Starting phenix.real_space_refine on Sat Dec 16 16:23:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpw_16788/12_2023/8cpw_16788_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpw_16788/12_2023/8cpw_16788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpw_16788/12_2023/8cpw_16788.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpw_16788/12_2023/8cpw_16788.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpw_16788/12_2023/8cpw_16788_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpw_16788/12_2023/8cpw_16788_updated.pdb" } resolution = 1.79 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= 0.005 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: 6 Type Number sf(0) Gaussians Mg 14 5.21 5 S 168 5.16 5 Na 24 4.78 5 C 21312 2.51 5 N 5976 2.21 5 O 8510 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 GLU 62": "OE1" <-> "OE2" Residue "1 GLU 94": "OE1" <-> "OE2" Residue "1 GLU 116": "OE1" <-> "OE2" Residue "2 GLU 62": "OE1" <-> "OE2" Residue "2 ASP 91": "OD1" <-> "OD2" Residue "2 ASP 92": "OD1" <-> "OD2" Residue "2 GLU 94": "OE1" <-> "OE2" Residue "4 GLU 62": "OE1" <-> "OE2" Residue "4 GLU 94": "OE1" <-> "OE2" Residue "4 GLU 140": "OE1" <-> "OE2" Residue "6 ASP 15": "OD1" <-> "OD2" Residue "6 GLU 62": "OE1" <-> "OE2" Residue "6 ASP 91": "OD1" <-> "OD2" Residue "6 GLU 94": "OE1" <-> "OE2" Residue "6 GLU 116": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "E GLU 62": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "F ASP 15": "OD1" <-> "OD2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "G GLU 62": "OE1" <-> "OE2" Residue "G GLU 94": "OE1" <-> "OE2" Residue "G GLU 116": "OE1" <-> "OE2" Residue "H GLU 94": "OE1" <-> "OE2" Residue "H GLU 140": "OE1" <-> "OE2" Residue "I GLU 62": "OE1" <-> "OE2" Residue "I GLU 94": "OE1" <-> "OE2" Residue "I GLU 140": "OE1" <-> "OE2" Residue "K ASP 15": "OD1" <-> "OD2" Residue "K GLU 62": "OE1" <-> "OE2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "K GLU 140": "OE1" <-> "OE2" Residue "M ASP 91": "OD1" <-> "OD2" Residue "M ASP 92": "OD1" <-> "OD2" Residue "M GLU 94": "OE1" <-> "OE2" Residue "M GLU 116": "OE1" <-> "OE2" Residue "O GLU 62": "OE1" <-> "OE2" Residue "O ASP 91": "OD1" <-> "OD2" Residue "O ASP 92": "OD1" <-> "OD2" Residue "O GLU 94": "OE1" <-> "OE2" Residue "O GLU 116": "OE1" <-> "OE2" Residue "P GLU 94": "OE1" <-> "OE2" Residue "P GLU 140": "OE1" <-> "OE2" Residue "Q GLU 62": "OE1" <-> "OE2" Residue "Q GLU 94": "OE1" <-> "OE2" Residue "Q GLU 116": "OE1" <-> "OE2" Residue "Q ASP 123": "OD1" <-> "OD2" Residue "Q ASP 131": "OD1" <-> "OD2" Residue "S GLU 94": "OE1" <-> "OE2" Residue "S GLU 140": "OE1" <-> "OE2" Residue "U GLU 94": "OE1" <-> "OE2" Residue "U GLU 140": "OE1" <-> "OE2" Residue "W GLU 62": "OE1" <-> "OE2" Residue "W ASP 91": "OD1" <-> "OD2" Residue "W ASP 92": "OD1" <-> "OD2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "W GLU 116": "OE1" <-> "OE2" Residue "X GLU 62": "OE1" <-> "OE2" Residue "X ASP 91": "OD1" <-> "OD2" Residue "X ASP 92": "OD1" <-> "OD2" Residue "X GLU 94": "OE1" <-> "OE2" Residue "Y ASP 91": "OD1" <-> "OD2" Residue "Y GLU 94": "OE1" <-> "OE2" Residue "Y GLU 140": "OE1" <-> "OE2" Residue "a GLU 62": "OE1" <-> "OE2" Residue "a GLU 94": "OE1" <-> "OE2" Residue "a GLU 116": "OE1" <-> "OE2" Residue "e GLU 62": "OE1" <-> "OE2" Residue "e GLU 94": "OE1" <-> "OE2" Residue "e GLU 140": "OE1" <-> "OE2" Residue "r GLU 94": "OE1" <-> "OE2" Residue "r GLU 116": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 36004 Number of models: 1 Model: "" Number of chains: 72 Chain: "1" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "6" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' NA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' NA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "4" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "6" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' NA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' NA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "2" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "4" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "6" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "A" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "B" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "E" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "F" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "G" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "H" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "I" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "K" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "M" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "O" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "P" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "Q" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "S" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "U" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "W" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "X" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "Y" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "a" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "e" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "r" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Time