Starting phenix.real_space_refine on Fri Dec 15 22:52:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5a_35984/12_2023/8j5a_35984.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5a_35984/12_2023/8j5a_35984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5a_35984/12_2023/8j5a_35984.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5a_35984/12_2023/8j5a_35984.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5a_35984/12_2023/8j5a_35984.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5a_35984/12_2023/8j5a_35984.pdb" } resolution = 1.19 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 38736 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 264 5.16 5 Na 24 4.78 5 C 22728 2.51 5 N 6144 2.21 5 O 10008 1.98 5 H 17040 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 ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 92": "OD1" <-> "OD2" Residue "B PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 92": "OD1" <-> "OD2" Residue "C PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 92": "OD1" <-> "OD2" Residue "D PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 92": "OD1" <-> "OD2" Residue "E PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 92": "OD1" <-> "OD2" Residue "F PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 92": "OD1" <-> "OD2" Residue "G PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 92": "OD1" <-> "OD2" Residue "H PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 92": "OD1" <-> "OD2" Residue "I PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ASP 92": "OD1" <-> "OD2" Residue "J PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ASP 92": "OD1" <-> "OD2" Residue "K PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ASP 92": "OD1" <-> "OD2" Residue "L PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ASP 92": "OD1" <-> "OD2" Residue "M PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ASP 92": "OD1" <-> "OD2" Residue "N PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ASP 92": "OD1" <-> "OD2" Residue "O PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ASP 92": "OD1" <-> "OD2" Residue "P PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ASP 92": "OD1" <-> "OD2" Residue "Q PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ASP 92": "OD1" <-> "OD2" Residue "R PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ASP 92": "OD1" <-> "OD2" Residue "S PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S ASP 92": "OD1" <-> "OD2" Residue "T PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ASP 92": "OD1" <-> "OD2" Residue "U PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ASP 92": "OD1" <-> "OD2" Residue "V PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ASP 92": "OD1" <-> "OD2" Residue "W PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ASP 92": "OD1" <-> "OD2" Residue "X PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X ASP 92": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 56208 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2342 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY A 176 " pdbres=" NA A 201 " Not linked: pdbres=" NA A 201 " pdbres="HOH A 301 " Not linked: pdbres="HOH A 301 " pdbres="HOH A 302 " Not linked: pdbres="HOH A 302 " pdbres="HOH A 303 " Not linked: pdbres="HOH A 303 " pdbres="HOH A 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY A 176 " pdbres=" NA A 201 " Not linked: pdbres=" NA A 201 " pdbres="HOH A 301 " Not linked: pdbres="HOH A 301 " pdbres="HOH A 302 " Not linked: pdbres="HOH A 302 " pdbres="HOH A 303 " Not linked: pdbres="HOH A 303 " pdbres="HOH A 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 1874 Chain: "B" Number of atoms: 2342 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY B 176 " pdbres=" NA B 201 " Not linked: pdbres=" NA B 201 " pdbres="HOH B 301 " Not linked: pdbres="HOH B 301 " pdbres="HOH B 302 " Not linked: pdbres="HOH B 302 " pdbres="HOH B 303 " Not linked: pdbres="HOH B 303 " pdbres="HOH B 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY B 176 " pdbres=" NA B 201 " Not linked: pdbres=" NA B 201 " pdbres="HOH B 301 " Not linked: pdbres="HOH B 301 " pdbres="HOH B 302 " Not linked: pdbres="HOH B 302 " pdbres="HOH B 303 " Not linked: pdbres="HOH B 303 " pdbres="HOH B 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 1874 Chain: "C" Number of atoms: 2342 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY C 176 " pdbres=" NA C 201 " Not linked: pdbres=" NA C 201 " pdbres="HOH C 301 " Not linked: pdbres="HOH C 301 " pdbres="HOH C 302 " Not linked: pdbres="HOH C 302 " pdbres="HOH C 303 " Not linked: pdbres="HOH C 303 " pdbres="HOH C 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY C 176 " pdbres=" NA C 201 " Not linked: pdbres=" NA C 201 " pdbres="HOH C 301 " Not linked: pdbres="HOH C 301 " pdbres="HOH C 302 " Not linked: pdbres="HOH C 302 " pdbres="HOH C 303 " Not linked: pdbres="HOH C 303 " pdbres="HOH C 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 1874 Chain: "D" Number of atoms: 2342 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY D 176 " pdbres=" NA D 201 " Not linked: pdbres=" NA D 201 " pdbres="HOH D 301 " Not linked: pdbres="HOH D 301 " pdbres="HOH D 302 " Not linked: pdbres="HOH D 302 " pdbres="HOH D 303 " Not linked: pdbres="HOH D 303 " pdbres="HOH D 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY D 176 " pdbres=" NA D 201 " Not linked: pdbres=" NA D 201 " pdbres="HOH D 301 " Not linked: pdbres="HOH D 301 " pdbres="HOH D 302 " Not linked: pdbres="HOH D 302 " pdbres="HOH D 303 " Not linked: pdbres="HOH D 303 " pdbres="HOH D 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 1874 Chain: "E" Number of atoms: 2342 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY E 176 " pdbres=" NA E 201 " Not linked: pdbres=" NA E 201 " pdbres="HOH E 301 " Not linked: pdbres="HOH E 301 " pdbres="HOH E 302 " Not linked: pdbres="HOH E 302 " pdbres="HOH E 303 " Not linked: pdbres="HOH E 303 " pdbres="HOH E 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY E 176 " pdbres=" NA E 201 " Not linked: pdbres=" NA E 201 " pdbres="HOH E 301 " Not linked: pdbres="HOH E 301 " pdbres="HOH E 302 " Not linked: pdbres="HOH E 302 " pdbres="HOH E 303 " Not linked: pdbres="HOH E 303 " pdbres="HOH E 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 1874 Chain: "F" Number of atoms: 2342 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY F 176 " pdbres=" NA F 201 " Not linked: pdbres=" NA F 201 " pdbres="HOH F 301 " Not linked: pdbres="HOH F 301 " pdbres="HOH F 302 " Not linked: pdbres="HOH F 302 " pdbres="HOH F 303 " Not linked: pdbres="HOH F 303 " pdbres="HOH F 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY F 176 " pdbres=" NA F 201 " Not linked: pdbres=" NA F 201 " pdbres="HOH F 301 " Not linked: pdbres="HOH F 301 " pdbres="HOH F 302 " Not linked: pdbres="HOH F 302 " pdbres="HOH F 303 " Not linked: pdbres="HOH F 303 " pdbres="HOH F 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 1874 Chain: "G" Number of atoms: 2342 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY G 176 " pdbres=" NA G 201 " Not linked: pdbres=" NA G 201 " pdbres="HOH G 301 " Not linked: pdbres="HOH G 301 " pdbres="HOH G 302 " Not linked: pdbres="HOH G 302 " pdbres="HOH G 303 " Not linked: pdbres="HOH G 303 " pdbres="HOH G 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY G 176 " pdbres=" NA G 201 " Not linked: pdbres=" NA G 201 " pdbres="HOH G 301 " Not linked: pdbres="HOH G 301 " pdbres="HOH G 302 " Not linked: pdbres="HOH G 302 " pdbres="HOH G 303 " Not linked: pdbres="HOH G 303 " pdbres="HOH G 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 1874 Chain: "H" Number of atoms: 2342 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY H 176 " pdbres=" NA H 201 " Not linked: pdbres=" NA H 201 " pdbres="HOH H 301 " Not linked: pdbres="HOH H 301 " pdbres="HOH H 302 " Not linked: pdbres="HOH H 302 " pdbres="HOH H 303 " Not linked: pdbres="HOH H 303 " pdbres="HOH H 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY H 176 " pdbres=" NA H 201 " Not linked: pdbres=" NA H 201 " pdbres="HOH H 301 " Not linked: pdbres="HOH H 301 " pdbres="HOH H 302 " Not linked: pdbres="HOH H 302 " pdbres="HOH H 303 " Not linked: pdbres="HOH H 303 " pdbres="HOH H 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 1874 Chain: "I" Number of atoms: 2342 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY I 176 " pdbres=" NA I 201 " Not linked: pdbres=" NA I 201 " pdbres="HOH I 301 " Not linked: pdbres="HOH I 301 " pdbres="HOH I 302 " Not linked: pdbres="HOH I 302 " pdbres="HOH I 303 " Not linked: pdbres="HOH I 303 " pdbres="HOH I 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY I 176 " pdbres=" NA I 201 " Not linked: pdbres=" NA I 201 " pdbres="HOH I 301 " Not linked: pdbres="HOH I 301 " pdbres="HOH I 302 " Not linked: pdbres="HOH I 302 " pdbres="HOH I 303 " Not linked: pdbres="HOH I 303 " pdbres="HOH I 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 1874 Chain: "J" Number of atoms: 2342 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY J 176 " pdbres=" NA J 201 " Not linked: pdbres=" NA J 201 " pdbres="HOH J 301 " Not linked: pdbres="HOH J 301 " pdbres="HOH J 302 " Not linked: pdbres="HOH J 302 " pdbres="HOH J 303 " Not linked: pdbres="HOH J 303 " pdbres="HOH J 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY J 176 " pdbres=" NA J 201 " Not linked: pdbres=" NA J 201 " pdbres="HOH J 301 " Not linked: pdbres="HOH J 301 " pdbres="HOH J 302 " Not linked: pdbres="HOH J 302 " pdbres="HOH J 303 " Not linked: pdbres="HOH J 303 " pdbres="HOH J 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 1874 Chain: "K" Number of atoms: 2342 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY K 176 " pdbres=" NA K 201 " Not linked: pdbres=" NA K 201 " pdbres="HOH K 301 " Not linked: pdbres="HOH K 301 " pdbres="HOH K 302 " Not linked: pdbres="HOH K 302 " pdbres="HOH K 303 " Not linked: pdbres="HOH K 303 " pdbres="HOH K 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY K 176 " pdbres=" NA K 201 " Not linked: pdbres=" NA K 201 " pdbres="HOH K 301 " Not linked: pdbres="HOH K 301 " pdbres="HOH K 302 " Not linked: pdbres="HOH K 302 " pdbres="HOH K 303 " Not linked: pdbres="HOH K 303 " pdbres="HOH K 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 1874 Chain: "L" Number of atoms: 2342 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY L 176 " pdbres=" NA L 201 " Not linked: pdbres=" NA L 201 " pdbres="HOH L 301 " Not linked: pdbres="HOH L 301 " pdbres="HOH L 302 " Not linked: pdbres="HOH L 302 " pdbres="HOH L 303 " Not linked: pdbres="HOH L 303 " pdbres="HOH L 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY L 176 " pdbres=" NA L 201 " Not linked: pdbres=" NA L 201 " pdbres="HOH L 301 " Not linked: pdbres="HOH L 301 " pdbres="HOH L 302 " Not linked: pdbres="HOH L 302 " pdbres="HOH L 303 " Not linked: pdbres="HOH L 303 " pdbres="HOH L 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 1874 Chain: "M" Number of atoms: 2342 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY M 176 " pdbres=" NA M 201 " Not linked: pdbres=" NA M 201 " pdbres="HOH M 301 " Not linked: pdbres="HOH M 301 " pdbres="HOH M 302 " Not linked: pdbres="HOH M 302 " pdbres="HOH M 303 " Not linked: pdbres="HOH M 303 " pdbres="HOH M 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY M 176 " pdbres=" NA M 201 " Not linked: pdbres=" NA M 201 " pdbres="HOH M 301 " Not linked: pdbres="HOH M 301 " pdbres="HOH M 302 " Not linked: pdbres="HOH M 302 " pdbres="HOH M 303 " Not linked: pdbres="HOH M 303 " pdbres="HOH M 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 1874 Chain: "N" Number of atoms: 2342 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY N 176 " pdbres=" NA N 201 " Not linked: pdbres=" NA N 201 " pdbres="HOH N 301 " Not linked: pdbres="HOH N 301 " pdbres="HOH N 302 " Not linked: pdbres="HOH N 302 " pdbres="HOH N 303 " Not linked: pdbres="HOH N 303 " pdbres="HOH N 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY N 176 " pdbres=" NA N 201 " Not linked: pdbres=" NA N 201 " pdbres="HOH N 301 " Not linked: pdbres="HOH N 301 " pdbres="HOH N 302 " Not linked: pdbres="HOH N 302 " pdbres="HOH N 303 " Not linked: pdbres="HOH N 303 " pdbres="HOH N 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 1874 Chain: "O" Number of atoms: 2342 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY O 176 " pdbres=" NA O 201 " Not linked: pdbres=" NA O 201 " pdbres="HOH O 301 " Not linked: pdbres="HOH O 301 " pdbres="HOH O 302 " Not linked: pdbres="HOH O 302 " pdbres="HOH O 303 " Not linked: pdbres="HOH O 303 " pdbres="HOH O 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY O 176 " pdbres=" NA O 201 " Not linked: pdbres=" NA O 201 " pdbres="HOH O 301 " Not linked: pdbres="HOH O 301 " pdbres="HOH O 302 " Not linked: pdbres="HOH O 302 " pdbres="HOH O 