Starting phenix.real_space_refine on Sat Jun 29 04:35:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bqw_16189/06_2024/8bqw_16189.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bqw_16189/06_2024/8bqw_16189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bqw_16189/06_2024/8bqw_16189.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bqw_16189/06_2024/8bqw_16189.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bqw_16189/06_2024/8bqw_16189.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bqw_16189/06_2024/8bqw_16189.pdb" } resolution = 2.3 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 10740 2.51 5 N 3060 2.21 5 O 3585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "M GLU 83": "OE1" <-> "OE2" Residue "Q GLU 83": "OE1" <-> "OE2" Residue "U GLU 83": "OE1" <-> "OE2" Residue "Y GLU 83": "OE1" <-> "OE2" Residue "2 GLU 83": "OE1" <-> "OE2" Residue "6 GLU 83": "OE1" <-> "OE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "I GLU 83": "OE1" <-> "OE2" Residue "a GLU 83": "OE1" <-> "OE2" Residue "e GLU 83": "OE1" <-> "OE2" Residue "i GLU 83": "OE1" <-> "OE2" Residue "m GLU 83": "OE1" <-> "OE2" Residue "q GLU 83": "OE1" <-> "OE2" Residue "u GLU 83": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 17385 Number of models: 1 Model: "" Number of chains: 90 Chain: "M" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "N" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "O" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "P" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "M" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "N" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "Q" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "R" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "S" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "T" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "Q" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "R" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "U" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "V" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "W" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "X" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "U" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "V" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "Y" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "Z" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "0" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "1" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "Y" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "Z" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "2" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "3" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "4" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "5" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "2" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "3" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "6" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "7" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "8" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "9" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "6" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "7" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "C" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "F" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "G" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "J" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "K" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "J" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "a" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "b" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "c" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "d" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "a" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "b" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "e" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "f" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "g" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "h" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "e" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "f" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "i" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "j" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "k" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "l" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "i" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "j" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "m" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "n" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "o" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "p" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "m" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "n" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "q" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "r" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "s" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "t" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "q" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "r" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "u" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "v" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "w" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "x" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "u" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "v" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 