building chain proxies: 18.95, per 1000 atoms: 0.53 Number of scatterers: 36004 At special positions: 0 Unit cell: (131.856, 131.856, 131.856, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 168 16.00 Mg 14 11.99 Na 24 11.00 O 8510 8.00 N 5976 7.00 C 21312 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: 16.81 Conformation dependent library (CDL) restraints added in 5.9 seconds 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7968 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 144 helices and 0 sheets defined 72.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.58 Creating SS restraints... Processing helix chain '1' and resid 14 through 41 Processing helix chain '1' and resid 49 through 76 Processing helix chain '1' and resid 96 through 123 Processing helix chain '1' and resid 127 through 136 Processing helix chain '1' and resid 138 through 158 Processing helix chain '1' and resid 164 through 173 Processing helix chain '2' and resid 14 through 41 Processing helix chain '2' and resid 49 through 76 Processing helix chain '2' and resid 96 through 123 Processing helix chain '2' and resid 127 through 136 Processing helix chain '2' and resid 138 through 158 Processing helix chain '2' and resid 164 through 173 Processing helix chain '4' and resid 14 through 41 Processing helix chain '4' and resid 49 through 76 Processing helix chain '4' and resid 96 through 123 Processing helix chain '4' and resid 127 through 136 Processing helix chain '4' and resid 138 through 158 Processing helix chain '4' and resid 164 through 173 Processing helix chain '6' and resid 14 through 41 Processing helix chain '6' and resid 49 through 75 Processing helix chain '6' and resid 96 through 123 Processing helix chain '6' and resid 127 through 136 Processing helix chain '6' and resid 138 through 158 Processing helix chain '6' and resid 164 through 173 Processing helix chain 'A' and resid 14 through 41 Processing helix chain 'A' and resid 49 through 76 Processing helix chain 'A' and resid 96 through 123 Processing helix chain 'A' and resid 127 through 136 Processing helix chain 'A' and resid 138 through 158 Processing helix chain 'A' and resid 164 through 173 Processing helix chain 'B' and resid 14 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 96 through 123 Processing helix chain 'B' and resid 127 through 136 Processing helix chain 'B' and resid 138 through 158 Processing helix chain 'B' and resid 164 through 173 Processing helix chain 'E' and resid 14 through 41 Processing helix chain 'E' and resid 49 through 76 Processing helix chain 'E' and resid 96 through 123 Processing helix chain 'E' and resid 127 through 136 Processing helix chain 'E' and resid 138 through 158 Processing helix chain 'E' and resid 164 through 173 Processing helix chain 'F' and resid 14 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 96 through 123 Processing helix chain 'F' and resid 127 through 136 Processing helix chain 'F' and resid 138 through 158 Processing helix chain 'F' and resid 164 through 173 Processing helix chain 'G' and resid 14 through 41 Processing helix chain 'G' and resid 49 through 75 Processing helix chain 'G' and resid 96 through 123 Processing helix chain 'G' and resid 127 through 136 Processing helix chain 'G' and resid 138 through 158 Processing helix chain 'G' and resid 164 through 173 Processing helix chain 'H' and resid 14 through 41 Processing helix chain 'H' and resid 49 through 76 Processing helix chain 'H' and resid 96 through 123 Processing helix chain 'H' and resid 127 through 136 Processing helix chain 'H' and resid 138 through 158 Processing helix chain 'H' and resid 164 through 173 Processing helix chain 'I' and resid 14 through 41 Processing helix chain 'I' and resid 49 through 76 Processing helix chain 'I' and resid 96 through 123 Processing helix chain 'I' and resid 127 through 136 Processing helix chain 'I' and resid 138 through 158 Processing helix chain 'I' and resid 164 through 173 Processing helix chain 'K' and resid 14 through 41 Processing helix chain 'K' and resid 49 through 76 Processing helix chain 'K' and resid 96 through 