Starting phenix.real_space_refine on Mon Apr 15 15:14:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cu8_26996/04_2024/8cu8_26996.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cu8_26996/04_2024/8cu8_26996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cu8_26996/04_2024/8cu8_26996.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cu8_26996/04_2024/8cu8_26996.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cu8_26996/04_2024/8cu8_26996.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cu8_26996/04_2024/8cu8_26996.pdb" } resolution = 1.91 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= 0.026 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: 5 Type Number sf(0) Gaussians Fe 24 7.16 5 S 72 5.16 5 C 20784 2.51 5 N 5688 2.21 5 O 8703 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 13": "OE1" <-> "OE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A ASP 87": "OD1" <-> "OD2" Residue "A GLU 88": "OE1" <-> "OE2" Residue "A GLU 103": "OE1" <-> "OE2" Residue "A ASP 135": "OD1" <-> "OD2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "C GLU 13": "OE1" <-> "OE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C GLU 60": "OE1" <-> "OE2" Residue "C ASP 87": "OD1" <-> "OD2" Residue "C GLU 88": "OE1" <-> "OE2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "C ASP 135": "OD1" <-> "OD2" Residue "D GLU 13": "OE1" <-> "OE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D GLU 60": "OE1" <-> "OE2" Residue "D GLU 85": "OE1" <-> "OE2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D ASP 135": "OD1" <-> "OD2" Residue "D GLU 136": "OE1" <-> "OE2" Residue "E GLU 13": "OE1" <-> "OE2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E GLU 60": "OE1" <-> "OE2" Residue "E GLU 88": "OE1" <-> "OE2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "E ASP 135": "OD1" <-> "OD2" Residue "E GLU 136": "OE1" <-> "OE2" Residue "F GLU 13": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "F GLU 60": "OE1" <-> "OE2" Residue "F GLU 88": "OE1" <-> "OE2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F ASP 135": "OD1" <-> "OD2" Residue "F GLU 136": "OE1" <-> "OE2" Residue "G GLU 13": "OE1" <-> "OE2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G ASP 87": "OD1" <-> "OD2" Residue "G GLU 88": "OE1" <-> "OE2" Residue "G GLU 103": "OE1" <-> "OE2" Residue "G GLU 131": "OE1" <-> "OE2" Residue "G ASP 135": "OD1" <-> "OD2" Residue "H GLU 13": "OE1" <-> "OE2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H ASP 87": "OD1" <-> "OD2" Residue "H GLU 88": "OE1" <-> "OE2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "H ASP 135": "OD1" <-> "OD2" Residue "H GLU 136": "OE1" <-> "OE2" Residue "I GLU 13": "OE1" <-> "OE2" Residue "I GLU 57": "OE1" <-> "OE2" Residue "I GLU 60": "OE1" <-> "OE2" Residue "I ASP 87": "OD1" <-> "OD2" Residue "I GLU 88": "OE1" <-> "OE2" Residue "I GLU 103": "OE1" <-> "OE2" Residue "I ASP 135": "OD1" <-> "OD2" Residue "I GLU 136": "OE1" <-> "OE2" Residue "J GLU 13": "OE1" <-> "OE2" Residue "J GLU 57": "OE1" <-> "OE2" Residue "J GLU 60": "OE1" <-> "OE2" Residue "J ASP 87": "OD1" <-> "OD2" Residue "J GLU 88": "OE1" <-> "OE2" Residue "J GLU 103": "OE1" <-> "OE2" Residue "J ASP 135": "OD1" <-> "OD2" Residue "J GLU 136": "OE1" <-> "OE2" Residue "K GLU 13": "OE1" <-> "OE2" Residue "K GLU 57": "OE1" <-> "OE2" Residue "K GLU 60": "OE1" <-> "OE2" Residue "K ASP 87": "OD1" <-> "OD2" Residue "K GLU 88": "OE1" <-> "OE2" Residue "K GLU 103": "OE1" <-> "OE2" Residue "K ASP 135": "OD1" <-> "OD2" Residue "K GLU 136": "OE1" <-> "OE2" Residue "L GLU 13": "OE1" <-> "OE2" Residue "L GLU 57": "OE1" <-> "OE2" Residue "L GLU 60": "OE1" <-> "OE2" Residue "L ASP 87": "OD1" <-> "OD2" Residue "L GLU 88": "OE1" <-> "OE2" Residue "L GLU 103": "OE1" <-> "OE2" Residue "L ASP 135": "OD1" <-> "OD2" Residue "L GLU 136": "OE1" <-> "OE2" Residue "M GLU 13": "OE1" <-> "OE2" Residue "M GLU 57": "OE1" <-> "OE2" Residue "M GLU 60": "OE1" <-> "OE2" Residue "M ASP 87": "OD1" <-> "OD2" Residue "M GLU 88": "OE1" <-> "OE2" Residue "M GLU 103": "OE1" <-> "OE2" Residue "M ASP 135": "OD1" <-> "OD2" Residue "M GLU 136": "OE1" <-> "OE2" Residue "N GLU 13": "OE1" <-> "OE2" Residue "N GLU 57": "OE1" <-> "OE2" Residue "N GLU 60": "OE1" <-> "OE2" Residue "N ASP 87": "OD1" <-> "OD2" Residue "N GLU 88": "OE1" <-> "OE2" Residue "N GLU 103": "OE1" <-> "OE2" Residue "N ASP 135": "OD1" <-> "OD2" Residue "N GLU 136": "OE1" <-> "OE2" Residue "O GLU 13": "OE1" <-> "OE2" Residue "O GLU 57": "OE1" <-> "OE2" Residue "O GLU 60": "OE1" <-> "OE2" Residue "O GLU 88": "OE1" <-> "OE2" Residue "O GLU 103": "OE1" <-> "OE2" Residue "O ASP 135": "OD1" <-> "OD2" Residue "O GLU 136": "OE1" <-> "OE2" Residue "P GLU 13": "OE1" <-> "OE2" Residue "P GLU 57": "OE1" <-> "OE2" Residue "P GLU 60": "OE1" <-> "OE2" Residue "P GLU 88": "OE1" <-> "OE2" Residue "P GLU 103": "OE1" <-> "OE2" Residue "P ASP 127": "OD1" <-> "OD2" Residue "P ASP 