303 " Not linked: pdbres="HOH O 303 " pdbres="HOH O 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 1874 Chain: "P" Number of atoms: 2342 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY P 176 " pdbres=" NA P 201 " Not linked: pdbres=" NA P 201 " pdbres="HOH P 301 " Not linked: pdbres="HOH P 301 " pdbres="HOH P 302 " Not linked: pdbres="HOH P 302 " pdbres="HOH P 303 " Not linked: pdbres="HOH P 303 " pdbres="HOH P 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY P 176 " pdbres=" NA P 201 " Not linked: pdbres=" NA P 201 " pdbres="HOH P 301 " Not linked: pdbres="HOH P 301 " pdbres="HOH P 302 " Not linked: pdbres="HOH P 302 " pdbres="HOH P 303 " Not linked: pdbres="HOH P 303 " pdbres="HOH P 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 1874 Chain: "Q" Number of atoms: 2342 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY Q 176 " pdbres=" NA Q 201 " Not linked: pdbres=" NA Q 201 " pdbres="HOH Q 301 " Not linked: pdbres="HOH Q 301 " pdbres="HOH Q 302 " Not linked: pdbres="HOH Q 302 " pdbres="HOH Q 303 " Not linked: pdbres="HOH Q 303 " pdbres="HOH Q 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY Q 176 " pdbres=" NA Q 201 " Not linked: pdbres=" NA Q 201 " pdbres="HOH Q 301 " Not linked: pdbres="HOH Q 301 " pdbres="HOH Q 302 " Not linked: pdbres="HOH Q 302 " pdbres="HOH Q 303 " Not linked: pdbres="HOH Q 303 " pdbres="HOH Q 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 1874 Chain: "R" Number of atoms: 2342 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY R 176 " pdbres=" NA R 201 " Not linked: pdbres=" NA R 201 " pdbres="HOH R 301 " Not linked: pdbres="HOH R 301 " pdbres="HOH R 302 " Not linked: pdbres="HOH R 302 " pdbres="HOH R 303 " Not linked: pdbres="HOH R 303 " pdbres="HOH R 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY R 176 " pdbres=" NA R 201 " Not linked: pdbres=" NA R 201 " pdbres="HOH R 301 " Not linked: pdbres="HOH R 301 " pdbres="HOH R 302 " Not linked: pdbres="HOH R 302 " pdbres="HOH R 303 " Not linked: pdbres="HOH R 303 " pdbres="HOH R 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 1874 Chain: "S" Number of atoms: 2342 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY S 176 " pdbres=" NA S 201 " Not linked: pdbres=" NA S 201 " pdbres="HOH S 301 " Not linked: pdbres="HOH S 301 " pdbres="HOH S 302 " Not linked: pdbres="HOH S 302 " pdbres="HOH S 303 " Not linked: pdbres="HOH S 303 " pdbres="HOH S 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY S 176 " pdbres=" NA S 201 " Not linked: pdbres=" NA S 201 " pdbres="HOH S 301 " Not linked: pdbres="HOH S 301 " pdbres="HOH S 302 " Not linked: pdbres="HOH S 302 " pdbres="HOH S 303 " Not linked: pdbres="HOH S 303 " pdbres="HOH S 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 1874 Chain: "T" Number of atoms: 2342 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY T 176 " pdbres=" NA T 201 " Not linked: pdbres=" NA T 201 " pdbres="HOH T 301 " Not linked: pdbres="HOH T 301 " pdbres="HOH T 302 " Not linked: pdbres="HOH T 302 " pdbres="HOH T 303 " Not linked: pdbres="HOH T 303 " pdbres="HOH T 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY T 176 " pdbres=" NA T 201 " Not linked: pdbres=" NA T 201 " pdbres="HOH T 301 " Not linked: pdbres="HOH T 301 " pdbres="HOH T 302 " Not linked: pdbres="HOH T 302 " pdbres="HOH T 303 " Not linked: pdbres="HOH T 303 " pdbres="HOH T 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 1874 Chain: "U" Number of atoms: 2342 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY U 176 " pdbres=" NA U 201 " Not linked: pdbres=" NA U 201 " pdbres="HOH U 301 " Not linked: pdbres="HOH U 301 " pdbres="HOH U 302 " Not linked: pdbres="HOH U 302 " pdbres="HOH U 303 " Not linked: pdbres="HOH U 303 " pdbres="HOH U 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY U 176 " pdbres=" NA U 201 " Not linked: pdbres=" NA U 201 " pdbres="HOH U 301 " Not linked: pdbres="HOH U 301 " pdbres="HOH U 302 " Not linked: pdbres="HOH U 302 " pdbres="HOH U 303 " Not linked: pdbres="HOH U 303 " pdbres="HOH U 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 1874 Chain: "V" Number of atoms: 2342 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY V 176 " pdbres=" NA V 201 " Not linked: pdbres=" NA V 201 " pdbres="HOH V 301 " Not linked: pdbres="HOH V 301 " pdbres="HOH V 302 " Not linked: pdbres="HOH V 302 " pdbres="HOH V 303 " Not linked: pdbres="HOH V 303 " pdbres="HOH V 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY V 176 " pdbres=" NA V 201 " Not linked: pdbres=" NA V 201 " pdbres="HOH V 301 " Not linked: pdbres="HOH V 301 " pdbres="HOH V 302 " Not linked: pdbres="HOH V 302 " pdbres="HOH V 303 " Not linked: pdbres="HOH V 303 " pdbres="HOH V 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 1874 Chain: "W" Number of atoms: 2342 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY W 176 " pdbres=" NA W 201 " Not linked: pdbres=" NA W 201 " pdbres="HOH W 301 " Not linked: pdbres="HOH W 301 " pdbres="HOH W 302 " Not linked: pdbres="HOH W 302 " pdbres="HOH W 303 " Not linked: pdbres="HOH W 303 " pdbres="HOH W 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY W 176 " pdbres=" NA W 201 " Not linked: pdbres=" NA W 201 " pdbres="HOH W 301 " Not linked: pdbres="HOH W 301 " pdbres="HOH W 302 " Not linked: pdbres="HOH W 302 " pdbres="HOH W 303 " Not linked: pdbres="HOH W 303 " pdbres="HOH W 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 1874 Chain: "X" Number of atoms: 2342 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY X 176 " pdbres=" NA X 201 " Not linked: pdbres=" NA X 201 " pdbres="HOH X 301 " Not linked: pdbres="HOH X 301 " pdbres="HOH X 302 " Not linked: pdbres="HOH X 302 " pdbres="HOH X 303 " Not linked: pdbres="HOH X 303 " pdbres="HOH X 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 314, 2176 Unusual residues: {' NA': 1} Classifications: {'peptide': 172, 'undetermined': 1, 'water': 141} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168, None: 142} Not linked: pdbres="GLY X 176 " pdbres=" NA X 201 " Not linked: pdbres=" NA X 201 " pdbres="HOH X 301 " Not linked: pdbres="HOH X 301 " pdbres="HOH X 302 " Not linked: pdbres="HOH X 302 " pdbres="HOH X 303 " Not linked: pdbres="HOH X 303 " pdbres="HOH X 304 " ... (remaining 137 not shown) Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 1874 Residues with excluded nonbonded symmetry interactions: 408 residue: pdb=" N ATYR A 34 