123 Processing helix chain 'K' and resid 127 through 136 Processing helix chain 'K' and resid 138 through 158 Processing helix chain 'K' and resid 164 through 173 Processing helix chain 'M' and resid 14 through 41 Processing helix chain 'M' and resid 49 through 75 Processing helix chain 'M' and resid 96 through 123 Processing helix chain 'M' and resid 127 through 136 Processing helix chain 'M' and resid 138 through 158 Processing helix chain 'M' and resid 164 through 173 Processing helix chain 'O' and resid 14 through 41 Processing helix chain 'O' and resid 49 through 76 Processing helix chain 'O' and resid 96 through 123 Processing helix chain 'O' and resid 127 through 136 Processing helix chain 'O' and resid 138 through 158 Processing helix chain 'O' and resid 164 through 173 Processing helix chain 'P' and resid 14 through 41 Processing helix chain 'P' and resid 49 through 76 Processing helix chain 'P' and resid 96 through 123 Processing helix chain 'P' and resid 127 through 136 Processing helix chain 'P' and resid 138 through 158 Processing helix chain 'P' and resid 164 through 173 Processing helix chain 'Q' and resid 14 through 41 Processing helix chain 'Q' and resid 49 through 75 Processing helix chain 'Q' and resid 96 through 123 Processing helix chain 'Q' and resid 127 through 136 Processing helix chain 'Q' and resid 138 through 158 Processing helix chain 'Q' and resid 164 through 173 Processing helix chain 'S' and resid 14 through 41 Processing helix chain 'S' and resid 49 through 76 Processing helix chain 'S' and resid 96 through 123 Processing helix chain 'S' and resid 127 through 136 Processing helix chain 'S' and resid 138 through 158 Processing helix chain 'S' and resid 164 through 173 Processing helix chain 'U' and resid 14 through 41 Processing helix chain 'U' and resid 49 through 76 Processing helix chain 'U' and resid 96 through 123 Processing helix chain 'U' and resid 127 through 136 Processing helix chain 'U' and resid 138 through 158 Processing helix chain 'U' and resid 164 through 173 Processing helix chain 'W' and resid 14 through 41 Processing helix chain 'W' and resid 49 through 75 Processing helix chain 'W' and resid 96 through 123 Processing helix chain 'W' and resid 127 through 136 Processing helix chain 'W' and resid 138 through 158 Processing helix chain 'W' and resid 164 through 173 Processing helix chain 'X' and resid 14 through 41 Processing helix chain 'X' and resid 49 through 76 Processing helix chain 'X' and resid 96 through 123 Processing helix chain 'X' and resid 127 through 136 Processing helix chain 'X' and resid 138 through 158 Processing helix chain 'X' and resid 164 through 173 Processing helix chain 'Y' and resid 14 through 41 Processing helix chain 'Y' and resid 49 through 76 Processing helix chain 'Y' and resid 96 through 123 Processing helix chain 'Y' and resid 127 through 136 Processing helix chain 'Y' and resid 138 through 158 Processing helix chain 'Y' and resid 164 through 173 Processing helix chain 'a' and resid 14 through 41 Processing helix chain 'a' and resid 49 through 75 Processing helix chain 'a' and resid 96 through 123 Processing helix chain 'a' and resid 127 through 136 Processing helix chain 'a' and resid 138 through 158 Processing helix chain 'a' and resid 164 through 173 Processing helix chain 'e' and resid 14 through 41 Processing helix chain 'e' and resid 49 through 76 Processing helix chain 'e' and resid 96 through 123 Processing helix chain 'e' and resid 127 through 136 Processing helix chain 'e' and resid 138 through 158 Processing helix chain 'e' and resid 164 through 173 Processing helix chain 'r' and resid 14 through 41 Processing helix chain 'r' and resid 49 through 76 Processing helix chain 'r' and resid 96 through 123 Processing helix chain 'r' and resid 127 through 136 Processing helix chain 'r' and resid 138 through 158 Processing helix chain 'r' and resid 164 through 173 2418 hydrogen bonds defined for protein. 7254 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: 11.22 Time building geometry restraints manager: 17.74 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: 11624 1.34 - 1.46: 4988 1.46 - 1.57: 17900 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 34776 Sorted by residual: bond pdb=" CB CSX A 90 " pdb=" SG CSX A 90 " ideal model delta sigma weight residual 1.831 1.755 0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" CB CSX G 90 " pdb=" SG CSX G 90 " ideal model delta sigma weight residual 1.831 1.756 0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" CB CSX Y 90 " pdb=" SG CSX Y 90 " ideal model delta sigma weight residual 1.831 1.756 0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" CB CSX Q 90 " pdb=" SG