135": "OD1" <-> "OD2" Residue "P GLU 136": "OE1" <-> "OE2" Residue "Q GLU 13": "OE1" <-> "OE2" Residue "Q GLU 57": "OE1" <-> "OE2" Residue "Q GLU 60": "OE1" <-> "OE2" Residue "Q GLU 88": "OE1" <-> "OE2" Residue "Q GLU 103": "OE1" <-> "OE2" Residue "Q GLU 136": "OE1" <-> "OE2" Residue "R GLU 13": "OE1" <-> "OE2" Residue "R GLU 57": "OE1" <-> "OE2" Residue "R GLU 60": "OE1" <-> "OE2" Residue "R ASP 87": "OD1" <-> "OD2" Residue "R GLU 88": "OE1" <-> "OE2" Residue "R GLU 103": "OE1" <-> "OE2" Residue "R ASP 135": "OD1" <-> "OD2" Residue "R GLU 136": "OE1" <-> "OE2" Residue "S GLU 13": "OE1" <-> "OE2" Residue "S GLU 57": "OE1" <-> "OE2" Residue "S GLU 60": "OE1" <-> "OE2" Residue "S ASP 87": "OD1" <-> "OD2" Residue "S GLU 88": "OE1" <-> "OE2" Residue "S GLU 103": "OE1" <-> "OE2" Residue "S ASP 135": "OD1" <-> "OD2" Residue "S GLU 136": "OE1" <-> "OE2" Residue "T GLU 13": "OE1" <-> "OE2" Residue "T GLU 57": "OE1" <-> "OE2" Residue "T GLU 60": "OE1" <-> "OE2" Residue "T ASP 87": "OD1" <-> "OD2" Residue "T GLU 88": "OE1" <-> "OE2" Residue "T GLU 103": "OE1" <-> "OE2" Residue "T ASP 135": "OD1" <-> "OD2" Residue "T GLU 136": "OE1" <-> "OE2" Residue "U GLU 13": "OE1" <-> "OE2" Residue "U GLU 57": "OE1" <-> "OE2" Residue "U GLU 60": "OE1" <-> "OE2" Residue "U ASP 87": "OD1" <-> "OD2" Residue "U GLU 88": "OE1" <-> "OE2" Residue "U GLU 103": "OE1" <-> "OE2" Residue "U ASP 135": "OD1" <-> "OD2" Residue "U GLU 136": "OE1" <-> "OE2" Residue "V GLU 13": "OE1" <-> "OE2" Residue "V GLU 57": "OE1" <-> "OE2" Residue "V GLU 60": "OE1" <-> "OE2" Residue "V GLU 85": "OE1" <-> "OE2" Residue "V GLU 88": "OE1" <-> "OE2" Residue "V GLU 103": "OE1" <-> "OE2" Residue "V ASP 135": "OD1" <-> "OD2" Residue "W GLU 13": "OE1" <-> "OE2" Residue "W GLU 57": "OE1" <-> "OE2" Residue "W GLU 60": "OE1" <-> "OE2" Residue "W GLU 88": "OE1" <-> "OE2" Residue "W GLU 103": "OE1" <-> "OE2" Residue "W ASP 135": "OD1" <-> "OD2" Residue "W GLU 136": "OE1" <-> "OE2" Residue "X GLU 13": "OE1" <-> "OE2" Residue "X GLU 57": "OE1" <-> "OE2" Residue "X GLU 60": "OE1" <-> "OE2" Residue "X GLU 88": "OE1" <-> "OE2" Residue "X GLU 103": "OE1" <-> "OE2" Residue "X ASP 135": "OD1" <-> "OD2" Residue "X GLU 136": "OE1" <-> "OE2" Residue "Y GLU 13": "OE1" <-> "OE2" Residue "Y GLU 57": "OE1" <-> "OE2" Residue "Y GLU 60": "OE1" <-> "OE2" Residue "Y GLU 88": "OE1" <-> "OE2" Residue "Y GLU 103": "OE1" <-> "OE2" Residue "Y GLU 131": "OE1" <-> "OE2" Residue "Y ASP 135": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 35271 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "C" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "D" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "E" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "F" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "G" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "H" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "I" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "J" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "K" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "L" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "M" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "N" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "O" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "P" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "Q" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "R" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "S" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "T" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "U" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "V" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "W" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "X" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "Y" Number of atoms: 1374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Conformer: "B" Number of residues, atoms: 168, 1366 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} bond proxies already assigned to first conformer: 1384 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "C" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "D" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "E" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "F" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Chain: "G" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "H" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "I" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Chain: "J" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "K" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Chain: "L" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "M" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "N" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "O" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "P" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "Q" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Chain: "R" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "S" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "T" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "U" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Chain: "V" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Chain: "W" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "X" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Chain: "Y" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Residues with excluded nonbonded symmetry interactions: 48 residue: pdb=" N AASN A 106 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 106 " occ=0.50 residue: pdb=" N AASN C 106 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN C 106 " occ=0.50 residue: pdb=" N AASN D 106 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN D 106 " occ=0.50 residue: pdb=" N AASN E 106 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN E 106 " occ=0.50 residue: pdb=" N AASN F 106 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN F 106 " occ=0.50 residue: pdb=" N AASN G 106 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN G 106 " occ=0.50 residue: pdb=" N AASN H 106 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN H 106 " occ=0.50 residue: pdb=" N AASN I 106 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN I 106 " occ=0.50 residue: pdb=" N AASN J 106 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN J 106 " occ=0.50 residue: pdb=" N AASN K 106 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN K 106 " occ=0.50 residue: pdb=" N AASN L 106 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN L 106 " occ=0.50 residue: pdb=" N AASN M 106 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN M 106 " occ=0.50 ... (remaining 36 not shown) Time building chain proxies: 31.21, per 1000 atoms: 0.88 Number of scatterers: 35271 At special positions: 0 Unit cell: (128.74, 128.74, 128.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 24 26.01 S 72 16.00 O 8703 8.00 N 5688 7.00 C 20784 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: 14.26 Conformation dependent library (CDL) restraints added in 10.9 seconds 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7776 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 79.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 9 through 37 Processing helix chain 'A' and resid 44 through 72 Processing helix chain 'A' and resid 91 through 120 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 133 through 155 Processing helix chain 'A' and resid 157 through 167 Processing helix chain 'C' and resid 9 through 37 Processing helix chain 'C' and resid 44 through 72 Processing helix chain 'C' and resid 91 through 120 Processing helix chain 'C' and resid 122 through 133 Processing helix chain 'C' and resid 133 through 155 Processing helix chain 'C' and resid 157 through 167 Processing helix chain 'D' and resid 9 through 37 Processing helix chain 'D' and resid 44 through 72 Processing helix chain 'D' and resid 91 through 120 Processing helix chain 'D' and resid 122 through 133 Processing helix chain 'D' and resid 133 through 155 Processing helix chain 'D' and resid 157 through 167 Processing helix chain 'E' and resid 9 through 37 Processing helix chain 'E' and resid 44 through 72 Processing helix chain 'E' and resid 91 through 120 Processing helix chain 'E' and resid 122 through 133 Processing helix chain 'E' and resid 133 through 155 Processing helix chain 'E' and resid 157 through 167 Processing helix chain 'F' and resid 9 through 37 Processing helix chain 'F' and resid 44 through 72 Processing helix chain 'F' and resid 91 through 120 Processing helix chain 'F' and resid 122 through 133 Processing helix chain 'F' and resid 133 through 155 Processing helix chain 'F' and resid 157 through 167 Processing helix chain 'G' and resid 9 through 37 Processing helix chain 'G' and resid 44 through 72 Processing helix chain 'G' and resid 91 through 120 Processing helix chain 'G' and resid 122 through 133 Processing helix chain 'G' and resid 133 through 155 Processing helix chain 'G' and resid 157 through 167 Processing helix chain 'H' and resid 9 through 37 Processing helix chain 'H' and resid 44 through 72 Processing helix chain 'H' and resid 91 through 120 Processing helix chain 'H' and resid 122 through 133 Processing helix chain 'H' and resid 133 through 155 Processing helix chain 'H' and resid 157 through 167 Processing helix chain 'I' and resid 9 through 37 Processing helix chain 'I' and resid 44 through 72 Processing helix chain 'I' and resid 91 through 120 Processing helix chain 'I' and resid 122 through 133 Processing helix chain 'I' and resid 133 through 155 Processing helix chain 'I' and resid 157 through 167 Processing helix chain 'J' and resid 9 through 37 Processing helix chain 'J' and resid 44 through 72 Processing helix chain 'J' and