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 34 " occ=0.50 residue: pdb=" N ASER A 38 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 38 " occ=0.50 residue: pdb=" N AGLN A 58 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 58 " occ=0.50 residue: pdb=" N ALYS A 68 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 68 " occ=0.50 residue: pdb=" N AMET A 70 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET A 70 " occ=0.50 residue: pdb=" N ALEU A 104 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU A 104 " occ=0.50 residue: pdb=" N AGLU A 107 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 107 " occ=0.50 residue: pdb=" N ASER A 109 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 109 " occ=0.50 residue: pdb=" N ASER A 113 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 113 " occ=0.50 residue: pdb=" N ALEU A 117 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU A 117 " occ=0.50 residue: pdb=" N ALEU A 120 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU A 120 " occ=0.50 residue: pdb=" N APHE A 132 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 132 " occ=0.50 ... (remaining 396 not shown) Time building chain proxies: 34.62, per 1000 atoms: 0.62 Number of scatterers: 56208 At special positions: 0 Unit cell: (128.7, 128.7, 128.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 264 16.00 Na 24 11.00 O 10008 8.00 N 6144 7.00 C 22728 6.00 H 17040 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: 35.73 Conformation dependent library (CDL) restraints added in 9.4 seconds 10224 Ramachandran restraints generated. 5112 Oldfield, 0 Emsley, 5112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9024 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 79.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.71 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 removed outlier: 4.309A pdb=" N GLU A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 42 Processing helix chain 'B' and resid 48 through 76 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 163 through 174 removed outlier: 4.309A pdb=" N GLU B 167 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 42 Processing helix chain 'C' and resid 48 through 76 Processing helix chain 'C' and resid 95 through 124 Processing helix chain 'C' and resid 126 through 137 Processing helix chain 'C' and resid 137 through 159 Processing helix chain 'C' and resid 163 through 174 removed outlier: 4.309A pdb=" N GLU C 167 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 42 Processing helix chain 'D' and resid 48 through 76 Processing helix chain 'D' and resid 95 through 124 Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 137 through 159 Processing helix chain 'D' and resid 163 through 174 removed outlier: 4.309A pdb=" N GLU D 167 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR D 168 " --> pdb=" O GLY D 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 42 Processing helix chain 'E' and resid 48 through 76 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 163 through 174 removed outlier: 4.309A pdb=" N GLU E 167 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR E 168 " --> pdb=" O GLY E 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 42 Processing helix chain 'F' and resid 48 through 76 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 163 through 174 removed outlier: 4.309A pdb=" N GLU F 167 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR F 168 " --> pdb=" O GLY F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 42 Processing helix chain 'G' and resid 48 through 76 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 137 through 159 Processing helix chain 'G' and resid 163 through 174 removed outlier: 4.309A pdb=" N GLU G 167 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR G 168 " --> pdb=" O GLY G 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 42 Processing helix chain 'H' and resid 48 through 76 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 137 through 159 Processing helix chain 'H' and resid 163 through 174 removed outlier: 4.309A pdb=" N GLU H 167 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR H 168 " --> pdb=" O GLY H 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 42 Processing helix chain 'I' and resid 48 through 76 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 Processing helix chain 'I' and resid 137 through 159 Processing helix chain 'I' and resid 163 through 174 removed outlier: 4.309A pdb=" N GLU I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR I 168 " --> pdb=" O GLY I 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 42 Processing helix chain 'J' and resid 48 through 76 Processing helix chain 'J' and resid 95 through 124 Processing helix chain 'J' and resid 126 through 137 Processing helix chain 'J' and resid 137 through 159 Processing helix chain 'J' and resid 163 through 174 removed outlier: 4.309A pdb=" N GLU J 167 " --> pdb=" O ALA J 163 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR J 168 " --> pdb=" O GLY J 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 42 Processing helix chain 'K' and resid 48 through 76 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 137 through 159 Processing helix chain 'K' and resid 163 through 174 removed outlier: 4.309A pdb=" N GLU K 167 " --> pdb=" O ALA K 163 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR K 168 " --> pdb=" O GLY K 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 42 Processing helix chain 'L' and resid 48 through 76 Processing helix chain 'L' and resid 95 through 124 Processing helix chain 'L' and resid 126 through 137 Processing helix chain 'L' and resid 137 through 159 Processing helix chain 'L' and resid 163 through 174 removed outlier: 4.309A pdb=" N GLU L 167 " --> pdb=" O ALA L 163 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR L 168 " --> pdb=" O GLY L 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 42 Processing helix chain 'M' and resid 48 through 76 Processing helix chain 'M' and resid 95 through 124 Processing helix chain 'M' and resid 126 through 137 Processing helix chain 'M' and resid 137 through 159 Processing helix chain 'M' and resid 163 through 174 removed outlier: 4.309A pdb=" N GLU M 167 " --> pdb=" O ALA M 163 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR M 168 " --> pdb=" O GLY M 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 42 Processing helix chain 'N' and