Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 17 15:34:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5a_35984/10_2023/8j5a_35984.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5a_35984/10_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_35984/10_2023/8j5a_35984.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5a_35984/10_2023/8j5a_35984.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5a_35984/10_2023/8j5a_35984.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5a_35984/10_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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 35.04, 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: 37.22 Conformation dependent library (CDL) restraints added in 8.1 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: 2.35 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: 18.39 Time building geometry restraints manager: 38.82 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: 23952 15.40 - 30.81: 1896 30.81 - 46.21: 504 46.21 - 61.61: 144 61.61 - 77.02: 96 Dihedral angle restraints: 26592 sinusoidal: 10752 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 26589 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.460 Construct map_model_manager: 2.130 Extract box with map and model: 11.250 Check model and map are aligned: 0.640 Set scattering table: 0.400 Process input model: 159.220 Find NCS groups from input model: 2.320 Set up NCS constraints: 0.220 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:10.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 188.720 ------------------------------------------------------------------------------- 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 *********************** 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 : 3.521 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 720 average time/residue: 1.9058 time to fit residues: 1690.2317 Evaluate side-chains 696 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 696 time to evaluate : 3.534 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 628 optimal weight: 4.9990 chunk 563 optimal weight: 10.0000 chunk 312 optimal weight: 7.9990 chunk 192 optimal weight: 0.0980 chunk 380 optimal weight: 6.9990 chunk 301 optimal weight: 50.0000 chunk 583 optimal weight: 50.0000 chunk 225 optimal weight: 8.9990 chunk 354 optimal weight: 8.9990 chunk 434 optimal weight: 10.0000 chunk 675 optimal weight: 50.0000 overall best weight: 5.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.0211 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 : 4.406 17.880 5544 Min Nonbonded Distance : 1.560 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 2.56 % Allowed : 3.21 % Favored : 94.23 % 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 *********************** REFINEMENT MACRO_CYCLE 2 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 696 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 696 time to evaluate : 3.672 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 696 average time/residue: 1.9627 time to fit residues: 1688.6049 Evaluate side-chains 696 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 696 time to evaluate : 3.527 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 375 optimal weight: 3.9990 chunk 209 optimal weight: 50.0000 chunk 562 optimal weight: 5.9990 chunk 460 optimal weight: 50.0000 chunk 186 optimal weight: 5.9990 chunk 676 optimal weight: 50.0000 chunk 731 optimal weight: 50.0000 chunk 602 optimal weight: 5.9990 chunk 671 optimal weight: 50.0000 chunk 230 optimal weight: 5.9990 chunk 542 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS B ** A 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 HIS B ** B 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 HIS B ** C 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 HIS B ** D 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS B ** E 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 HIS B ** F 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 HIS B ** G 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 HIS B ** H 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 HIS B ** I 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 HIS B ** J 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 HIS B ** K 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** L 105 HIS B ** L 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 HIS B ** M 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** N 105 HIS B ** N 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** O 105 HIS B ** O 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 HIS B ** P 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Q 105 HIS B ** Q 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** R 105 HIS B ** R 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** S 105 HIS B ** S 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** T 105 HIS B ** T 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** U 105 HIS B ** U 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** V 105 HIS B ** V 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** W 105 HIS B ** W 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** X 105 HIS B ** X 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 37008 Z= 0.361 Angle : 0.760 6.090 50952 Z= 0.432 Chirality : 0.039 0.147 5544 Planarity : 0.004 0.020 6816 Dihedral : 4.401 19.858 5544 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.56 % Allowed : 4.49 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.84 (0.11), residues: 5112 helix: 3.56 (0.07), residues: 4224 sheet: None (None), residues: 0 loop : 1.17 (0.26), residues: 888 *********************** REFINEMENT MACRO_CYCLE 3 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 696 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 696 time to evaluate : 4.623 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 696 average time/residue: 2.0556 time to fit residues: 1755.1313 Evaluate side-chains 672 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 672 time to evaluate : 3.517 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 668 optimal weight: 20.0000 chunk 508 optimal weight: 7.9990 chunk 351 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 323 optimal weight: 4.9990 chunk 454 optimal weight: 50.0000 chunk 679 optimal weight: 50.0000 chunk 719 optimal weight: 0.9990 chunk 354 optimal weight: 0.9990 chunk 643 optimal weight: 50.0000 chunk 193 optimal weight: 8.9990 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 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 37008 Z= 0.304 Angle : 0.676 6.072 50952 Z= 0.380 Chirality : 0.037 0.124 5544 Planarity : 0.004 0.020 6816 Dihedral : 4.335 20.208 5544 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.56 % Allowed : 4.49 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.18 (0.11), residues: 5112 helix: 3.81 (0.07), residues: 4224 sheet: None (None), residues: 0 loop : 1.22 (0.27), residues: 888 *********************** REFINEMENT MACRO_CYCLE 4 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 696 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 696 time to evaluate : 3.533 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 696 average time/residue: 2.0692 time to fit residues: 1764.8818 Evaluate side-chains 696 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 696 time to evaluate : 3.528 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 598 optimal weight: 8.9990 chunk 408 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 535 optimal weight: 6.9990 chunk 296 optimal weight: 0.0670 chunk 613 optimal weight: 50.0000 chunk 497 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 367 optimal weight: 50.0000 chunk 645 optimal weight: 50.0000 chunk 181 optimal weight: 50.0000 overall best weight: 4.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 37008 Z= 0.310 Angle : 0.680 5.854 50952 Z= 0.382 Chirality : 0.037 0.123 5544 Planarity : 0.004 0.021 6816 Dihedral : 4.296 20.323 5544 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.56 % Allowed : 4.49 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.17 (0.11), residues: 5112 helix: 3.82 (0.07), residues: 4224 sheet: None (None), residues: 0 loop : 1.12 (0.27), residues: 888 *********************** REFINEMENT MACRO_CYCLE 5 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 696 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 696 time to evaluate : 3.589 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 696 average time/residue: 2.0800 time to fit residues: 1777.4552 Evaluate side-chains 696 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 696 time to evaluate : 3.550 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 241 optimal weight: 50.0000 chunk 647 optimal weight: 50.0000 chunk 142 optimal weight: 50.0000 chunk 422 optimal weight: 50.0000 chunk 177 optimal weight: 50.0000 chunk 719 optimal weight: 4.9990 chunk 597 optimal weight: 5.9990 chunk 333 optimal weight: 50.0000 chunk 59 optimal weight: 50.0000 chunk 238 optimal weight: 50.0000 chunk 377 optimal weight: 9.9990 overall best weight: 24.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.071 37008 Z= 0.792 Angle : 1.188 7.170 50952 Z= 0.670 Chirality : 0.056 0.301 5544 Planarity : 0.008 0.052 6816 Dihedral : 4.350 17.925 5544 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 2.56 % Allowed : 5.66 % Favored : 91.77 % 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: 4.19 (0.11), residues: 5112 helix: 3.15 (0.07), residues: 4224 sheet: None (None), residues: 0 loop : 0.77 (0.25), residues: 888 *********************** REFINEMENT MACRO_CYCLE 6 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 648 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 648 time to evaluate : 3.530 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 648 average time/residue: 2.0865 time to fit residues: 1648.3504 Evaluate side-chains 648 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 648 time to evaluate : 3.586 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 694 optimal weight: 1.9990 chunk 81 optimal weight: 50.0000 chunk 410 optimal weight: 2.9990 chunk 525 optimal weight: 50.0000 chunk 407 optimal weight: 0.9990 chunk 605 optimal weight: 0.7980 chunk 401 optimal weight: 50.0000 chunk 717 optimal weight: 0.9990 chunk 448 optimal weight: 0.9980 chunk 437 optimal weight: 1.9990 chunk 331 optimal weight: 50.0000 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 37008 Z= 0.158 Angle : 0.511 4.884 50952 Z= 0.285 Chirality : 0.033 0.125 5544 Planarity : 0.003 0.021 6816 Dihedral : 4.165 21.315 5544 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.56 % Allowed : 5.77 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.69 (0.11), residues: 5112 helix: 4.18 (0.07), residues: 4224 sheet: None (None), residues: 0 loop : 1.28 (0.27), residues: 888 *********************** REFINEMENT MACRO_CYCLE 7 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 720 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 720 time to evaluate : 3.626 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 720 average time/residue: 2.0153 time to fit residues: 1789.4319 Evaluate side-chains 720 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 720 time to evaluate : 3.566 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 443 optimal weight: 10.0000 chunk 286 optimal weight: 8.9990 chunk 428 optimal weight: 50.0000 chunk 216 optimal weight: 50.0000 chunk 140 optimal weight: 8.9990 chunk 138 optimal weight: 4.9990 chunk 455 optimal weight: 50.0000 chunk 488 optimal weight: 50.0000 chunk 354 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 563 optimal weight: 4.