resid 91 through 120 Processing helix chain 'J' and resid 122 through 133 Processing helix chain 'J' and resid 133 through 155 Processing helix chain 'J' and resid 157 through 167 Processing helix chain 'K' and resid 9 through 37 Processing helix chain 'K' and resid 44 through 72 Processing helix chain 'K' and resid 91 through 120 Processing helix chain 'K' and resid 122 through 133 Processing helix chain 'K' and resid 133 through 155 Processing helix chain 'K' and resid 157 through 167 Processing helix chain 'L' and resid 9 through 37 Processing helix chain 'L' and resid 44 through 72 Processing helix chain 'L' and resid 91 through 120 Processing helix chain 'L' and resid 122 through 133 Processing helix chain 'L' and resid 133 through 155 Processing helix chain 'L' and resid 157 through 167 Processing helix chain 'M' and resid 9 through 37 Processing helix chain 'M' and resid 44 through 72 Processing helix chain 'M' and resid 91 through 120 Processing helix chain 'M' and resid 122 through 133 Processing helix chain 'M' and resid 133 through 155 Processing helix chain 'M' and resid 157 through 167 Processing helix chain 'N' and resid 9 through 37 Processing helix chain 'N' and resid 44 through 72 Processing helix chain 'N' and resid 91 through 120 Processing helix chain 'N' and resid 122 through 133 Processing helix chain 'N' and resid 133 through 155 Processing helix chain 'N' and resid 157 through 167 Processing helix chain 'O' and resid 9 through 37 Processing helix chain 'O' and resid 44 through 72 Processing helix chain 'O' and resid 91 through 120 Processing helix chain 'O' and resid 122 through 133 Processing helix chain 'O' and resid 133 through 155 Processing helix chain 'O' and resid 157 through 167 Processing helix chain 'P' and resid 9 through 37 Processing helix chain 'P' and resid 44 through 72 Processing helix chain 'P' and resid 91 through 120 Processing helix chain 'P' and resid 122 through 133 Processing helix chain 'P' and resid 133 through 155 Processing helix chain 'P' and resid 157 through 167 Processing helix chain 'Q' and resid 9 through 37 Processing helix chain 'Q' and resid 44 through 72 Processing helix chain 'Q' and resid 91 through 120 Processing helix chain 'Q' and resid 122 through 133 Processing helix chain 'Q' and resid 133 through 155 Processing helix chain 'Q' and resid 157 through 167 Processing helix chain 'R' and resid 9 through 37 Processing helix chain 'R' and resid 44 through 72 Processing helix chain 'R' and resid 91 through 120 Processing helix chain 'R' and resid 122 through 133 Processing helix chain 'R' and resid 133 through 155 Processing helix chain 'R' and resid 157 through 167 Processing helix chain 'S' and resid 9 through 37 Processing helix chain 'S' and resid 44 through 72 Processing helix chain 'S' and resid 91 through 120 Processing helix chain 'S' and resid 122 through 133 Processing helix chain 'S' and resid 133 through 155 Processing helix chain 'S' and resid 157 through 167 Processing helix chain 'T' and resid 9 through 37 Processing helix chain 'T' and resid 44 through 72 Processing helix chain 'T' and resid 91 through 120 Processing helix chain 'T' and resid 122 through 133 Processing helix chain 'T' and resid 133 through 155 Processing helix chain 'T' and resid 157 through 167 Processing helix chain 'U' and resid 9 through 37 Processing helix chain 'U' and resid 44 through 72 Processing helix chain 'U' and resid 91 through 120 Processing helix chain 'U' and resid 122 through 133 Processing helix chain 'U' and resid 133 through 155 Processing helix chain 'U' and resid 157 through 167 Processing helix chain 'V' and resid 9 through 37 Processing helix chain 'V' and resid 44 through 72 Processing helix chain 'V' and resid 91 through 120 Processing helix chain 'V' and resid 122 through 133 Processing helix chain 'V' and resid 133 through 155 Processing helix chain 'V' and resid 157 through 167 Processing helix chain 'W' and resid 9 through 37 Processing helix chain 'W' and resid 44 through 72 Processing helix chain 'W' and resid 91 through 120 Processing helix chain 'W' and resid 122 through 133 Processing helix chain 'W' and resid 133 through 155 Processing helix chain 'W' and resid 157 through 167 Processing helix chain 'X' and resid 9 through 37 Processing helix chain 'X' and resid 44 through 72 Processing helix chain 'X' and resid 91 through 120 Processing helix chain 'X' and resid 122 through 133 Processing helix chain 'X' and resid 133 through 155 Processing helix chain 'X' and resid 157 through 167 Processing helix chain 'Y' and resid 9 through 37 Processing helix chain 'Y' and resid 44 through 72 Processing helix chain 'Y' and resid 91 through 120 Processing helix chain 'Y' and resid 122 through 133 Processing helix chain 'Y' and resid 133 through 155 Processing helix chain 'Y' and resid 157 through 167 2688 hydrogen bonds defined for protein. 