resid 48 through 76 Processing helix chain 'N' and resid 95 through 124 Processing helix chain 'N' and resid 126 through 137 Processing helix chain 'N' and resid 137 through 159 Processing helix chain 'N' and resid 163 through 174 removed outlier: 4.309A pdb=" N GLU N 167 " --> pdb=" O ALA N 163 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR N 168 " --> pdb=" O GLY N 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 42 Processing helix chain 'O' and resid 48 through 76 Processing helix chain 'O' and resid 95 through 124 Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 137 through 159 Processing helix chain 'O' and resid 163 through 174 removed outlier: 4.309A pdb=" N GLU O 167 " --> pdb=" O ALA O 163 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR O 168 " --> pdb=" O GLY O 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 42 Processing helix chain 'P' and resid 48 through 76 Processing helix chain 'P' and resid 95 through 124 Processing helix chain 'P' and resid 126 through 137 Processing helix chain 'P' and resid 137 through 159 Processing helix chain 'P' and resid 163 through 174 removed outlier: 4.309A pdb=" N GLU P 167 " --> pdb=" O ALA P 163 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR P 168 " --> pdb=" O GLY P 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 42 Processing helix chain 'Q' and resid 48 through 76 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 Processing helix chain 'Q' and resid 137 through 159 Processing helix chain 'Q' and resid 163 through 174 removed outlier: 4.309A pdb=" N GLU Q 167 " --> pdb=" O ALA Q 163 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR Q 168 " --> pdb=" O GLY Q 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 42 Processing helix chain 'R' and resid 48 through 76 Processing helix chain 'R' and resid 95 through 124 Processing helix chain 'R' and resid 126 through 137 Processing helix chain 'R' and resid 137 through 159 Processing helix chain 'R' and resid 163 through 174 removed outlier: 4.309A pdb=" N GLU R 167 " --> pdb=" O ALA R 163 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR R 168 " --> pdb=" O GLY R 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 42 Processing helix chain 'S' and resid 48 through 76 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 Processing helix chain 'S' and resid 137 through 159 Processing helix chain 'S' and resid 163 through 174 removed outlier: 4.309A pdb=" N GLU S 167 " --> pdb=" O ALA S 163 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR S 168 " --> pdb=" O GLY S 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 42 Processing helix chain 'T' and resid 48 through 76 Processing helix chain 'T' and resid 95 through 124 Processing helix chain 'T' and resid 126 through 137 Processing helix chain 'T' and resid 137 through 159 Processing helix chain 'T' and resid 163 through 174 removed outlier: 4.309A pdb=" N GLU T 167 " --> pdb=" O ALA T 163 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR T 168 " --> pdb=" O GLY T 164 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 42 Processing helix chain 'U' and resid 48 through 76 Processing helix chain 'U' and resid 95 through 124 Processing helix chain 'U' and resid 126 through 137 Processing helix chain 'U' and resid 137 through 159 Processing helix chain 'U' and resid 163 through 174 removed outlier: 4.309A pdb=" N GLU U 167 " --> pdb=" O ALA U 163 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR U 168 " --> pdb=" O GLY U 164 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 42 Processing helix chain 'V' and resid 48 through 76 Processing helix chain 'V' and resid 95 through 124 Processing helix chain 'V' and resid 126 through 137 Processing helix chain 'V' and resid 137 through 159 Processing helix chain 'V' and resid 163 through 174 removed outlier: 4.309A pdb=" N GLU V 167 " --> pdb=" O ALA V 163 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR V 168 " --> pdb=" O GLY V 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 42 Processing helix chain 'W' and resid 48 through 76 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 Processing helix chain 'W' and resid 137 through 159 Processing helix chain 'W' and resid 163 through 174 removed outlier: 4.309A pdb=" N GLU W 167 " --> pdb=" O ALA W 163 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR W 168 " --> pdb=" O GLY W 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 42 Processing helix chain 'X' and resid 48 through 76 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 Processing helix chain 'X' and resid 137 through 159 Processing helix chain 'X' and resid 163 through 174 removed outlier: 4.309A pdb=" N GLU X 167 " --> pdb=" O ALA X 163 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR X 168 " --> pdb=" O GLY X 164 " (cutoff:3.500A) 3144 hydrogen bonds defined for protein. 9504 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: 18.30 Time building geometry restraints manager: 37.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.11: 17040 1.11 - 1.29: 5808 1.29 - 1.47: 15120 1.47 - 1.64: 15672 1.64 - 1.82: 408 Bond restraints: 54048 Sorted by residual: bond pdb=" N ALA D 166 " pdb=" H AALA D 166 " ideal model delta sigma weight residual 0.860 1.046 -0.186 2.00e-02 2.50e+03 8.63e+01 bond pdb=" N ALA D 166 " pdb=" H BALA D 166 " ideal model delta sigma weight residual 0.860 1.046 -0.186 2.00e-02 2.50e+03 8.63e+01 bond pdb=" N ALA H 166 " pdb=" H AALA H 166 " ideal model delta sigma weight residual 0.860 1.046 -0.186 2.00e-02 2.50e+03 8.63e+01 bond pdb=" N ALA H 166 " pdb=" H BALA H 166 " ideal model delta sigma weight residual 0.860 1.046 -0.186 2.00e-02 2.50e+03 8.63e+01 bond pdb=" N ALA L 166 " pdb=" H AALA L 166 " ideal model delta sigma weight residual 0.860 1.046 -0.186 2.00e-02 2.50e+03 8.63e+01 ... (remaining 54043 not shown) Histogram of bond angle deviations from ideal: 98.26 - 105.41: 576 105.41 - 112.57: 49152 112.57 - 119.72: 17328 119.72 - 126.87: 21792 126.87 - 134.02: 336 Bond angle restraints: 89184 Sorted by residual: angle pdb=" CA PHE N 41 " pdb=" CB PHE N 41 " pdb=" CG PHE N 41 " ideal model delta sigma weight residual 113.80 108.38 5.42 1.00e+00 1.00e+00 2.93e+01 angle pdb=" CA PHE D 41 " pdb=" CB PHE D 41 " pdb=" CG PHE D 41 " ideal model delta sigma weight residual 113.80 108.38 5.42 1.00e+00 1.00e+00 2.93e+01 angle pdb=" CA PHE L 41 " pdb=" CB PHE L 41 " pdb=" CG PHE L 41 " ideal model delta sigma weight residual 113.80 108.38 5.42 1.00e+00 1.00e+00 2.93e+01 angle pdb=" CA PHE S 41 " pdb=" CB PHE S 41 " pdb=" CG PHE S 41 " ideal model delta sigma weight residual 113.80 108.38 5.42 1.00e+00 1.00e+00 2.93e+01 angle pdb=" CA PHE X 41 " pdb=" CB PHE X 41 " pdb=" CG PHE X 41 " ideal model delta sigma weight residual 113.80 108.38 5.42 1.00e+00 1.00e+00 2.93e+01 ... (remaining 89179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.40: 26040 15.40 - 30.81: 1968 30.81 - 46.21: 504 46.21 - 61.61: 168 61.61 - 77.02: 96 Dihedral angle restraints: 28776 sinusoidal: 12936 harmonic: 15840 Sorted by residual: dihedral pdb=" CA VAL B 46 " pdb=" C VAL B 46 " pdb=" N ALA B 47 " pdb=" CA ALA B 47 " ideal model delta harmonic sigma weight residual 180.00 162.12 17.88 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA VAL J 46 " pdb=" C VAL J 46 " pdb=" N ALA J 47 " pdb=" CA ALA J 47 " ideal model delta harmonic sigma weight residual 180.00 162.12 17.88 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA VAL F 46 " pdb=" C VAL F 46 " pdb=" N ALA F 47 " pdb=" CA ALA F 47 " ideal model delta harmonic sigma weight residual 180.00 162.12 17.88 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 28773 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.065: 3360 0.065 - 0.129: 1656 0.129 - 0.193: 384 0.193 - 0.257: 120 0.257 - 0.321: 24 Chirality restraints: 5544 Sorted by residual: chirality pdb=" CA GLU G 167 " pdb=" N GLU G 167 " pdb=" C GLU G 167 " pdb=" CB GLU G 167 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA GLU N 167 " pdb=" N GLU N 167 " pdb=" C GLU N 167 " pdb=" CB GLU N 167 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA GLU X 167 " pdb=" N GLU X 167 " pdb=" C GLU X 167 " pdb=" CB GLU X 167 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 5541 not shown) Planarity restraints: 9096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN Q 73 " 0.202 2.00e-02 2.50e+03 2.02e-01 6.10e+02 pdb=" CD GLN Q 73 " -0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN Q 73 " -0.200 2.00e-02 2.50e+03 pdb=" NE2 GLN Q 73 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN Q 73 " -0.281 2.00e-02 2.50e+03 pdb="HE22 GLN Q 73 " 0.290 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN F 73 " 0.202 2.00e-02 2.50e+03 2.02e-01 6.10e+02 pdb=" CD GLN F 73 " -0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN F 73 " -0.200 2.00e-02 2.50e+03 pdb=" NE2 GLN F 73 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN F 73 " -0.281 2.00e-02 2.50e+03 pdb="HE22 GLN F 73 " 0.290 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN S 73 " 0.202 2.00e-02 2.50e+03 2.02e-01 6.10e+02 pdb=" CD GLN S 73 " -0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN S 73 " -0.200 2.00e-02 2.50e+03 pdb=" NE2 GLN S 73 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN S 73 " -0.281 2.00e-02 2.50e+03 pdb="HE22 GLN S 73 " 0.290 2.00e-02 2.50e+03 ... (remaining 9093 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 3252 2.17 - 2.78: 83316 2.78 - 3.38: 156168 3.38 - 3.99: 236160 3.99 - 4.60: 349572 Nonbonded interactions: 828468 Sorted by model distance: nonbonded pdb=" SG CYS A 39 " pdb=" CE BMET M 70 " model vdw 1.560 3.500 nonbonded pdb=" CE BMET K 70 " pdb=" SG CYS Q 39 " model vdw 1.560 3.500 nonbonded pdb=" SG CYS I 39 " pdb=" CE BMET T 70 " model vdw 1.560 3.500 nonbonded pdb=" CE BMET D 70 " pdb=" SG CYS O 39 " model vdw 1.560 3.500 nonbonded pdb=" CE BMET G 70 " pdb=" SG CYS V 39 " model vdw 1.560 3.500 ... (remaining 828463 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 33 or resid 36 through 37 or resid 39 or resid 4 \ 1 through 42 or resid 44 through 57 or resid 60 through 67 or resid 71 or resid \ 73 through 74 or resid 76 through 101 or resid 103 or resid 106 or resid 111 thr \ ough 112 or resid 115 through 116 or resid 118 through 119 or resid 121 or resid \ 123 through 125 or resid 127 through 129 or resid 131 or resid 134 through 138 \ or resid 140 through 143 or resid 145 through 165 or resid 167 through 171 or re \ sid 174 through 201)) selection = (chain 'B' and (resid 5 through 33 or resid 36 through 37 or resid 39 or resid 4 \ 1 through 42 or resid 44 through 57 or resid 60 through 67 or resid 71 or resid \ 73 through 74 or resid 76 through 101 or resid 103 or resid 106 or resid 111 thr \ ough 112 or resid 115 through 116 or resid 118 through 119 or resid 121 or resid \ 123 through 125 or resid 127 through 129 or resid 131 or resid 134 through 138 \ or resid 140 through 143 or resid 145 through 165 or resid 167 through 171 or re \ sid 174 through 201)) selection = (chain 'C' and (resid 5 through 33 or resid 36 through 37 or resid 39 or resid 4 \ 1 through 42 or resid 44 through 57 or resid 60 through 67 or resid 71 or resid \ 73 through 74 or resid 76 through 101 or resid 103 or resid 106 or resid 111 thr \ ough 112 or resid 115 through 116 or resid 118 through 119 or resid 121 or resid \ 123 through 125 or resid 127 through 129 or resid 131 or resid 134 through 138 \ or resid 140 through 143 or resid 145 through 165 or resid 167 through 171 or re \ sid 174 through 201)) selection = (chain 'D' and (resid 5 through 33 or resid 36 through 37 or resid 39 or resid 4 \ 1 through 42 or resid 44 through 57 or resid 60 through 67 or resid 71 or resid \ 73 through 74 or resid 76 through 101 or resid 103 or resid 106 or resid 111 thr \ ough 112 or resid 115 through 116 or resid 118 through 119 or resid 121 or resid \ 123 through 125 or resid 127 through 129 or resid 131 or resid 134 through 138 \ or resid 140 through 143 or resid 145 through 165 or resid 167 through 171 or re \ sid 174 through 201)) selection = (chain 'E' and (resid 5 through 33 or resid 36 through 37 or resid 39 or resid 4 \ 1 through 42 or resid 44 through 57 or resid 60 through 67 or resid 71 or resid \ 73 through 74 or resid 76 through 101 or resid 103 or resid 106 or resid 111 thr \ ough 112 or resid 115 through 116 or resid 118 through 119 or resid 121 or resid \ 123 through 125 or resid 127 through 129 or resid 131 or resid 134 through 138 \ or resid 140 through 143 or resid 145 through 165 or resid 167 through 171 or re \ sid 174 through 201)) selection = (chain 'F' and (resid 5 through 33 or resid 36 through 37 or resid 39 or resid 4 \ 1 through 42 or resid 44 through 57 or resid 60 through 67 or resid 71 or resid \ 73 through 74 or resid 76 through 101 