Starting phenix.real_space_refine on Sat Dec 16 13:16:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cu8_26996/12_2023/8cu8_26996.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cu8_26996/12_2023/8cu8_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_26996/12_2023/8cu8_26996.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cu8_26996/12_2023/8cu8_26996.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cu8_26996/12_2023/8cu8_26996.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cu8_26996/12_2023/8cu8_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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 32.13, per 1000 atoms: 0.91 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: 13.56 Conformation dependent library (CDL) restraints added in 11.4 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: 2.55 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: 10.78 Time building geometry restraints manager: 14.43 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: 1.770 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: 0.030 Extract box with map and model: 9.730 Check model and map are aligned: 0.470 Set scattering table: 0.280 Process input model: 105.750 Find NCS groups from input model: 2.660 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:13.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.200 ------------------------------------------------------------------------------- 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 : 4.333 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 720 average time/residue: 1.9891 time to fit residues: 1647.0489 Evaluate side-chains 574 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 574 time to evaluate : 4.086 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.7215 ------------------------------------------------------------------------------- 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: 4.9990 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: 3.1990 ------------------------------------------------------------------------------- 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: 0.8999 moved from start: 0.0908 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= 0.249 Angle : 0.523 6.405 45408 Z= 0.292 Chirality : 0.041 0.149 4800 Planarity : 0.004 0.031 6072 Dihedral : 4.241 15.143 4416 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % 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: 4.29 (0.13), residues: 4056 helix: 3.42 (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 Y 114 PHE 0.018 0.002 PHE P 35 TYR 0.047 0.003 TYR Q 28 ARG 0.002 0.000 ARG L 59 *********************** 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 552 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 552 time to evaluate : 4.121 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 552 average time/residue: 1.6902 time to fit residues: 1101.2102 Evaluate side-chains 624 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 624 time to evaluate : 4.022 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4605 ------------------------------------------------------------------------------- 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: 10.0000 chunk 290 optimal weight: 6.9990 chunk 237 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 349 optimal weight: 4.9990 chunk 377 optimal weight: 2.9990 chunk 311 optimal weight: 6.9990 chunk 346 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 280 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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: 0.8993 moved from start: 0.0954 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= 0.235 Angle : 0.500 6.391 45408 Z= 0.280 Chirality : 0.040 0.147 4800 Planarity : 0.003 0.029 6072 Dihedral : 4.146 14.455 4416 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 0.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.09 % Allowed : 5.62 % Favored : 94.29 % 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 V 89 HIS 0.003 0.001 HIS G 114 PHE 0.018 0.002 PHE R 35 TYR 0.037 0.003 TYR F 28 ARG 0.001 0.000 ARG X 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 555 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 552 time to evaluate : 3.781 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 552 average time/residue: 1.6693 time to fit residues: 1088.3363 Evaluate side-chains 528 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 3.828 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9968 ------------------------------------------------------------------------------- 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: 0.9990 chunk 262 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 166 optimal weight: 7.9990 chunk 234 optimal weight: 3.9990 chunk 350 optimal weight: 2.9990 chunk 371 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 332 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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: 0.8966 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 33648 Z= 0.179 Angle : 0.462 6.456 45408 Z= 0.257 Chirality : 0.039 0.137 4800 Planarity : 0.003 0.028 6072 Dihedral : 4.030 14.450 4416 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.14 % Allowed : 6.93 % Favored : 92.92 % 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: 5.44 (0.13), residues: 4056 helix: 4.24 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.05 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 89 HIS 0.002 0.001 HIS G 114 PHE 0.016 0.002 PHE X 35 TYR 0.025 0.002 TYR F 28 ARG 0.001 0.000 ARG F 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 : 4.468 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 528 average time/residue: 1.4900 time to fit residues: 924.0281 Evaluate side-chains 696 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 696 time to evaluate : 3.074 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9593 ------------------------------------------------------------------------------- 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: 1.9990 chunk 276 optimal weight: 0.8980 chunk 153 optimal weight: 0.6980 chunk 316 optimal weight: 7.9990 chunk 256 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 7.9990 chunk 333 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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: 0.8969 moved from start: 0.1122 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= 0.185 Angle : 0.475 6.312 45408 Z= 0.261 Chirality : 0.039 0.139 4800 Planarity : 0.003 0.028 6072 Dihedral : 3.992 14.155 4416 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.09 % Allowed : 7.96 % Favored : 91.95 % 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: 5.57 (0.13), residues: 4056 helix: 4.32 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : 0.06 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 89 HIS 0.002 0.001 HIS E 114 PHE 0.016 0.002 PHE W 35 TYR 0.023 0.002 TYR F 28 ARG 0.001 0.000 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 5 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 699 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 696 time to evaluate : 4.927 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 696 average time/residue: 2.0243 time to fit residues: 1620.6460 Evaluate side-chains 598 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 598 time to evaluate : 4.347 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 0.8980 chunk 334 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 217 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 371 optimal weight: 6.9990 chunk 308 optimal weight: 3.9990 chunk 172 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 195 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 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: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 33648 Z= 0.171 