8.68, per 1000 atoms: 0.50 Number of scatterers: 17385 At special positions: 0 Unit cell: (141.765, 90.148, 57.433, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 3585 8.00 N 3060 7.00 C 10740 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 21.21 Conformation dependent library (CDL) restraints added in 3.1 seconds 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4440 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... No hydrogen bonds 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: 0.01 Time building geometry restraints manager: 21.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 3090 1.29 - 1.35: 2730 1.35 - 1.42: 450 1.42 - 1.48: 3088 1.48 - 1.55: 7892 Bond restraints: 17250 Sorted by residual: bond pdb=" CA ALA q 89 " pdb=" CB ALA q 89 " ideal model delta sigma weight residual 1.529 1.495 0.034 1.62e-02 3.81e+03 4.50e+00 bond pdb=" CA ALA U 89 " pdb=" CB ALA U 89 " ideal model delta sigma weight residual 1.529 1.495 0.034 1.62e-02 3.81e+03 4.48e+00 bond pdb=" CA ALA m 89 " pdb=" CB ALA m 89 " ideal model delta sigma weight residual 1.529 1.495 0.034 1.62e-02 3.81e+03 4.46e+00 bond pdb=" CA ALA Y 89 " pdb=" CB ALA Y 89 " ideal model delta sigma weight residual 1.529 1.495 0.034 1.62e-02 3.81e+03 4.43e+00 bond pdb=" CA ALA u 89 " pdb=" CB ALA u 89 " ideal model delta sigma weight residual 1.529 1.495 0.034 1.62e-02 3.81e+03 4.42e+00 ... (remaining 17245 not shown) Histogram of bond angle deviations from ideal: 106.08 - 111.39: 6836 111.39 - 116.69: 6646 116.69 - 121.99: 4912 121.99 - 127.29: 4826 127.29 - 132.59: 30 Bond angle restraints: 23250 Sorted by residual: angle pdb=" C HIS m 50 " pdb=" CA HIS m 50 " pdb=" CB HIS m 50 " ideal model delta sigma weight residual 109.65 116.13 -6.48 1.75e+00 3.27e-01 1.37e+01 angle pdb=" C HIS E 50 " pdb=" CA HIS E 50 " pdb=" CB HIS E 50 " ideal model delta sigma weight residual 109.65 116.12 -6.47 1.75e+00 3.27e-01 1.37e+01 angle pdb=" C HIS 2 50 " pdb=" CA HIS 2 50 " pdb=" CB HIS 2 50 " ideal model delta sigma weight residual 109.65 116.11 -6.46 1.75e+00 3.27e-01 1.36e+01 angle pdb=" C HIS I 50 " pdb=" CA HIS I 50 " pdb=" CB HIS I 50 " ideal model delta sigma weight residual 109.65 116.11 -6.46 1.75e+00 3.27e-01 1.36e+01 angle pdb=" C HIS a 50 " pdb=" CA HIS a 50 " pdb=" CB HIS a 50 " ideal model delta sigma weight residual 109.65 116.11 -6.46 1.75e+00 3.27e-01 1.36e+01 ... (remaining 23245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.58: 9075 9.58 - 19.16: 840 19.16 - 28.74: 135 28.74 - 38.32: 30 38.32 - 47.90: 60 Dihedral angle restraints: 10140 sinusoidal: 3180 harmonic: 6960 Sorted by residual: dihedral pdb=" CA GLY I 14 " pdb=" C GLY I 14 " pdb=" N VAL I 15 " pdb=" CA VAL I 15 " ideal model delta harmonic sigma weight residual -180.00 -164.80 -15.20 0 5.00e+00 4.00e-02 9.25e+00 dihedral pdb=" CA GLY i 14 " pdb=" C GLY i 14 " pdb=" N VAL i 15 " pdb=" CA VAL i 15 " ideal model delta harmonic sigma weight residual -180.00 -164.82 -15.18 0 5.00e+00 4.00e-02 9.22e+00 dihedral pdb=" CA GLY E 14 " pdb=" C GLY E 14 " pdb=" N VAL E 15 " pdb=" CA VAL E 15 " ideal model delta harmonic sigma weight residual -180.00 -164.82 -15.18 0 5.00e+00 4.00e-02 9.21e+00 ... (remaining 10137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 964 0.028 - 0.056: 457 0.056 - 0.084: 422 0.084 - 0.112: 927 0.112 - 0.140: 290 Chirality restraints: 3060 Sorted by residual: chirality pdb=" CA ILE 7 88 " pdb=" N ILE 7 88 " pdb=" C ILE 7 88 " pdb=" CB ILE 7 88 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE N 88 " pdb=" N ILE N 88 " pdb=" C ILE N 88 " pdb=" CB ILE N 88 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA ILE f 88 " pdb=" N ILE f 88 " pdb=" C ILE f 88 " pdb=" CB ILE f 88 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 3057 not shown) Planarity restraints: 2910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL i 49 " -0.005 2.00e-02 2.50e+03 1.04e-02 1.09e+00 pdb=" C VAL i 49 " 0.018 2.00e-02 2.50e+03 pdb=" O VAL i 49 " -0.007 2.00e-02 2.50e+03 pdb=" N HIS i 50 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL m 49 " -0.005 2.00e-02 2.50e+03 1.04e-02 1.09e+00 pdb=" C VAL m 49 " 0.018 2.00e-02 2.50e+03 pdb=" O VAL m 49 " -0.007 2.00e-02 2.50e+03 pdb=" N HIS m 50 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 49 " 0.005 2.00e-02 2.50e+03 1.04e-02 1.09e+00 pdb=" C VAL R 49 " -0.018 2.00e-02 2.50e+03 pdb=" O VAL R 49 " 0.007 2.00e-02 2.50e+03 pdb=" N HIS R 50 " 0.006 2.00e-02 2.50e+03 ... (remaining 2907 not shown) Histogram of nonbonded interaction distances: 0.05 - 1.02: 12931 1.02 - 1.99: 25226 1.99 - 2.96: 54325 2.96 - 3.93: 110722 3.93 - 4.90: 242386 Warning: very small nonbonded interaction distances. Nonbonded interactions: 445590 Sorted