CSX Q 90 " ideal model delta sigma weight residual 1.831 1.756 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" CB CSX K 90 " pdb=" SG CSX K 90 " ideal model delta sigma weight residual 1.831 1.756 0.075 2.00e-02 2.50e+03 1.40e+01 ... (remaining 34771 not shown) Histogram of bond angle deviations from ideal: 99.62 - 106.49: 710 106.49 - 113.36: 19008 113.36 - 120.23: 12843 120.23 - 127.10: 13951 127.10 - 133.97: 336 Bond angle restraints: 46848 Sorted by residual: angle pdb=" CA TYR E 39 " pdb=" CB TYR E 39 " pdb=" CG TYR E 39 " ideal model delta sigma weight residual 113.90 108.14 5.76 1.80e+00 3.09e-01 1.02e+01 angle pdb=" CA TYR I 39 " pdb=" CB TYR I 39 " pdb=" CG TYR I 39 " ideal model delta sigma weight residual 113.90 108.16 5.74 1.80e+00 3.09e-01 1.02e+01 angle pdb=" CA TYR 2 39 " pdb=" CB TYR 2 39 " pdb=" CG TYR 2 39 " ideal model delta sigma weight residual 113.90 108.18 5.72 1.80e+00 3.09e-01 1.01e+01 angle pdb=" CA TYR 4 39 " pdb=" CB TYR 4 39 " pdb=" CG TYR 4 39 " ideal model delta sigma weight residual 113.90 108.18 5.72 1.80e+00 3.09e-01 1.01e+01 angle pdb=" CA TYR M 39 " pdb=" CB TYR M 39 " pdb=" CG TYR M 39 " ideal model delta sigma weight residual 113.90 108.18 5.72 1.80e+00 3.09e-01 1.01e+01 ... (remaining 46843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 18967 16.52 - 33.04: 1481 33.04 - 49.55: 347 49.55 - 66.07: 96 66.07 - 82.59: 109 Dihedral angle restraints: 21000 sinusoidal: 8688 harmonic: 12312 Sorted by residual: dihedral pdb=" CA VAL U 46 " pdb=" C VAL U 46 " pdb=" N ALA U 47 " pdb=" CA ALA U 47 " ideal model delta harmonic sigma weight residual 180.00 162.63 17.37 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA VAL K 46 " pdb=" C VAL K 46 " pdb=" N ALA K 47 " pdb=" CA ALA K 47 " ideal model delta harmonic sigma weight residual 180.00 162.63 17.37 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA VAL E 46 " pdb=" C VAL E 46 " pdb=" N ALA E 47 " pdb=" CA ALA E 47 " ideal model delta harmonic sigma weight residual 180.00 162.63 17.37 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 20997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3454 0.056 - 0.112: 1163 0.112 - 0.168: 212 0.168 - 0.225: 68 0.225 - 0.281: 23 Chirality restraints: 4920 Sorted by residual: chirality pdb=" CA TYR I 137 " pdb=" N TYR I 137 " pdb=" C TYR I 137 " pdb=" CB TYR I 137 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA TYR O 137 " pdb=" N TYR O 137 " pdb=" C TYR O 137 " pdb=" CB TYR O 137 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA TYR E 137 " pdb=" N TYR E 137 " pdb=" C TYR E 137 " pdb=" CB TYR E 137 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 4917 not shown) Planarity restraints: 6192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 2 137 " -0.023 2.00e-02 2.50e+03 1.69e-02 5.69e+00 pdb=" CG TYR 2 137 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR 2 137 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR 2 137 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR 2 137 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR 2 137 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR 2 137 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR 2 137 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 1 137 " 0.023 2.00e-02 2.50e+03 1.68e-02 5.66e+00 pdb=" CG TYR 1 137 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR 1 137 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR 1 137 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR 1 137 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR 1 137 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR 1 137 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR 1 137 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 137 " 0.023 2.00e-02 2.50e+03 1.68e-02 5.65e+00 pdb=" CG TYR A 137 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 137 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 137 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 137 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR A 137 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 137 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 137 " 0.021 2.00e-02 2.50e+03 ... (remaining 6189 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 2972 2.72 - 3.27: 39798 3.27 - 3.81: 72133 3.81 - 4.36: 90362 4.36 - 4.90: 141831 Nonbonded interactions: 347096 Sorted by model distance: nonbonded pdb=" OE1 GLU M 116 " pdb=" O HOH M 301 " model vdw 2.180 2.440 nonbonded pdb=" OE1 GLU Q 116 " pdb=" O HOH Q 601 " model vdw 2.181 2.440 nonbonded pdb=" OE1 GLU W 116 " pdb=" O HOH W 601 " model vdw 2.181 2.440 nonbonded pdb=" OE1 GLU a 116 " pdb=" O HOH a 301 " model vdw 2.181 2.440 nonbonded pdb=" OE1 GLU 6 116 " pdb=" O HOH 6 301 " model vdw 2.181 2.440 ... (remaining 347091 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 '1' and resid 4 through 176) selection = (chain '2' and resid 4 through 176) selection = (chain '4' and resid 4 through 176) selection = (chain '6' and resid 4 through 176) selection = (chain 'A' and resid 4 through 176) selection = (chain 'B' and resid 4 through 176) selection = (chain 'E' and resid 4 through 176) selection = (chain 'F' and resid 4 through 176) selection = (chain 'G' and resid 4 through 176) selection = (chain 'H' and resid 4 through 176) selection = (chain 'I' and resid 4 through 176) selection = (chain 'K' and resid 4 through 176) selection = (chain 'M' and resid 4 through 176) selection = (chain 'O' and resid 4 through 176) selection = (chain 'P' and resid 4 through 176) selection = (chain 'Q' and resid 4 through 176) selection = (chain 'S' and resid 4 through 176) selection = (chain 'U' and resid 4 through 176) selection = (chain 'W' and resid 4 through 176) selection = (chain 'X' and resid 4 through 176) selection = (chain 'Y' and resid 4 through 176) selection = (chain 'a' and resid 4 through 176) selection = (chain 'e' and resid 4 through 176) selection = (chain 'r' and resid 4 through 176) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 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: 7.700 Check model and map are aligned: 0.570 Set scattering table: 0.350 Process input model: 94.670 Find NCS groups from input model: 3.120 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 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 0.076 34776 Z= 0.344 Angle : 0.840 6.653 46848 Z= 0.483 Chirality : 0.060 0.281 4920 Planarity : 0.008 0.059 6192 Dihedral : 14.346 82.591 13032 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.63 % Allowed : 2.18 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.13), residues: 4032 helix: 1.61 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.83 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP e 93 HIS 0.011 0.004 HIS U 136 PHE 0.028 0.006 PHE K 41 TYR 0.029 0.006 TYR 1 137 ARG 0.015 0.003 ARG H 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 560 time to evaluate : 4.552 Fit side-chains outliers start: 23 outliers final: 23 residues processed: 560 average time/residue: 1.9590 time to fit residues: 1271.3246 Evaluate side-chains 569 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 546 time to evaluate : 4.478 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.4628 time to fit residues: 23.3620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 7.9990 chunk 309 optimal weight: 10.0000 chunk 171 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 208 optimal weight: 7.9990 chunk 165 optimal weight: 0.4980 chunk 319 optimal weight: 0.9990 chunk 123 optimal weight: 7.9990 chunk 194 optimal weight: 1.9990 chunk 238 optimal weight: 7.9990 chunk 370 optimal weight: 0.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 112 GLN 2 14 GLN 4 112 GLN 6 14 GLN 6 112 GLN A 112 GLN B 14 GLN B 112 GLN E 14 GLN E 112 GLN F 14 GLN F 112 GLN G 112 GLN H 14 GLN K 14 GLN K 112 GLN M 14 GLN M 112 GLN O 112 GLN P 112 GLN Q 14 GLN Q 112 GLN S 14 GLN S 112 GLN U 14 GLN U 112 GLN U 125 ASN W 14 GLN W 112 GLN X 14 GLN X 112 GLN Y 14 GLN Y 112 GLN a 14 GLN a 112 GLN a 125 ASN e 112 GLN e 125 ASN r 112 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.0640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 34776 Z= 0.141 Angle : 0.532 5.582 46848 Z= 0.294 Chirality : 0.039 0.147 4920 Planarity : 0.003 0.033 6192 Dihedral : 4.357 19.395 4536 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 1.33 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.58 (0.13), residues: 4032 helix: 3.51 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.81 (0.26), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 93 HIS 0.004 0.002 HIS O 65 PHE 0.017 0.003 PHE A 41 TYR 0.020 0.002 TYR X 39 ARG 0.007 0.000 ARG 6 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 611 time to evaluate : 4.479 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 611 average time/residue: 1.8279 time to fit residues: 1305.8409 Evaluate side-chains 603 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 579 time to evaluate : 4.358 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.4680 time to fit residues: 24.1598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 308 optimal weight: 20.0000 chunk 252 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 371 optimal weight: 5.9990 chunk 400 optimal weight: 0.7980 chunk 330 optimal weight: 20.0000 chunk 368 optimal weight: 1.9990 chunk 126 optimal weight: 20.0000 chunk 297 optimal weight: 9.