8088 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: 11.09 Time building geometry restraints manager: 15.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10156 1.34 - 1.45: 5035 1.45 - 1.57: 18313 1.57 - 1.69: 0 1.69 - 1.80: 144 Bond restraints: 33648 Sorted by residual: bond pdb=" C GLY W 157 " pdb=" O GLY W 157 " ideal model delta sigma weight residual 1.235 1.252 -0.017 1.35e-02 5.49e+03 1.57e+00 bond pdb=" C GLY D 157 " pdb=" O GLY D 157 " ideal model delta sigma weight residual 1.235 1.252 -0.017 1.35e-02 5.49e+03 1.57e+00 bond pdb=" C GLY C 157 " pdb=" O GLY C 157 " ideal model delta sigma weight residual 1.235 1.252 -0.017 1.35e-02 5.49e+03 1.57e+00 bond pdb=" C GLY F 157 " pdb=" O GLY F 157 " ideal model delta sigma weight residual 1.235 1.252 -0.017 1.35e-02 5.49e+03 1.57e+00 bond pdb=" C GLY H 157 " pdb=" O GLY H 157 " ideal model delta sigma weight residual 1.235 1.252 -0.017 1.35e-02 5.49e+03 1.57e+00 ... (remaining 33643 not shown) Histogram of bond angle deviations from ideal: 100.13 - 106.90: 528 106.90 - 113.66: 18184 113.66 - 120.43: 14215 120.43 - 127.19: 12217 127.19 - 133.95: 264 Bond angle restraints: 45408 Sorted by residual: angle pdb=" C SER E 34 " pdb=" N PHE E 35 " pdb=" CA PHE E 35 " ideal model delta sigma weight residual 122.06 116.42 5.64 1.86e+00 2.89e-01 9.18e+00 angle pdb=" C SER H 34 " pdb=" N PHE H 35 " pdb=" CA PHE H 35 " ideal model delta sigma weight residual 122.06 116.43 5.63 1.86e+00 2.89e-01 9.18e+00 angle pdb=" C SER Y 34 " pdb=" N PHE Y 35 " pdb=" CA PHE Y 35 " ideal model delta sigma weight residual 122.06 116.44 5.62 1.86e+00 2.89e-01 9.13e+00 angle pdb=" C SER C 34 " pdb=" N PHE C 35 " pdb=" CA PHE C 35 " ideal model delta sigma weight residual 122.06 116.46 5.60 1.86e+00 2.89e-01 9.06e+00 angle pdb=" C SER W 34 " pdb=" N PHE W 35 " pdb=" CA PHE W 35 " ideal model delta sigma weight residual 122.06 116.46 5.60 1.86e+00 2.89e-01 9.06e+00 ... (remaining 45403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 18204 16.69 - 33.37: 1605 33.37 - 50.06: 331 50.06 - 66.75: 68 66.75 - 83.44: 48 Dihedral angle restraints: 20256 sinusoidal: 8256 harmonic: 12000 Sorted by residual: dihedral pdb=" CA VAL S 42 " pdb=" C VAL S 42 " pdb=" N ALA S 43 " pdb=" CA ALA S 43 " ideal model delta harmonic sigma weight residual 180.00 163.97 16.03 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA VAL O 42 " pdb=" C VAL O 42 " pdb=" N ALA O 43 " pdb=" CA ALA O 43 " ideal model delta harmonic sigma weight residual 180.00 163.98 16.02 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA VAL J 42 " pdb=" C VAL J 42 " pdb=" N ALA J 43 " pdb=" CA ALA J 43 " ideal model delta harmonic sigma weight residual 180.00 164.00 16.00 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 20253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2801 0.033 - 0.066: 1228 0.066 - 0.099: 527 0.099 - 0.132: 168 0.132 - 0.165: 76 Chirality restraints: 4800 Sorted by residual: chirality pdb=" CA PHE N 35 " pdb=" N PHE N 35 " pdb=" C PHE N 35 " pdb=" CB PHE N 35 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.83e-01 chirality pdb=" CA PHE T 35 " pdb=" N PHE T 35 " pdb=" C PHE T 35 " pdb=" CB PHE T 35 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.83e-01 chirality pdb=" CA PHE A 35 " pdb=" N PHE A 35 " pdb=" C PHE A 35 " pdb=" CB PHE A 35 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.83e-01 ... (remaining 4797 not shown) Planarity restraints: 6072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 28 " -0.036 2.00e-02 2.50e+03 2.91e-02 1.69e+01 pdb=" CG TYR Q 28 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 28 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 28 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 28 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 28 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR Q 28 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR Q 28 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 28 " 0.036 2.00e-02 2.50e+03 2.90e-02 1.69e+01 pdb=" CG TYR F 28 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 TYR F 28 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR F 28 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR F 28 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR F 28 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR F 28 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR F 28 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR T 28 " -0.036 2.00e-02 2.50e+03 2.90e-02 1.68e+01 pdb=" CG TYR T 28 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 TYR T 28 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR T 28 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR T 28 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR T 28 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR T 28 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR T 28 " -0.005 