chain 'S' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 201 through 206)) selection = (chain 'T' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 201 through 206)) selection = (chain 'U' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 201 through 206)) selection = (chain 'V' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 201 through 206)) selection = (chain 'W' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 201 through 206)) selection = (chain 'X' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 through 63 or resid 6 \ 5 through 93 or resid 95 through 101 or resid 103 through 155 or resid 157 throu \ gh 161 or resid 163 through 176 or resid 201 through 206)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.33 max=1.00 mean=0.96 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.250 Extract box with map and model: 22.330 Check model and map are aligned: 0.800 Set scattering table: 0.500 Process input model: 226.250 Find NCS groups from input model: 3.500 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:10.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 270.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 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 : 0.003 0.021 36120 Z= 0.194 Angle : 0.610 5.532 48672 Z= 0.346 Chirality : 0.036 0.137 5184 Planarity : 0.005 0.070 6360 Dihedral : 14.219 74.167 13920 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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: 4.01 (0.13), residues: 4080 helix: 2.98 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.23 (0.27), residues: 792 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 4.354 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 2.7198 time to fit residues: 963.3098 Evaluate side-chains 312 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 4.298 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1176 ------------------------------------------------------------------------------- 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: 6.9990 chunk 309 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 208 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 319 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 238 optimal weight: 6.9990 chunk 370 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN B 109 ASN C 109 ASN D 109 ASN E 109 ASN F 109 ASN G 109 ASN H 109 ASN I 109 ASN J 109 ASN K 109 ASN L 109 ASN M 109 ASN N 109 ASN O 109 ASN P 109 ASN Q 109 ASN R 109 ASN S 109 ASN T 109 ASN U 109 ASN V 109 ASN W 109 ASN X 109 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.0222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.021 36120 Z= 0.234 Angle : 0.661 5.788 48672 Z= 0.371 Chirality : 0.037 0.131 5184 Planarity : 0.005 0.046 6360 Dihedral : 4.678 17.926 4536 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 0.61 % 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: 3.93 (0.13), residues: 4080 helix: 2.91 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.29 (0.27), residues: 792 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 328 time to evaluate : 4.308 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 328 average time/residue: 2.8428 time to fit residues: 1133.0982 Evaluate side-chains 504 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 4.350 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1439 ------------------------------------------------------------------------------- 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: 3.9990 chunk 114 optimal weight: 4.9990 chunk 308 optimal weight: 5.9990 chunk 252 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 371 optimal weight: 5.9990 chunk 400 optimal weight: 6.9990 chunk 330 optimal weight: 5.9990 chunk 368 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 297 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN B 109 ASN C 109 ASN D 109 ASN E 109 ASN F 109 ASN G 109 ASN H 109 ASN I 109 ASN J 109 ASN K 109 ASN L 109 ASN M 109 ASN N 109 ASN O 109 ASN P 109 ASN Q 109 ASN R 109 ASN S 109 ASN T 109 ASN U 109 ASN V 109 ASN W 109 ASN X 109 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.0524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.022 36120 Z= 0.247 Angle : 0.674 5.876 48672 Z= 0.379 Chirality : 0.038 0.130 5184 Planarity : 0.006 0.071 6360 Dihedral : 4.679 17.621 4536 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 1.89 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: 3.93 (0.13), residues: 4080 helix: 2.91 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.30 (0.27), residues: 792 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 489 time to evaluate : 4.384 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 489 average time/residue: 3.8403 time to fit residues: 2183.7288 Evaluate side-chains 505 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 505 time to evaluate : 4.476 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1878 ------------------------------------------------------------------------------- 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: 6.9990 chunk 279 optimal weight: 3.9990 chunk 192 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 249 optimal weight: 8.9990 chunk 372 optimal weight: 1.9990 chunk 394 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 353 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN B 109 ASN C 109 ASN D 109 ASN E 109 ASN F 109 ASN G 109 ASN H 109 ASN I 109 ASN J 109 ASN K 109 ASN L 109 ASN M 109 ASN N 109 ASN O 109 ASN P 109 ASN Q 109 ASN R 109 ASN S 109 ASN T 109 ASN U 109 ASN V 109 ASN W 109 ASN X 109 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.0567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.023 36120 Z= 0.250 Angle : 0.679 5.896 48672 Z= 0.381 Chirality : 0.038 0.128 5184 Planarity : 0.006 0.065 6360 Dihedral : 4.695 17.645 4536 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 1.86 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: 3.90 (0.13), residues: 4080 helix: 2.88 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.28 (0.27), residues: 792 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 4.364 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 3.8492 time to fit residues: 2142.8138 Evaluate side-chains 504 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 4.334 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2358 ------------------------------------------------------------------------------- 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: 5.9990 chunk 223 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 293 optimal weight: 0.6980 chunk 162 optimal weight: 6.9990 chunk 336 optimal weight: 4.9990 chunk 272 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 201 optimal weight: 7.9990 chunk 353 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN B 109 ASN C 109 ASN D 109 ASN E 109 ASN F 109 ASN G 109 ASN H 109 ASN I 109 ASN J 109 ASN K 109 ASN L 109 ASN M 109 ASN N 109 ASN O 109 ASN P 109 ASN Q 109 ASN R 109 ASN S 109 ASN T 109 ASN U 109 ASN V 109 ASN W 109 ASN X 109 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.0557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.019 36120 Z= 0.226 Angle : 0.646 5.666 48672 Z= 0.363 Chirality : 0.037 0.128 5184 Planarity : 0.005 0.068 6360 Dihedral : 4.679 17.968 4536 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 1.96 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: 3.96 (0.13), residues: 4080 helix: 2.94 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.26 (0.27), residues: 792 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 4.261 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 504 average time/residue: 3.7933 time to fit residues: 2222.6391 Evaluate side-chains 504 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 4.305 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0616 ------------------------------------------------------------------------------- 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: 5.9990 chunk 355 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 231 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 394 optimal weight: 5.9990 chunk 327 optimal weight: 0.3980 chunk 182 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN B 109 ASN C 109 ASN D 109 ASN E 109 ASN F 109 ASN G 109 ASN H 109 ASN I 109 ASN J 109 ASN K 109 ASN L 109 ASN M 109 ASN N 109 ASN O 109 ASN P 109 ASN Q 109 ASN R 109 ASN S 109 ASN T 109 ASN U 109 ASN V 109 ASN W 109 ASN X 109 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.0598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.024 36120 Z= 0.259 Angle : 0.690 5.997 48672 Z= 0.388 Chirality : 0.038 0.132 5184 Planarity : 0.005 0.064 6360 Dihedral : 4.687 17.530 4536 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 2.17 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: 3.89 (0.13), residues: 4080 helix: 2.88 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.29 (0.27), residues: 792 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 4.331 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 3.8143 time to fit residues: 2127.5311 Evaluate side-chains 504 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 4.310 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1641 ------------------------------------------------------------------------------- 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: 4.9990 chunk 44 optimal weight: 6.9990 chunk 224 optimal weight: 4.9990 chunk 288 optimal weight: 7.9990 chunk 223 optimal weight: 4.9990 chunk 332 optimal weight: 6.9990 chunk 220 optimal weight: 5.9990 chunk 393 optimal weight: 6.9990 chunk 246 optimal weight: 3.9990 chunk 239 optimal weight: 3.9990 chunk 181 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN B 109 ASN C 109 ASN D 109 ASN E 109 ASN F 109 ASN G 109 ASN H 109 ASN I 109 ASN J 109 ASN K 109 ASN L 109 ASN M 109 ASN N 109 ASN O 109 ASN P 109 ASN Q 109 ASN R 109 ASN S 109 ASN T 109 ASN U 109 ASN V 109 ASN W 109 ASN X 109 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.0607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.023 36120 Z= 0.264 Angle : 0.689 5.848 48672 Z= 0.387 Chirality : 0.038 0.128 5184 Planarity : 0.006 0.069 6360 Dihedral : 4.703 17.698 4536 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 1.91 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: 3.85 (0.13), residues: 4080 helix: 2.85 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.29 (0.27), residues: 792 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 4.397 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 3.8001 time to fit residues: 2121.5601 Evaluate side-chains 504 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 4.268 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1258 ------------------------------------------------------------------------------- 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: 6.9990 chunk 157 optimal weight: 7.9990 chunk 234 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 250 optimal weight: 4.9990 chunk 267 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 309 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN B 109 ASN C 109 ASN D 109 ASN E 109 ASN F 109 ASN G 109 ASN H 109 ASN I 109 ASN J 109 ASN K 109 ASN L 109 ASN M 