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 112 GLN 1 125 ASN 2 112 GLN 2 125 ASN 4 112 GLN 4 125 ASN 6 112 GLN 6 125 ASN A 112 GLN A 125 ASN B 112 GLN B 125 ASN E 112 GLN E 125 ASN F 112 GLN F 125 ASN G 112 GLN G 125 ASN H 112 GLN H 125 ASN I 112 GLN I 125 ASN K 112 GLN K 125 ASN M 112 GLN O 112 GLN O 125 ASN P 112 GLN P 125 ASN Q 112 GLN S 112 GLN S 125 ASN U 112 GLN U 125 ASN W 112 GLN X 112 GLN X 125 ASN Y 112 GLN Y 125 ASN a 112 GLN a 125 ASN e 112 GLN e 125 ASN r 112 GLN r 125 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.0713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 34776 Z= 0.248 Angle : 0.669 6.906 46848 Z= 0.371 Chirality : 0.043 0.154 4920 Planarity : 0.004 0.061 6192 Dihedral : 4.516 17.678 4536 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 1.42 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.02 (0.13), residues: 4032 helix: 3.09 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.74 (0.26), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP Q 93 HIS 0.008 0.002 HIS H 136 PHE 0.024 0.004 PHE S 41 TYR 0.026 0.003 TYR a 39 ARG 0.012 0.001 ARG 2 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 589 time to evaluate : 4.380 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 589 average time/residue: 1.9349 time to fit residues: 1324.0172 Evaluate side-chains 530 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 506 time to evaluate : 4.237 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.4551 time to fit residues: 23.5609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 2.9990 chunk 279 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 249 optimal weight: 20.0000 chunk 372 optimal weight: 9.9990 chunk 394 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 353 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 112 GLN 1 125 ASN 2 112 GLN 2 125 ASN 4 112 GLN 4 125 ASN 6 112 GLN 6 125 ASN A 112 GLN A 125 ASN B 112 GLN B 125 ASN E 112 GLN E 125 ASN F 112 GLN F 125 ASN G 125 ASN H 112 GLN H 125 ASN I 112 GLN I 125 ASN K 112 GLN K 125 ASN M 112 GLN O 112 GLN O 125 ASN P 112 GLN P 125 ASN Q 112 GLN Q 125 ASN S 112 GLN S 125 ASN U 112 GLN U 125 ASN W 112 GLN X 112 GLN X 125 ASN Y 112 GLN Y 125 ASN a 112 GLN a 125 ASN e 112 GLN e 125 ASN r 112 GLN r 125 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.0795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 34776 Z= 0.185 Angle : 0.589 6.518 46848 Z= 0.326 Chirality : 0.040 0.141 4920 Planarity : 0.003 0.038 6192 Dihedral : 4.394 17.920 4536 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 1.33 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.20 (0.13), residues: 4032 helix: 3.25 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.63 (0.26), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP P 93 HIS 0.005 0.002 HIS X 136 PHE 0.020 0.003 PHE E 41 TYR 0.022 0.002 TYR B 39 ARG 0.008 0.001 ARG 2 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 558 time to evaluate : 4.629 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 558 average time/residue: 1.8814 time to fit residues: 1222.3889 Evaluate side-chains 545 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 521 time to evaluate : 4.196 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.4506 time to fit residues: 23.1924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 0.8980 chunk 223 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 293 optimal weight: 5.9990 chunk 162 optimal weight: 8.9990 chunk 336 optimal weight: 20.0000 chunk 272 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 201 optimal weight: 6.9990 chunk 353 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 125 ASN 2 125 ASN 4 125 ASN 6 125 ASN A 125 ASN B 125 ASN E 125 ASN F 125 ASN G 112 GLN G 125 ASN H 125 ASN I 125 ASN K 125 ASN O 125 ASN P 125 ASN Q 125 ASN S 125 ASN U 125 ASN W 125 ASN X 125 ASN Y 125 ASN a 125 ASN e 125 ASN r 125 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.0771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 34776 Z= 0.249 Angle : 0.673 6.970 46848 Z= 0.372 Chirality : 0.042 0.151 4920 Planarity : 0.004 0.031 6192 Dihedral : 4.474 17.595 4536 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 1.31 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.91 (0.13), residues: 4032 helix: 3.04 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.59 (0.26), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP X 93 HIS 0.007 0.002 HIS X 136 PHE 0.024 0.004 PHE E 41 TYR 0.028 0.003 TYR e 39 ARG 0.009 0.001 ARG K 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 556 time to evaluate : 4.668 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 24 residues processed: 556 average time/residue: 1.8973 time to fit residues: 1228.6680 Evaluate side-chains 545 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 521 time to evaluate : 4.363 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.4676 time to fit residues: 24.3567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 10.0000 chunk 355 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 231 optimal weight: 9.9990 chunk 97 optimal weight: 0.8980 chunk 394 optimal weight: 9.9990 chunk 327 optimal weight: 7.9990 chunk 182 optimal weight: 8.9990 chunk 32 optimal weight: 0.0980 chunk 130 optimal weight: 2.9990 chunk 207 optimal weight: 9.