2.00e-02 2.50e+03 ... (remaining 6069 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 535 2.61 - 3.19: 30507 3.19 - 3.76: 58587 3.76 - 4.33: 86796 4.33 - 4.90: 133849 Nonbonded interactions: 310274 Sorted by model distance: nonbonded pdb="FE FE A 201 " pdb=" O HOH A 360 " model vdw 2.043 2.260 nonbonded pdb="FE FE F 201 " pdb=" O HOH F 359 " model vdw 2.043 2.260 nonbonded pdb="FE FE U 201 " pdb=" O HOH U 359 " model vdw 2.043 2.260 nonbonded pdb="FE FE V 201 " pdb=" O HOH V 359 " model vdw 2.043 2.260 nonbonded pdb="FE FE I 201 " pdb=" O HOH I 359 " model vdw 2.043 2.260 ... (remaining 310269 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 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'C' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'D' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'E' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'F' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'G' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'H' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'I' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'J' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'K' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'L' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'M' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'N' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'O' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'P' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'Q' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'R' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'S' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'T' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'U' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'V' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'W' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'X' and (resid 2 through 105 or resid 107 through 169 or resid 201)) selection = (chain 'Y' and (resid 2 through 105 or resid 107 through 169 or resid 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=0.99 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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 9.410 Check model and map are aligned: 0.470 Set scattering table: 0.320 Process input model: 104.220 Find NCS groups from input model: 2.510 Set up NCS constraints: 0.210 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:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9019 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 33648 Z= 0.337 Angle : 0.650 7.527 45408 Z= 0.398 Chirality : 0.048 0.165 4800 Planarity : 0.005 0.040 6072 Dihedral : 13.913 83.436 12480 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 0.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.28 (0.11), residues: 4056 helix: 1.29 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : -0.89 (0.18), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 89 HIS 0.004 0.001 HIS V 114 PHE 0.023 0.003 PHE H 35 TYR 0.071 0.004 TYR Q 28 ARG 0.002 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 720 time to evaluate : 4.310 Fit side-chains REVERT: A 147 MET cc_start: 0.9134 (mtm) cc_final: 0.8859 (mtt) REVERT: C 147 MET cc_start: 0.9132 (mtm) cc_final: 0.8858 (mtt) REVERT: D 147 MET cc_start: 0.9135 (mtm) cc_final: 0.8860 (mtt) REVERT: E 147 MET cc_start: 0.9134 (mtm) cc_final: 0.8863 (mtt) REVERT: F 147 MET cc_start: 0.9136 (mtm) cc_final: 0.8860 (mtt) REVERT: G 147 MET cc_start: 0.9140 (mtm) cc_final: 0.8866 (mtt) REVERT: H 147 MET cc_start: 0.9135 (mtm) cc_final: 0.8861 (mtt) REVERT: I 147 MET cc_start: 0.9134 (mtm) cc_final: 0.8859 (mtt) REVERT: J 147 MET cc_start: 0.9141 (mtm) cc_final: 0.8871 (mtt) REVERT: K 147 MET cc_start: 0.9138 (mtm) cc_final: 0.8863 (mtt) REVERT: L 147 MET cc_start: 0.9141 (mtm) cc_final: 0.8868 (mtt) REVERT: M 147 MET cc_start: 0.9133 (mtm) cc_final: 0.8860 (mtt) REVERT: N 147 MET cc_start: 0.9144 (mtm) cc_final: 0.8869 (mtt) REVERT: O 147 MET cc_start: 0.9137 (mtm) cc_final: 0.8862 (mtt) REVERT: P 147 MET cc_start: 0.9141 (mtm) cc_final: 0.8867 (mtt) REVERT: Q 147 MET cc_start: 0.9137 (mtm) cc_final: 0.8863 (mtt) REVERT: R 147 MET cc_start: 0.9139 (mtm) cc_final: 0.8865 (mtt) REVERT: S 147 MET cc_start: 0.9139 (mtm) cc_final: 0.8864 (mtt) REVERT: T 147 MET cc_start: 0.9136 (mtm) cc_final: 0.8862 (mtt) REVERT: U 147 MET cc_start: 0.9133 (mtm) cc_final: 0.8861 (mtt) REVERT: V 147 MET cc_start: 0.9139 (mtm) cc_final: 0.8863 (mtt) REVERT: W 147 MET cc_start: 0.9134 (mtm) cc_final: 0.8862 (mtt) REVERT: X 147 MET cc_start: 0.9135 (mtm) cc_final: 0.8857 (mtt) REVERT: Y 147 MET cc_start: 0.9142 (mtm) cc_final: 0.8870 (mtt) outliers start: 0 outliers final: 0 residues processed: 720 average time/residue: 1.9209 time to fit residues: 1588.0337 Evaluate side-chains 574 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 574 time to evaluate : 4.