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 37008 Z= 0.402 Angle : 0.779 6.264 50952 Z= 0.440 Chirality : 0.040 0.152 5544 Planarity : 0.005 0.029 6816 Dihedral : 4.271 19.391 5544 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.56 % Allowed : 5.77 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.01 (0.11), residues: 5112 helix: 3.71 (0.07), residues: 4224 sheet: None (None), residues: 0 loop : 1.09 (0.27), residues: 888 *********************** REFINEMENT MACRO_CYCLE 8 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 696 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 696 time to evaluate : 3.557 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 696 average time/residue: 2.0926 time to fit residues: 1785.2997 Evaluate side-chains 696 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 696 time to evaluate : 3.551 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 652 optimal weight: 9.9990 chunk 686 optimal weight: 9.9990 chunk 626 optimal weight: 5.9990 chunk 668 optimal weight: 10.0000 chunk 402 optimal weight: 50.0000 chunk 291 optimal weight: 6.9990 chunk 524 optimal weight: 50.0000 chunk 205 optimal weight: 50.0000 chunk 603 optimal weight: 4.9990 chunk 632 optimal weight: 5.9990 chunk 665 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 37008 Z= 0.357 Angle : 0.728 5.839 50952 Z= 0.411 Chirality : 0.038 0.133 5544 Planarity : 0.004 0.026 6816 Dihedral : 4.294 20.082 5544 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.56 % Allowed : 5.77 % Favored : 91.67 % 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: 4.99 (0.11), residues: 5112 helix: 3.69 (0.07), residues: 4224 sheet: None (None), residues: 0 loop : 1.11 (0.27), residues: 888 *********************** REFINEMENT MACRO_CYCLE 9 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 696 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 696 time to evaluate : 3.816 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 696 average time/residue: 2.1220 time to fit residues: 1811.2895 Evaluate side-chains 696 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 696 time to evaluate : 3.585 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 438 optimal weight: 9.9990 chunk 706 optimal weight: 50.0000 chunk 431 optimal weight: 50.0000 chunk 335 optimal weight: 50.0000 chunk 491 optimal weight: 50.0000 chunk 741 optimal weight: 50.0000 chunk 682 optimal weight: 3.9990 chunk 590 optimal weight: 9.9990 chunk 61 optimal weight: 50.0000 chunk 455 optimal weight: 50.0000 chunk 361 optimal weight: 50.0000 overall best weight: 24.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.073 37008 Z= 0.808 Angle : 1.192 8.027 50952 Z= 0.674 Chirality : 0.057 0.295 5544 Planarity : 0.008 0.056 6816 Dihedral : 4.320 17.902 5544 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 2.56 % Allowed : 5.77 % Favored : 91.67 % 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: 4.20 (0.11), residues: 5112 helix: 3.15 (0.07), residues: 4224 sheet: None (None), residues: 0 loop : 0.79 (0.25), residues: 888 ********************** REFINEMENT MACRO_CYCLE 10 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 672 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 672 time to evaluate : 3.517 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 672 average time/residue: 2.1332 time to fit residues: 1745.6923 Evaluate side-chains 693 residues out of total 2880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 693 time to evaluate : 3.551 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 744 random chunks: chunk 468 optimal weight: 1.9990 chunk 628 optimal weight: 2.9990 chunk 180 optimal weight: 50.0000 chunk 544 optimal weight: 5.9990 chunk 87 optimal weight: 50.0000 chunk 164 optimal weight: 0.9990 chunk 591 optimal weight: 4.9990 chunk 247 optimal weight: 50.0000 chunk 607 optimal weight: 50.0000 chunk 74 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.166809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.133405 restraints weight = 158337.262| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.05 r_work: 0.3169 rms_B_bonded: 0.99 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 1.50 restraints_weight: 0.2500 r_work: 0.2909 rms_B_bonded: 2.60 restraints_weight: 0.1250 r_work: 0.2874 rms_B_bonded: 3.45 restraints_weight: 0.0625 r_work: 0.2855 rms_B_bonded: 4.61 restraints_weight: 0.0312 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 37008 Z= 0.194 Angle : 0.555 4.899 50952 Z= 0.312 Chirality : 0.034 0.126 5544 Planarity : 0.003 0.023 6816 Dihedral : 4.249 21.540 5544 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.56 % Allowed : 5.77 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.36 (0.11), residues: 5112 helix: 3.95 (0.07), residues: 4224 sheet: None (None), residues: 0 loop : 1.19 (0.27), residues: 888 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31203.02 seconds wall clock time: 540 minutes 23.94 seconds (32423.94 seconds total)