by model distance: nonbonded pdb=" OE1 GLN V 24 " pdb=" OE1 GLN Z 24 " model vdw 0.052 3.040 nonbonded pdb=" OE1 GLN b 24 " pdb=" OE1 GLN r 24 " model vdw 0.052 3.040 nonbonded pdb=" OE1 GLN j 24 " pdb=" OE1 GLN n 24 " model vdw 0.053 3.040 nonbonded pdb=" OE1 GLN Z 24 " pdb=" OE1 GLN F 24 " model vdw 0.053 3.040 nonbonded pdb=" OE1 GLN N 24 " pdb=" OE1 GLN 3 24 " model vdw 0.053 3.040 ... (remaining 445585 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 '0' selection = chain '1' selection = chain '4' selection = chain '5' selection = chain '8' selection = chain '9' selection = chain 'B' selection = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'X' selection = chain 'c' selection = chain 'd' selection = chain 'g' selection = chain 'h' selection = chain 'k' selection = chain 'l' selection = chain 'o' selection = chain 'p' selection = chain 's' selection = chain 't' selection = chain 'w' selection = chain 'x' } ncs_group { reference = chain '2' selection = chain '3' selection = chain '6' selection = chain '7' selection = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'U' selection = chain 'V' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'e' selection = chain 'f' selection = chain 'i' selection = chain 'j' selection = chain 'm' selection = chain 'n' selection = chain 'q' selection = chain 'r' selection = chain 'u' selection = chain 'v' } 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=1.00 max=1.00 mean=1.00 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.130 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 65.310 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.280 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: 0.000 Load rotamer database and sin/cos tables:10.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 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 : 0.008 0.034 17250 Z= 0.545 Angle : 1.138 6.480 23250 Z= 0.687 Chirality : 0.074 0.140 3060 Planarity : 0.003 0.010 2910 Dihedral : 8.963 47.901 5700 Min Nonbonded Distance : 0.052 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.78 (0.14), residues: 2190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.11), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS U 50 PHE 0.010 0.003 PHE v 94 TYR 0.005 0.002 TYR v 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 509 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 58 LYS cc_start: 0.8296 (mttt) cc_final: 0.8067 (mttp) REVERT: Q 97 LYS cc_start: 0.7843 (mttt) cc_final: 0.7605 (mttm) REVERT: R 21 LYS cc_start: 0.8251 (tttt) cc_final: 0.7780 (ttpm) REVERT: R 97 LYS cc_start: 0.7937 (mttt) cc_final: 0.7670 (mttm) REVERT: u 21 LYS cc_start: 0.8089 (tttt) cc_final: 0.7500 (ttpt) REVERT: u 80 LYS cc_start: 0.8505 (tttt) cc_final: 0.6872 (mptt) REVERT: v 80 LYS cc_start: 0.8462 (tttt) cc_final: 0.6818 (mptt) REVERT: v 97 LYS cc_start: 0.7835 (mttt) cc_final: 0.7522 (mttm) outliers start: 0 outliers final: 0 residues processed: 509 average time/residue: 1.4046 time to fit residues: 804.4594 Evaluate side-chains 509 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 509 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.6034 > 50: distance: 337 - 341: 3.711 distance: 341 - 342: 10.651 distance: 342 - 343: 19.340 distance: 342 - 345: 7.701 distance: 343 - 344: 37.477 distance: 343 - 350: 32.286 distance: 345 - 346: 20.337 distance: 346 - 347: 19.264 distance: 347 - 348: 16.045 distance: 348 - 349: 7.699 distance: 350 - 351: 14.176 distance: 351 - 352: 31.448 distance: 351 - 354: 18.904 distance: 352 - 353: 29.283 distance: 352 - 357: 32.308 distance: 354 - 355: 22.551 distance: 354 - 356: 24.607 distance: 357 - 358: 34.849 distance: 358 - 359: 32.574 distance: 358 - 361: 22.722 distance: 359 - 360: 29.244 distance: 359 - 366: 34.146 distance: 361 - 362: 18.067 distance: 362 - 363: 26.133 distance: 363 - 364: 19.604 distance: 364 - 365: 17.002 distance: 366 - 367: 6.993 distance: 367 - 368: 26.375 distance: 368 - 369: 18.305 distance: 368 - 375: 21.360 distance: 370 - 371: 32.793 distance: 371 - 372: 27.416 distance: 372 - 374: 18.852 distance: 375 - 376: 31.594 distance: 376 - 377: 19.226 distance: 377 - 378: 41.512 distance: 377 - 379: 32.350 distance: 379 - 380: 26.282 distance: 380 - 381: 7.028 distance: 380 - 383: 21.102 distance: 381 - 382: 17.358 distance: 381 - 386: 12.768 distance: 383 - 384: 25.134 distance: 383 - 385: 18.073 distance: 386 - 387: 17.371 distance: 387 - 388: 11.676 distance: 387 - 390: 26.941 distance: 388 - 389: 11.316 distance: 388 - 393: 16.928 distance: 390 - 391: 3.765 distance: 390 - 392: 11.845 distance: 393 - 394: 13.563 distance: 394 - 395: 15.340 distance: 394 - 397: 15.454 distance: 395 - 396: 31.767 distance: 395 - 403: 10.545 distance: 397 - 398: 12.123 distance: 398 - 399: 17.623 distance: 398 - 400: 17.487 distance: 399 - 401: 16.127 distance: 400 - 402: 20.195 distance: 401 - 402: 19.272 distance: 403 - 404: 15.900 distance: 404 - 405: 46.298 distance: 405 - 406: 41.411 distance: 405 - 407: 19.217 distance: 407 - 408: 10.712 distance: 408 - 409: 9.140 distance: 408 - 411: 24.093 distance: 409 - 410: 29.877 distance: 409 - 414: 27.393 distance: 411 - 412: 40.066 distance: 411 - 413: 34.247