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 2.9990 chunk 291 optimal weight: 3.9990 chunk 161 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 196 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 300 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 224 optimal weight: 10.0000 chunk 348 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 82 GLN A 167 HIS C 79 GLN C 82 GLN C 167 HIS D 79 GLN D 82 GLN D 167 HIS E 79 GLN E 82 GLN E 167 HIS F 79 GLN F 82 GLN F 167 HIS G 79 GLN G 82 GLN G 167 HIS H 79 GLN H 82 GLN H 167 HIS I 79 GLN I 167 HIS J 79 GLN J 82 GLN J 167 HIS K 79 GLN K 82 GLN K 167 HIS L 79 GLN L 82 GLN L 167 HIS M 79 GLN M 82 GLN M 167 HIS N 79 GLN N 82 GLN N 167 HIS O 79 GLN O 82 GLN O 167 HIS P 79 GLN P 82 GLN P 167 HIS Q 79 GLN Q 82 GLN Q 167 HIS R 79 GLN R 167 HIS S 79 GLN S 82 GLN S 167 HIS T 79 GLN T 82 GLN T 167 HIS U 79 GLN U 82 GLN U 167 HIS V 79 GLN V 167 HIS W 79 GLN W 82 GLN W 167 HIS X 79 GLN X 82 GLN X 167 HIS Y 79 GLN Y 82 GLN Y 167 HIS Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8996 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 33648 Z= 0.237 Angle : 0.518 6.393 45408 Z= 0.288 Chirality : 0.040 0.148 4800 Planarity : 0.004 0.031 6072 Dihedral : 4.227 15.111 4416 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % 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: 4.32 (0.13), residues: 4056 helix: 3.45 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.34 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 89 HIS 0.003 0.001 HIS G 114 PHE 0.018 0.002 PHE L 35 TYR 0.046 0.003 TYR F 28 ARG 0.002 0.000 ARG S 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 555 time to evaluate : 4.127 Fit side-chains REVERT: A 147 MET cc_start: 0.9082 (mtm) cc_final: 0.8811 (mtt) REVERT: C 147 MET cc_start: 0.9079 (mtm) cc_final: 0.8809 (mtt) REVERT: D 147 MET cc_start: 0.9080 (mtm) cc_final: 0.8810 (mtt) REVERT: E 147 MET cc_start: 0.9081 (mtm) cc_final: 0.8810 (mtt) REVERT: F 147 MET cc_start: 0.9083 (mtm) cc_final: 0.8809 (mtt) REVERT: G 147 MET cc_start: 0.9085 (mtm) cc_final: 0.8817 (mtt) REVERT: H 147 MET cc_start: 0.9082 (mtm) cc_final: 0.8810 (mtt) REVERT: I 147 MET cc_start: 0.9080 (mtm) cc_final: 0.8809 (mtt) REVERT: J 147 MET cc_start: 0.9084 (mtm) cc_final: 0.8815 (mtt) REVERT: K 147 MET cc_start: 0.9085 (mtm) cc_final: 0.8812 (mtt) REVERT: L 147 MET cc_start: 0.9084 (mtm) cc_final: 0.8818 (mtt) REVERT: M 147 MET cc_start: 0.9080 (mtm) cc_final: 0.8807 (mtt) REVERT: N 147 MET cc_start: 0.9086 (mtm) cc_final: 0.8817 (mtt) REVERT: O 147 MET cc_start: 0.9083 (mtm) cc_final: 0.8810 (mtt) REVERT: P 147 MET cc_start: 0.9085 (mtm) cc_final: 0.8815 (mtt) REVERT: Q 147 MET cc_start: 0.9083 (mtm) cc_final: 0.8811 (mtt) REVERT: R 147 MET cc_start: 0.9083 (mtm) cc_final: 0.8815 (mtt) REVERT: S 147 MET cc_start: 0.9082 (mtm) cc_final: 0.8815 (mtt) REVERT: T 147 MET cc_start: 0.9083 (mtm) cc_final: 0.8811 (mtt) REVERT: U 147 MET cc_start: 0.9081 (mtm) cc_final: 0.8810 (mtt) REVERT: V 147 MET cc_start: 0.9084 (mtm) cc_final: 0.8810 (mtt) REVERT: W 147 MET cc_start: 0.9082 (mtm) cc_final: 0.8810 (mtt) REVERT: X 147 MET cc_start: 0.9082 (mtm) cc_final: 0.8807 (mtt) REVERT: Y 147 MET cc_start: 0.9084 (mtm) cc_final: 0.8817 (mtt) outliers start: 0 outliers final: 0 residues processed: 555 average time/residue: 1.7107 time to fit residues: 1116.0954 Evaluate side-chains 645 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 645 time to evaluate : 4.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 290 optimal weight: 3.9990 chunk 237 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 349 optimal weight: 4.9990 chunk 377 optimal weight: 1.9990 chunk 311 optimal weight: 6.9990 chunk 346 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 280 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN C 82 GLN D 82 GLN E 82 GLN F 82 GLN G 82 GLN H 82 GLN J 82 GLN K 82 GLN L 82 GLN M 82 GLN N 82 GLN O 82 GLN P 82 GLN Q 82 GLN S 82 GLN T 82 GLN U 82 GLN W 82 GLN X 82 GLN Y 82 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 33648 Z= 0.236 Angle : 0.504 6.372 45408 Z= 0.281 Chirality : 0.040 0.147 4800 Planarity : 0.003 0.029 6072 Dihedral : 4.147 14.449 4416 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.09 % Allowed : 5.65 % Favored : 94.26 % 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: 5.06 (0.13), residues: 4056 helix: 3.97 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.14 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP O 89 HIS 0.003 0.001 HIS Y 114 PHE 0.018 0.002 PHE H 35 TYR 0.038 0.003 TYR F 28 ARG 0.001 0.000 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 549 time to evaluate : 4.575 Fit side-chains REVERT: A 147 MET cc_start: 0.9078 (mtm) cc_final: 0.8817 (mtt) REVERT: C 147 MET cc_start: 0.9077 (mtm) cc_final: 0.8813 (mtt) REVERT: D 147 MET cc_start: 0.9077 (mtm) cc_final: 0.8815 (mtt) REVERT: E 147 MET cc_start: 0.9077 (mtm) cc_final: 0.8817 (mtt) REVERT: F 147 MET cc_start: 0.9077 (mtm) cc_final: 0.8816 (mtt) REVERT: G 147 MET cc_start: 0.9077 (mtm) cc_final: 0.8819 (mtt) REVERT: H 147 MET cc_start: 0.9078 (mtm) cc_final: 0.8816 (mtt) REVERT: I 147 MET cc_start: 0.9076 (mtm) cc_final: 0.8814 (mtt) REVERT: J 147 MET cc_start: 0.9077 (mtm) cc_final: 0.8817 (mtt) REVERT: K 147 MET cc_start: 0.9082 (mtm) cc_final: 0.8819 (mtt) REVERT: L 147 MET cc_start: 0.9077 (mtm) cc_final: 0.8818 (mtt) REVERT: M 147 MET cc_start: 0.9078 (mtm) cc_final: 0.8815 (mtt) REVERT: N 147 MET cc_start: 0.9080 (mtm) cc_final: 0.8820 (mtt) REVERT: O 147 MET cc_start: 0.9080 (mtm) cc_final: 0.8817 (mtt) REVERT: P 147 MET cc_start: 0.9077 (mtm) cc_final: 0.8817 (mtt) REVERT: Q 147 MET cc_start: 0.9078 (mtm) cc_final: 0.8818 (mtt) REVERT: R 147 MET cc_start: 0.9075 (mtm) cc_final: 0.8815 (mtt) REVERT: S 147 MET cc_start: 0.9075 (mtm) cc_final: 0.8816 (mtt) REVERT: T 147 MET cc_start: 0.9081 (mtm) cc_final: 0.8817 (mtt) REVERT: U 147 MET cc_start: 0.9077 (mtm) cc_final: 0.8816 (mtt) REVERT: V 147 MET cc_start: 0.9081 (mtm) cc_final: 0.8817 (mtt) REVERT: W 147 MET cc_start: 0.9078 (mtm) cc_final: 0.8817 (mtt) REVERT: X 147 MET cc_start: 0.9079 (mtm) cc_final: 0.8814 (mtt) REVERT: Y 147 MET cc_start: 0.9078 (mtm) cc_final: 0.8820 (mtt) outliers start: 3 outliers final: 0 residues processed: 549 average time/residue: 1.7424 time to fit residues: 1124.8423 Evaluate side-chains 528 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 4.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 166 optimal weight: 7.9990 chunk 234 optimal weight: 2.9990 chunk 350 optimal weight: 3.9990 chunk 371 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 332 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN D 82 GLN E 82 GLN F 82 GLN G 82 GLN H 82 GLN J 82 GLN K 82 GLN L 82 GLN N 82 GLN O 82 GLN P 82 GLN Q 82 GLN S 82 GLN T 82 GLN U 82 GLN V 82 GLN W 82 GLN X 82 GLN Y 82 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 33648 Z= 0.188 Angle : 0.470 6.364 45408 Z= 0.261 Chirality : 0.039 0.140 4800 Planarity : 0.003 0.028 6072 Dihedral : 4.048 14.422 4416 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.14 % Allowed : 6.28 % Favored : 93.58 % 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: 5.38 (0.13), residues: 4056 helix: 4.20 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.06 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 89 HIS 0.002 0.001 HIS D 114 PHE 0.017 0.002 PHE O 35 TYR 0.026 0.002 TYR W 28 ARG 0.001 0.000 ARG Q 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 528 time to evaluate : 4.198 Fit side-chains REVERT: A 147 MET cc_start: 0.9066 (mtm) cc_final: 0.8822 (mtt) REVERT: C 131 GLU cc_start: 0.7476 (tp30) cc_final: 0.7236 (tp30) REVERT: C 147 MET cc_start: 0.9064 (mtm) cc_final: 0.8820 (mtt) REVERT: D 147 MET cc_start: 0.9065 (mtm) cc_final: 0.8822 (mtt) REVERT: E 131 GLU cc_start: 0.7470 (tp30) cc_final: 0.7238 (tp30) REVERT: E 147 MET cc_start: 0.9064 (mtm) cc_final: 0.8824 (mtt) REVERT: F 147 MET cc_start: 0.9067 (mtm) cc_final: 0.8822 (mtt) REVERT: G 147 MET cc_start: 0.9066 (mtm) cc_final: 0.8808 (mtt) REVERT: H 147 MET cc_start: 0.9066 (mtm) cc_final: 0.8822 (mtt) REVERT: I 147 MET cc_start: 0.9064 (mtm) cc_final: 0.8822 (mtt) REVERT: J 147 MET cc_start: 0.9065 (mtm) cc_final: 0.8806 (mtt) REVERT: K 147 MET cc_start: 0.9069 (mtm) cc_final: 0.8824 (mtt) REVERT: L 147 MET cc_start: 0.9065 (mtm) cc_final: 0.8807 (mtt) REVERT: M 131 GLU cc_start: 0.7475 (tp30) cc_final: 0.7239 (tp30) REVERT: M 147 MET cc_start: 0.9064 (mtm) cc_final: 0.8820 (mtt) REVERT: N 147 MET cc_start: 0.9068 (mtm) cc_final: 0.8809 (mtt) REVERT: O 147 MET cc_start: 0.9067 (mtm) cc_final: 0.8822 (mtt) REVERT: P 147 MET cc_start: 0.9066 (mtm) cc_final: 0.8806 (mtt) REVERT: Q 147 MET cc_start: 0.9067 (mtm) cc_final: 0.8824 (mtt) REVERT: R 147 MET cc_start: 0.9066 (mtm) cc_final: 0.8806 (mtt) REVERT: S 147 MET cc_start: 0.9063 (mtm) cc_final: 0.8805 (mtt) REVERT: T 147 MET cc_start: 0.9062 (mtm) cc_final: 0.8817 (mtt) REVERT: U 147 MET cc_start: 0.9067 (mtm) cc_final: 0.8822 (mtt) REVERT: V 147 MET cc_start: 0.9068 (mtm) cc_final: 0.8822 (mtt) REVERT: W 147 MET cc_start: 0.9065 (mtm) cc_final: 0.8820 (mtt) REVERT: X 147 MET cc_start: 0.9065 (mtm) cc_final: 0.8818 (mtt) REVERT: Y 147 MET cc_start: 0.9066 (mtm) cc_final: 0.8808 (mtt) outliers start: 5 outliers final: 0 residues processed: 528 average time/residue: 1.7840 time to fit residues: 1108.1523 Evaluate side-chains 696 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 696 time to evaluate : 4.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 276 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 316 optimal weight: 0.9990 chunk 256 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 8.9990 chunk 333 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: