Starting phenix.real_space_refine on Sat Mar 23 05:53:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpw_16788/03_2024/8cpw_16788_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpw_16788/03_2024/8cpw_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_16788/03_2024/8cpw_16788.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpw_16788/03_2024/8cpw_16788.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpw_16788/03_2024/8cpw_16788_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpw_16788/03_2024/8cpw_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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 19.24, 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: 18.30 Conformation dependent library (CDL) restraints added in 7.6 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: 5.62 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: 11.60 Time building geometry restraints manager: 19.26 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: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 7.620 Check model and map are aligned: 0.540 Set scattering table: 0.310 Process input model: 100.880 Find NCS groups from input model: 2.870 Set up NCS constraints: 0.300 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:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.200 ------------------------------------------------------------------------------- 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 : 4.311 Fit side-chains REVERT: 2 70 MET cc_start: 0.8657 (mtp) cc_final: 0.8362 (mtp) REVERT: S 70 MET cc_start: 0.8657 (mtp) cc_final: 0.8360 (mtp) REVERT: W 70 MET cc_start: 0.8664 (mtp) cc_final: 0.8317 (mtp) REVERT: a 70 MET cc_start: 0.8668 (mtp) cc_final: 0.8323 (mtp) outliers start: 23 outliers final: 23 residues processed: 560 average time/residue: 1.8709 time to fit residues: 1215.1179 Evaluate side-chains 569 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 546 time to evaluate : 4.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 109 ASN Chi-restraints excluded: chain 2 residue 109 ASN Chi-restraints excluded: chain 4 residue 109 ASN Chi-restraints excluded: chain 6 residue 109 ASN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain Q residue 109 ASN Chi-restraints excluded: chain S residue 109 ASN Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain W residue 109 ASN Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain a residue 109 ASN Chi-restraints excluded: chain e residue 109 ASN Chi-restraints excluded: chain r residue 109 ASN 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: 6.9990 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: 2.0988 ------------------------------------------------------------------------------- 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 E 125 ASN F 14 GLN F 112 GLN G 112 GLN H 14 GLN K 14 GLN K 112 GLN K 125 ASN 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 r 125 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.0602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 34776 Z= 0.155 Angle : 0.556 5.716 46848 Z= 0.308 Chirality : 0.039 0.149 4920 Planarity : 0.003 0.032 6192 Dihedral : 5.621 40.991 4582 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.03 % Allowed : 1.96 % 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: 4.44 (0.13), residues: 4032 helix: 3.40 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.84 (0.26), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP F 93 HIS 0.005 0.002 HIS O 65 PHE 0.018 0.003 PHE W 41 TYR 0.021 0.002 TYR 2 39 ARG 0.007 0.001 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 591 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 590 time to evaluate : 3.714 Fit side-chains REVERT: S 70 MET cc_start: 0.8691 (mtp) cc_final: 0.8216 (mtp) REVERT: W 70 MET cc_start: 0.8692 (mtp) cc_final: 0.8229 (mtp) REVERT: a 70 MET cc_start: 0.8693 (mtp) cc_final: 0.8233 (mtp) outliers start: 1 outliers final: 1 residues processed: 590 average time/residue: 1.8238 time to fit residues: 1252.5074 Evaluate side-chains 563 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 562 time to evaluate : 4.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 308 optimal weight: 4.9990 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: 4.9990 chunk 126 optimal weight: 20.0000 chunk 297 optimal weight: 5.9990 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 125 ASN B 125 ASN E 125 ASN 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 125 ASN P 125 ASN Q 112 GLN Q 125 ASN S 125 ASN U 125 ASN W 112 GLN W 125 ASN X 125 ASN Y 125 ASN a 112 GLN a 125 ASN e 125 ASN r 112 GLN r 125 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.0696 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 : 0.670 6.877 46848 Z= 0.372 Chirality : 0.043 0.154 4920 Planarity : 0.004 0.025 6192 Dihedral : 4.527 17.771 4536 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.15 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: 3.98 (0.13), residues: 4032 helix: 3.07 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.73 (0.26), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP O 93 HIS 0.008 0.002 HIS F 136 PHE 0.024 0.004 PHE r 41 TYR 0.026 0.003 TYR e 39 ARG 0.008 0.001 ARG K 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 609 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 585 time to evaluate : 4.573 Fit side-chains REVERT: W 70 MET cc_start: 0.8695 (mtp) cc_final: 0.8299 (mtp) REVERT: a 70 MET cc_start: 0.8696 (mtp) cc_final: 0.8297 (mtp) outliers start: 24 outliers final: 24 residues processed: 585 average time/residue: 1.8428 time to fit residues: 1253.5719 Evaluate side-chains 543 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 519 time to evaluate : 3.