Angle : 0.491 6.279 45408 Z= 0.259 Chirality : 0.038 0.135 4800 Planarity : 0.002 0.028 6072 Dihedral : 3.942 14.165 4416 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.14 % Allowed : 10.47 % Favored : 89.38 % 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: 5.70 (0.13), residues: 4056 helix: 4.40 (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 0.005 0.001 TRP L 89 HIS 0.002 0.001 HIS C 114 PHE 0.015 0.002 PHE F 35 TYR 0.019 0.002 TYR G 28 ARG 0.001 0.000 ARG P 72 *********************** REFINEMENT MACRO_CYCLE 6 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 557 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 552 time to evaluate : 4.077 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 552 average time/residue: 1.6730 time to fit residues: 1091.9390 Evaluate side-chains 528 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 4.061 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 211 optimal weight: 5.9990 chunk 271 optimal weight: 9.9990 chunk 210 optimal weight: 0.9990 chunk 312 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 370 optimal weight: 3.9990 chunk 231 optimal weight: 8.9990 chunk 225 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 W 82 GLN X 82 GLN Y 82 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 33648 Z= 0.183 Angle : 0.497 6.128 45408 Z= 0.264 Chirality : 0.038 0.137 4800 Planarity : 0.003 0.027 6072 Dihedral : 3.949 14.120 4416 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.09 % Allowed : 10.79 % Favored : 89.13 % 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: 5.69 (0.13), residues: 4056 helix: 4.38 (0.08), residues: 3336 sheet: None (None), residues: 0 loop : 0.19 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 89 HIS 0.002 0.001 HIS G 114 PHE 0.016 0.002 PHE O 35 TYR 0.019 0.002 TYR F 28 ARG 0.001 0.000 ARG R 72 *********************** REFINEMENT MACRO_CYCLE 7 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 531 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 528 time to evaluate : 4.155 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 528 average time/residue: 1.7710 time to fit residues: 1103.5233 Evaluate side-chains 528 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 4.099 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 221 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 235 optimal weight: 1.9990 chunk 252 optimal weight: 8.9990 chunk 182 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 290 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 W 82 GLN X 82 GLN Y 82 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.1134 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= 0.205 Angle : 0.511 6.209 45408 Z= 0.272 Chirality : 0.039 0.139 4800 Planarity : 0.003 0.027 6072 Dihedral : 3.980 14.214 4416 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % 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: 5.61 (0.13), residues: 4056 helix: 4.32 (0.08), residues: 3336 sheet: None (None), residues: 0 loop : 0.22 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 89 HIS 0.003 0.001 HIS D 114 PHE 0.016 0.002 PHE O 35 TYR 0.021 0.002 TYR F 28 ARG 0.001 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 8 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 528 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 4.135 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 1.7512 time to fit residues: 1086.3509 Evaluate side-chains 528 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 3.965 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 9.9990 chunk 354 optimal weight: 2.9990 chunk 323 optimal weight: 10.0000 chunk 344 optimal weight: 2.9990 chunk 207 optimal weight: 8.9990 chunk 150 optimal weight: 9.9990 chunk 270 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 311 optimal weight: 5.9990 chunk 326 optimal weight: 10.0000 chunk 343 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 R 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: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 33648 Z= 0.335 Angle : 0.571 6.512 45408 Z= 0.311 Chirality : 0.043 0.154 4800 Planarity : 0.003 0.028 6072 Dihedral : 4.147 14.843 4416 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.14 % Allowed : 11.33 % Favored : 88.53 % 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: 5.15 (0.13), residues: 4056 helix: 4.00 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : 0.04 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 89 HIS 0.004 0.001 HIS T 114 PHE 0.019 0.003 PHE W 35 TYR 0.029 0.003 TYR W 28 ARG 0.002 0.000 ARG J 72 *********************** REFINEMENT MACRO_CYCLE 9 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 507 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 502 time to evaluate : 4.426 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 502 average time/residue: 1.7961 time to fit residues: 1058.1722 Evaluate side-chains 502 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 502 time to evaluate : 3.945 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 6.9990 chunk 364 optimal weight: 0.9990 chunk 222 optimal weight: 0.9990 chunk 173 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 chunk 382 optimal weight: 1.9990 chunk 352 optimal weight: 3.9990 chunk 304 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 235 optimal weight: 7.9990 chunk 186 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 W 82 GLN X 82 GLN Y 82 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.1187 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= 0.183 Angle : 0.507 6.337 45408 Z= 0.268 Chirality : 0.038 0.139 4800 Planarity : 0.002 0.027 6072 Dihedral : 3.996 14.301 4416 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.09 % Allowed : 11.36 % Favored : 88.56 % 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: 5.66 (0.13), residues: 4056 helix: 4.36 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : 0.21 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP O 89 HIS 0.002 0.001 HIS G 114 PHE 0.017 0.002 PHE X 35 TYR 0.018 0.002 TYR F 28 ARG 0.001 0.000 ARG P 72 ********************** REFINEMENT MACRO_CYCLE 10 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 531 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 528 time to evaluate : 3.921 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 528 average time/residue: 1.7533 time to fit residues: 1089.1241 Evaluate side-chains 528 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 3.785 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 1.9990 chunk 324 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 280 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 305 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 313 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 W 82 GLN X 82 GLN Y 82 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.084259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.068028 restraints weight = 179292.400| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 3.27 r_work: 0.2507 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2540 r_free = 0.2540 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9183 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 33648 Z= 0.183 Angle : 0.503 6.160 45408 Z= 0.266 Chirality : 0.038 0.138 4800 Planarity : 0.002 0.027 6072 Dihedral : 3.969 14.107 4416 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.00 % Allowed : 11.44 % Favored : 88.56 % 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: 5.71 (0.13), residues: 4056 helix: 4.39 (0.08), residues: 3336 sheet: None (None), residues: 0 loop : 0.26 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 89 HIS 0.002 0.001 HIS Y 114 PHE 0.016 0.002 PHE O 35 TYR 0.019 0.002 TYR F 28 ARG 0.001 0.000 ARG N 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16514.56 seconds wall clock time: 328 minutes 51.31 seconds (19731.31 seconds total)