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 125 ASN 2 125 ASN 4 125 ASN 6 125 ASN A 125 ASN B 125 ASN E 125 ASN F 125 ASN G 112 GLN G 125 ASN H 125 ASN I 125 ASN K 125 ASN O 125 ASN P 125 ASN Q 125 ASN S 125 ASN U 125 ASN X 125 ASN Y 125 ASN a 125 ASN e 125 ASN r 125 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 34776 Z= 0.123 Angle : 0.501 5.863 46848 Z= 0.275 Chirality : 0.036 0.132 4920 Planarity : 0.003 0.052 6192 Dihedral : 4.190 18.804 4536 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 1.31 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.65 (0.13), residues: 4032 helix: 3.62 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.53 (0.27), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP X 93 HIS 0.003 0.001 HIS F 105 PHE 0.015 0.002 PHE O 41 TYR 0.020 0.002 TYR a 39 ARG 0.010 0.000 ARG 6 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 569 time to evaluate : 4.305 Fit side-chains outliers start: 24 outliers final: 17 residues processed: 569 average time/residue: 1.8146 time to fit residues: 1209.9800 Evaluate side-chains 558 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 541 time to evaluate : 4.518 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.4642 time to fit residues: 18.9903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 224 optimal weight: 5.9990 chunk 288 optimal weight: 8.9990 chunk 223 optimal weight: 10.0000 chunk 332 optimal weight: 3.9990 chunk 220 optimal weight: 20.0000 chunk 393 optimal weight: 9.9990 chunk 246 optimal weight: 5.9990 chunk 239 optimal weight: 6.9990 chunk 181 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 125 ASN 2 125 ASN 4 125 ASN 6 125 ASN A 125 ASN B 125 ASN E 125 ASN F 125 ASN G 125 ASN H 125 ASN I 125 ASN K 125 ASN O 125 ASN P 125 ASN Q 125 ASN S 125 ASN U 125 ASN W 125 ASN X 125 ASN Y 125 ASN a 125 ASN e 125 ASN r 125 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 34776 Z= 0.256 Angle : 0.676 7.164 46848 Z= 0.373 Chirality : 0.042 0.140 4920 Planarity : 0.004 0.027 6192 Dihedral : 4.402 17.198 4536 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 1.96 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.01 (0.13), residues: 4032 helix: 3.11 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.60 (0.26), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP 2 93 HIS 0.007 0.002 HIS H 136 PHE 0.023 0.004 PHE E 41 TYR 0.028 0.003 TYR e 39 ARG 0.010 0.001 ARG 6 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 512 time to evaluate : 4.531 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 512 average time/residue: 1.9941 time to fit residues: 1183.8165 Evaluate side-chains 543 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 519 time to evaluate : 4.414 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.4676 time to fit residues: 24.1308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 20.0000 chunk 157 optimal weight: 2.9990 chunk 234 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 250 optimal weight: 4.9990 chunk 267 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 309 optimal weight: 10.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 125 ASN 2 125 ASN 4 125 ASN 6 125 ASN A 125 ASN B 125 ASN E 125 ASN F 125 ASN G 125 ASN H 125 ASN I 125 ASN K 125 ASN O 125 ASN P 125 ASN Q 125 ASN S 125 ASN U 125 ASN X 125 ASN Y 125 ASN a 125 ASN e 125 ASN r 125 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 34776 Z= 0.176 Angle : 0.577 6.695 46848 Z= 0.319 Chirality : 0.039 0.138 4920 Planarity : 0.003 0.071 6192 Dihedral : 4.335 17.730 4536 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 1.99 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.29 (0.13), residues: 4032 helix: 3.33 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.56 (0.27), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP 2 93 HIS 0.006 0.002 HIS H 65 PHE 0.019 0.003 PHE G 41 TYR 0.022 0.002 TYR 2 39 ARG 0.011 0.001 ARG 6 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 545 time to evaluate : 4.304 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 545 average time/residue: 1.9542 time to fit residues: 1234.9133 Evaluate side-chains 555 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 531 time to evaluate : 4.441 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.4613 time to fit residues: 23.9488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 2.9990 chunk 376 optimal weight: 9.9990 chunk 343 optimal weight: 8.9990 chunk 366 optimal weight: 8.9990 chunk 220 optimal weight: 20.0000 chunk 159 optimal weight: 0.8980 chunk 287 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 331 optimal weight: 5.9990 chunk 346 optimal weight: 0.8980 chunk 365 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 125 ASN 2 125 ASN 4 125 ASN 6 125 ASN A 125 ASN B 125 ASN E 125 ASN F 125 ASN G 125 ASN H 125 ASN I 125 ASN K 125 ASN O 125 ASN P 125 ASN Q 125 ASN S 125 ASN U 125 ASN X 125 ASN Y 125 ASN a 125 ASN e 125 ASN r 125 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 34776 Z= 0.201 Angle : 0.615 6.995 46848 Z= 0.339 Chirality : 0.040 0.145 4920 Planarity : 0.004 0.066 6192 Dihedral : 4.359 17.697 4536 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 2.02 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.17 (0.13), residues: 4032 helix: 3.23 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.58 (0.26), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP 2 93 HIS 0.006 0.002 HIS 6 65 PHE 0.022 0.003 PHE F 41 TYR 0.026 0.002 TYR O 39 ARG 0.011 0.001 ARG 6 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 533 time to evaluate : 4.500 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 24 residues processed: 533 average time/residue: 1.9798 time to fit residues: 1222.5577 Evaluate side-chains 554 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 530 time to evaluate : 4.277 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.5061 time to fit residues: 25.7672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 3.9990 chunk 387 optimal weight: 9.9990 chunk 236 optimal weight: 7.9990 chunk 183 optimal weight: 20.0000 chunk 269 optimal weight: 6.9990 chunk 406 optimal weight: 0.8980 chunk 374 optimal weight: 5.9990 chunk 323 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 250 optimal weight: 4.9990 chunk 198 optimal weight: 2.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 125 ASN 2 125 ASN 4 125 ASN 6 125 ASN A 125 ASN B 125 ASN E 125 ASN F 125 ASN G 125 ASN H 125 ASN I 125 ASN K 125 ASN O 125 ASN P 125 ASN Q 125 ASN S 125 ASN U 125 ASN X 125 ASN Y 125 ASN a 125 ASN e 125 ASN r 125 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 34776 Z= 0.168 Angle : 0.570 6.735 46848 Z= 0.314 Chirality : 0.039 0.141 4920 Planarity : 0.003 0.053 6192 Dihedral : 4.315 18.046 4536 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.35 (0.13), residues: 4032 helix: 3.38 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.59 (0.27), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP X 93 HIS 0.007 0.002 HIS K 65 PHE 0.019 0.003 PHE B 41 TYR 0.022 0.002 TYR G 39 ARG 0.010 0.001 ARG K 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 554 time to evaluate : 4.248 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 554 average time/residue: 1.8976 time to fit residues: 1223.6067 Evaluate side-chains 529 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 529 time to evaluate : 4.087 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 3.9990 chunk 344 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 298 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 324 optimal weight: 7.9990 chunk 135 optimal weight: 9.9990 chunk 332 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 125 ASN 2 125 ASN 4 125 ASN 6 125 ASN A 125 ASN B 125 ASN E 125 ASN F 125 ASN G 125 ASN H 125 ASN I 125 ASN K 125 ASN O 125 ASN P 125 ASN S 125 ASN U 125 ASN X 125 ASN Y 125 ASN a 125 ASN e 125 ASN r 125 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.152208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.140534 restraints weight = 201178.711| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.77 r_work: 0.2758 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 34776 Z= 0.267 Angle : 0.695 7.355 46848 Z= 0.384 Chirality : 0.043 0.152 4920 Planarity : 0.004 0.067 6192 Dihedral : 4.422 17.218 4536 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 2.02 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.93 (0.13), residues: 4032 helix: 3.05 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.58 (0.26), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP 2 93 HIS 0.008 0.002 HIS H 136 PHE 0.025 0.004 PHE X 41 TYR 0.030 0.003 TYR A 39 ARG 0.011 0.001 ARG K 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17089.07 seconds wall clock time: 303 minutes 37.80 seconds (18217.80 seconds total)