or resid 103 or resid 106 or resid 111 thr \ ough 112 or resid 115 through 116 or resid 118 through 119 or resid 121 or resid \ 123 through 125 or resid 127 through 129 or resid 131 or resid 134 through 138 \ or resid 140 through 143 or resid 145 through 165 or resid 167 through 171 or re \ sid 174 through 201)) selection = (chain 'G' and (resid 5 through 33 or resid 36 through 37 or resid 39 or resid 4 \ 1 through 42 or resid 44 through 57 or resid 60 through 67 or resid 71 or resid \ 73 through 74 or resid 76 through 101 or resid 103 or resid 106 or resid 111 thr \ ough 112 or resid 115 through 116 or resid 118 through 119 or resid 121 or resid \ 123 through 125 or resid 127 through 129 or resid 131 or resid 134 through 138 \ or resid 140 through 143 or resid 145 through 165 or resid 167 through 171 or re \ sid 174 through 201)) selection = (chain 'H' and (resid 5 through 33 or resid 36 through 37 or resid 39 or resid 4 \ 1 through 42 or resid 44 through 57 or resid 60 through 67 or resid 71 or resid \ 73 through 74 or resid 76 through 101 or resid 103 or resid 106 or resid 111 thr \ ough 112 or resid 115 through 116 or resid 118 through 119 or resid 121 or resid \ 123 through 125 or resid 127 through 129 or resid 131 or resid 134 through 138 \ or resid 140 through 143 or resid 145 through 165 or resid 167 through 171 or re \ sid 174 through 201)) selection = (chain 'I' and (resid 5 through 33 or resid 36 through 37 or resid 39 or resid 4 \ 1 through 42 or resid 44 through 57 or resid 60 through 67 or resid 71 or resid \ 73 through 74 or resid 76 through 101 or resid 103 or resid 106 or resid 111 thr \ ough 112 or resid 115 through 116 or resid 118 through 119 or resid 121 or resid \ 123 through 125 or resid 127 through 129 or resid 131 or resid 134 through 138 \ or resid 140 through 143 or resid 145 through 165 or resid 167 through 171 or re \ sid 174 through 201)) selection = (chain 'J' and (resid 5 through 33 or resid 36 through 37 or resid 39 or resid 4 \ 1 through 42 or resid 44 through 57 or resid 60 through 67 or resid 71 or resid \ 73 through 74 or resid 76 through 101 or resid 103 or resid 106 or resid 111 thr \ ough 112 or resid 115 through 116 or resid 118 through 119 or resid 121 or resid \ 123 through 125 or resid 127 through 129 or resid 131 or resid 134 through 138 \ or resid 140 through 143 or resid 145 through 165 or resid 167 through 171 or re \ sid 174 through 201)) selection = (chain 'K' and (resid 5 through 33 or resid 36 through 37 or resid 39 or resid 4 \ 1 through 42 or resid 44 through 57 or resid 60 through 67 or resid 71 or resid \ 73 through 74 or resid 76 through 101 or resid 103 or resid 106 or resid 111 thr \ ough 112 or resid 115 through 116 or resid 118 through 119 or resid 121 or resid \ 123 through 125 or resid 127 through 129 or resid 131 or resid 134 through 138 \ or resid 140 through 143 or resid 145 through 165 or resid 167 through 171 or re \ sid 174 through 201)) selection = (chain 'L' and (resid 5 through 33 or resid 36 through 37 or resid 39 or resid 4 \ 1 through 42 or resid 44 through 57 or resid 60 through 67 or resid 71 or resid \ 73 through 74 or resid 76 through 101 or resid 103 or resid 106 or resid 111 thr \ ough 112 or resid 115 through 116 or resid 118 through 119 or resid 121 or resid \ 123 through 125 or resid 127 through 129 or resid 131 or resid 134 through 138 \ or resid 140 through 143 or resid 145 through 165 or resid 167 through 171 or re \ sid 174 through 201)) selection = (chain 'M' and (resid 5 through 33 or resid 36 through 37 or resid 39 or resid 4 \ 1 through 42 or resid 44 through 57 or resid 60 through 67 or resid 71 or resid \ 73 through 74 or resid 76 through 101 or resid 103 or resid 106 or resid 111 thr \ ough 112 or resid 115 through 116 or resid 118 through 119 or resid 121 or resid \ 123 through 125 or resid 127 through 129 or resid 131 or resid 134 through 138 \ or resid 140 through 143 or resid 145 through 165 or resid 167 through 171 or re \ sid 174 through 201)) selection = (chain 'N' and (resid 5 through 33 or resid 36 through 37 or resid 39 or resid 4 \ 1 through 42 or resid 44 through 57 or resid 60 through 67 or resid 71 or resid \ 73 through 74 or resid 76 through 101 or resid 103 or resid 106 or resid 111 thr \ ough 112 or resid 115 through 116 or resid 118 through 119 or resid 121 or resid \ 123 through 125 or resid 127 through 129 or resid 131 or resid 134 through 138 \ or resid 140 through 143 or resid 145 through 165 or resid 167 through 171 or re \ sid 174 through 201)) selection = (chain 'O' and (resid 5 through 33 or resid 36 through 37 or resid 39 or resid 4 \ 1 through 42 or resid 44 through 57 or resid 60 through 67 or resid 71 or resid \ 73 through 74 or resid 76 through 101 or resid 103 or resid 106 or resid 111 thr \ ough 112 or resid 115 through 116 or resid 118 through 119 or resid 121 or resid \ 123 through 125 or resid 127 through 129 or resid 131 or resid 134 through 138 \ or resid 140 through 143 or resid 145 through 165 or resid 167 through 171 or re \ sid 174 through 201)) selection = (chain 'P' and (resid 5 through 33 or resid 36 through 37 or resid 39 or resid 4 \ 1 through 42 or resid 44 through 57 or resid 60 through 67 or resid 71 or resid \ 73 through 74 or resid 76 through 101 or resid 103 or resid 106 or resid 111 thr \ ough 112 or resid 115 through 116 or resid 118 through 119 or resid 121 or resid \ 123 through 125 or resid 127 through 129 or resid 131 or resid 134 through 138 \ or resid 140 through 143 or resid 145 through 165 or resid 167 through 171 or re \ sid 174 through 201)) selection = (chain 'Q' and (resid 5 through 33 or resid 36 through 37 or resid 39 or resid 4 \ 1 through 42 or resid 44 through 57 or resid 60 through 67 or resid 71 or resid \ 73 through 74 or resid 76 through 101 or resid 103 or resid 106 or resid 111 thr \ ough 112 or resid 115 through 116 or resid 118 through 119 or resid 121 or resid \ 123 through 125 or resid 127 through 129 or resid 131 or resid 134 through 138 \ or resid 140 through 143 or resid 145 through 165 or resid 167 through 171 or re \ sid 174 through 201)) selection = (chain 'R' and (resid 5 through 33 or resid 36 through 37 or resid 39 or resid 4 \ 1 through 42 or resid 44 through 57 or resid 60 through 67 or resid 71 or resid \ 73 through 74 or resid 76 through 101 or resid 103 or resid 106 or resid 111 thr \ ough 112 or resid 115 through 116 or resid 118 through 119 or resid 121 or resid \ 123 through 125 or resid 127 through 129 or resid 131 or resid 134 through 138 \ or resid 140 through 143 or resid 145 through 165 or resid 167 through 171 or re \ sid 174 through 201)) selection = (chain 'S' and (resid 5 through 33 or resid 36 through 37 or resid 39 or resid 4 \ 1 through 42 or resid 44 through 57 or resid 60 through 67 or resid 71 or resid \ 73 through 74 or resid 76 through 101 or resid 103 or resid 106 or resid 111 thr \ ough 112 or resid 115 through 116 or resid 118 through 119 or resid 121 or resid \ 123 through 125 or resid 127 through 129 or resid 131 or resid 134 through 138 \ or resid 140 through 143 or resid 145 through 165 or resid 167 through 171 or re \ sid 174 through 201)) selection = (chain 'T' and (resid 5 through 33 or resid 36 through 37 or resid 39 or resid 4 \ 1 through 42 or resid 44 through 57 or resid 60 through 67 or resid 71 or resid \ 73 through 74 or resid 76 through 101 or resid 103 or resid 106 or resid 111 thr \ ough 112 or resid 115 through 116 or resid 118 through 119 or resid 121 or resid \ 123 through 125 or resid 127 through 129 or resid 131 or resid 134 through 138 \ or resid 140 through 143 or resid 145 through 165 or resid 167 through 171 or re \ sid 174 through 201)) selection = (chain 'U' and (resid 5 through 33 or resid 36 through 37 or resid 39 or resid 4 \ 1 through 42 or resid 44 through 57 or resid 60 through 67 or resid 71 or resid \ 73 through 74 or resid 76 through 101 or resid 103 or resid 106 or resid 111 thr \ ough 112 or resid 115 through 116 or resid 118 through 119 or resid 121 or resid \ 123 through 125 or resid 127 through 129 or resid 131 or resid 134 through 138 \ or resid 140 through 143 or resid 145 through 165 or resid 167 through 171 or re \ sid 174 through 201)) selection = (chain 'V' and (resid 5 through 33 or resid 36 through 37 or resid 39 or resid 4 \ 1 through 42 or resid 44 through 57 or resid 60 through 67 or resid 71 or resid \ 73 through 74 or resid 76 through 101 or resid 103 or resid 106 or resid 111 thr \ ough 112 or resid 115 through 116 or resid 118 through 119 or resid 121 or resid \ 123 through 125 or resid 127 through 129 or resid 131 or resid 134 through 138 \ or resid 140 through 143 or resid 145 through 165 or resid 167 through 171 or re \ sid 174 through 201)) selection = (chain 'W' and (resid 5 through 33 or resid 36 through 37 or resid 39 or resid 4 \ 1 through 42 or resid 44 through 57 or resid 60 through 67 or resid 71 or resid \ 73 through 74 or resid 76 through 101 or resid 103 or resid 106 or resid 111 thr \ ough 112 or resid 115 through 116 or resid 118 through 119 or resid 121 or resid \ 123 through 125 or resid 127 through 129 or resid 131 or resid 134 through 138 \ or resid 140 through 143 or resid 145 through 165 or resid 167 through 171 or re \ sid 174 through 201)) selection = (chain 'X' and (resid 5 through 33 or resid 36 through 37 or resid 39 or resid 4 \ 1 through 42 or resid 44 through 57 or resid 60 through 67 or resid 71 or resid \ 73 through 74 or resid 76 through 101 or resid 103 or resid 106 or resid 111 thr \ ough 112 or resid 115 through 116 or resid 118 through 119 or resid 121 or resid \ 123 through 125 or resid 127 through 129 or resid 131 or resid 134 through 138 \ or resid 140 through 143 or resid 145 through 165 or resid 167 through 171 or re \ sid 174 through 201)) } 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=0.50 max=1.00 mean=0.93 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: 2.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.410 Construct map_model_manager: 1.990 Extract box with map and model: 10.170 Check model and map are aligned: 0.630 Set scattering table: 0.380 Process input model: 158.070 Find NCS groups from input model: 2.380 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 185.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 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 : 0.014 0.070 37008 Z= 0.933 Angle : 1.484 9.652 50952 Z= 1.022 Chirality : 0.079 0.321 5544 Planarity : 0.008 0.039 6816 Dihedral : 13.930 77.016 13728 Min Nonbonded Distance : 1.560 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 3.21 % Allowed : 3.21 % Favored : 93.59 % 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: 3.37 (0.11), residues: 5112 helix: 2.67 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.14 (0.23), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.011 TRP F 93 HIS 0.019 0.008 HIS D 65 PHE 0.041 0.011 PHE F 41 TYR 0.073 0.014 TYR Q 137 ARG 0.012 0.003 ARG Q 43 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10224 Ramachandran restraints generated. 5112 Oldfield, 0 Emsley, 5112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10224 Ramachandran restraints generated. 5112 Oldfield, 0 Emsley, 5112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 720 time to evaluate : 3.344 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 720 average time/residue: 1.9074 time to fit residues: 1690.5972 Evaluate side-chains 696 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 696 time to evaluate : 3.338 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.3691 > 50: distance: 13 - 42: 3.028 distance: 121 - 146: 26.234 distance: 125 - 151: 36.252 distance: 130 - 161: 33.887 distance: 138 - 146: 29.638 distance: 139 - 171: 31.905 distance: 146 - 147: 42.252 distance: 147 - 148: 61.210 distance: 147 - 150: 3.576 distance: 148 - 149: 42.334 distance: 148 - 151: 10.376 distance: 149 - 180: 51.025 distance: 149 - 189: 50.502 distance: 151 - 152: 70.109 distance: 152 - 155: 39.668 distance: 153 - 154: 57.420 distance: 154 - 198: 66.332 distance: 155 - 156: 38.562 distance: 156 - 157: 68.112 distance: 156 - 158: 52.964 distance: 158 - 160: 40.552 distance: 159 - 160: 55.709 distance: 161 - 166: 69.540 distance: 162 - 163: 40.014 distance: 162 - 165: 57.801 distance: 162 - 167: 68.949 distance: 163 - 164: 40.336 distance: 163 - 171: 57.159 distance: 164 - 218: 38.346 distance: 164 - 226: 66.400 distance: 165 - 168: 55.871 distance: 165 - 169: 45.223 distance: 165 - 170: 39.226 distance: 171 - 172: 67.550 distance: 172 - 173: 43.458 distance: 172 - 175: 51.949 distance: 173 - 174: 19.947 distance: 173 - 180: 18.098 distance: 173 - 189: 40.734 distance: 174 - 234: 40.691 distance: 175 - 176: 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