109 ASN N 109 ASN O 109 ASN P 109 ASN Q 109 ASN R 109 ASN S 109 ASN T 109 ASN U 109 ASN V 109 ASN W 109 ASN X 109 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.0563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.019 36120 Z= 0.213 Angle : 0.629 5.583 48672 Z= 0.354 Chirality : 0.037 0.127 5184 Planarity : 0.005 0.063 6360 Dihedral : 4.674 18.149 4536 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 1.94 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: 4.01 (0.13), residues: 4080 helix: 2.97 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.27 (0.27), residues: 792 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 4.437 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 504 average time/residue: 3.8079 time to fit residues: 2232.6054 Evaluate side-chains 504 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 4.385 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3598 ------------------------------------------------------------------------------- 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: 8.9990 chunk 376 optimal weight: 6.9990 chunk 343 optimal weight: 5.9990 chunk 366 optimal weight: 5.9990 chunk 220 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 287 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 331 optimal weight: 0.8980 chunk 346 optimal weight: 7.9990 chunk 365 optimal weight: 0.9980 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN B 109 ASN C 109 ASN D 109 ASN E 109 ASN F 109 ASN G 109 ASN H 109 ASN I 109 ASN J 109 ASN K 109 ASN L 109 ASN M 109 ASN N 109 ASN O 109 ASN P 109 ASN Q 109 ASN R 109 ASN S 109 ASN T 109 ASN U 109 ASN V 109 ASN W 109 ASN X 109 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.0576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.019 36120 Z= 0.224 Angle : 0.647 5.660 48672 Z= 0.364 Chirality : 0.037 0.131 5184 Planarity : 0.005 0.060 6360 Dihedral : 4.667 17.968 4536 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 2.00 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: 3.98 (0.13), residues: 4080 helix: 2.94 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.29 (0.27), residues: 792 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 4.310 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 3.8106 time to fit residues: 2128.3750 Evaluate side-chains 504 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 4.346 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1679 ------------------------------------------------------------------------------- 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: 6.9990 chunk 387 optimal weight: 0.9990 chunk 236 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 269 optimal weight: 1.9990 chunk 406 optimal weight: 0.9990 chunk 374 optimal weight: 8.9990 chunk 323 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 250 optimal weight: 0.0980 chunk 198 optimal weight: 1.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN B 109 ASN C 109 ASN D 109 ASN E 109 ASN F 109 ASN G 109 ASN H 109 ASN I 109 ASN J 109 ASN K 109 ASN L 109 ASN M 109 ASN N 109 ASN O 109 ASN P 109 ASN Q 109 ASN R 109 ASN S 109 ASN T 109 ASN U 109 ASN V 109 ASN W 109 ASN X 109 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.0598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.016 36120 Z= 0.149 Angle : 0.540 5.300 48672 Z= 0.304 Chirality : 0.034 0.132 5184 Planarity : 0.004 0.049 6360 Dihedral : 4.558 18.723 4536 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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: 4.39 (0.13), residues: 4080 helix: 3.24 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.35 (0.27), residues: 792 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 4.397 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 3.8629 time to fit residues: 2164.2316 Evaluate side-chains 504 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 4.291 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1768 ------------------------------------------------------------------------------- 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: 5.9990 chunk 344 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 298 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 324 optimal weight: 5.9990 chunk 135 optimal weight: 7.9990 chunk 332 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN B 109 ASN C 109 ASN D 109 ASN E 109 ASN F 109 ASN G 109 ASN H 109 ASN I 109 ASN J 109 ASN K 109 ASN L 109 ASN M 109 ASN N 109 ASN O 109 ASN P 109 ASN Q 109 ASN R 109 ASN S 109 ASN T 109 ASN U 109 ASN V 109 ASN W 109 ASN X 109 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.200434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.153456 restraints weight = 44340.180| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 0.24 r_work: 0.3680 rms_B_bonded: 0.44 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 0.80 restraints_weight: 0.2500 r_work: 0.3335 rms_B_bonded: 1.99 restraints_weight: 0.1250 r_work: 0.3192 rms_B_bonded: 4.53 restraints_weight: 0.0625 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.0630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.025 36120 Z= 0.271 Angle : 0.693 5.848 48672 Z= 0.389 Chirality : 0.039 0.127 5184 Planarity : 0.005 0.051 6360 Dihedral : 4.675 17.971 4536 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 1.86 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: 3.90 (0.13), residues: 4080 helix: 2.88 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.32 (0.27), residues: 792 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32472.48 seconds wall clock time: 558 minutes 27.68 seconds (33507.68 seconds total)