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 109 ASN Chi-restraints excluded: chain 2 residue 109 ASN Chi-restraints excluded: chain 4 residue 109 ASN Chi-restraints excluded: chain 6 residue 109 ASN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain Q residue 109 ASN Chi-restraints excluded: chain S residue 109 ASN Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain W residue 109 ASN Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain a residue 109 ASN Chi-restraints excluded: chain e residue 109 ASN Chi-restraints excluded: chain r residue 109 ASN 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: 4.9990 chunk 192 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 177 optimal weight: 0.5980 chunk 249 optimal weight: 9.9990 chunk 372 optimal weight: 4.9990 chunk 394 optimal weight: 9.9990 chunk 194 optimal weight: 3.9990 chunk 353 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 2 125 ASN 4 112 GLN 4 125 ASN 6 112 GLN 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 112 GLN K 125 ASN M 112 GLN O 125 ASN P 125 ASN Q 112 GLN Q 125 ASN S 125 ASN U 125 ASN W 112 GLN X 125 ASN Y 125 ASN a 112 GLN a 125 ASN e 125 ASN r 112 GLN r 125 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.0805 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= 0.166 Angle : 0.564 6.374 46848 Z= 0.312 Chirality : 0.039 0.141 4920 Planarity : 0.003 0.056 6192 Dihedral : 4.354 18.264 4536 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.54 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: 4.30 (0.13), residues: 4032 helix: 3.33 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.61 (0.26), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP S 93 HIS 0.004 0.001 HIS H 136 PHE 0.019 0.003 PHE 2 41 TYR 0.021 0.002 TYR E 39 ARG 0.010 0.001 ARG 6 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 575 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 551 time to evaluate : 4.500 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 551 average time/residue: 1.8153 time to fit residues: 1166.7225 Evaluate side-chains 547 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 523 time to evaluate : 4.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 109 ASN Chi-restraints excluded: chain 2 residue 109 ASN Chi-restraints excluded: chain 4 residue 109 ASN Chi-restraints excluded: chain 6 residue 109 ASN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain Q residue 109 ASN Chi-restraints excluded: chain S residue 109 ASN Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain W residue 109 ASN Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain a residue 109 ASN Chi-restraints excluded: chain e residue 109 ASN Chi-restraints excluded: chain r residue 109 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 0.9980 chunk 223 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 293 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 336 optimal weight: 20.0000 chunk 272 optimal weight: 0.0470 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: 4.4084 ------------------------------------------------------------------------------- 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: 0.0772 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= 0.242 Angle : 0.667 7.074 46848 Z= 0.369 Chirality : 0.042 0.150 4920 Planarity : 0.004 0.040 6192 Dihedral : 4.458 17.489 4536 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 1.63 % Favored : 97.71 % 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: 3.95 (0.13), residues: 4032 helix: 3.07 (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 X 93 HIS 0.007 0.002 HIS H 136 PHE 0.024 0.004 PHE 2 41 TYR 0.028 0.003 TYR G 39 ARG 0.009 0.001 ARG 6 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 564 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 540 time to evaluate : 3.778 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 540 average time/residue: 1.8408 time to fit residues: 1157.2612 Evaluate side-chains 534 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 510 time to evaluate : 4.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 109 ASN Chi-restraints excluded: chain 2 residue 109 ASN Chi-restraints excluded: chain 4 residue 109 ASN Chi-restraints excluded: chain 6 residue 109 ASN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain Q residue 109 ASN Chi-restraints excluded: chain S residue 109 ASN Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain W residue 109 ASN Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain a residue 109 ASN Chi-restraints excluded: chain e residue 109 ASN Chi-restraints excluded: chain r residue 109 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 9.9990 chunk 355 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 231 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 394 optimal weight: 10.0000 chunk 327 optimal weight: 8.9990 chunk 182 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- 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 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: 0.8010 moved from start: 0.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 34776 Z= 0.211 Angle : 0.626 6.800 46848 Z= 0.345 Chirality : 0.041 0.141 4920 Planarity : 0.004 0.080 6192 Dihedral : 4.427 17.612 4536 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.69 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: 4.05 (0.13), residues: 4032 helix: 3.16 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.54 (0.26), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP 1 93 HIS 0.006 0.002 HIS e 136 PHE 0.022 0.003 PHE G 41 TYR 0.024 0.003 TYR a 39 ARG 0.010 0.001 ARG K 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 563 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 539 time to evaluate : 3.573 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 539 average time/residue: 1.8134 time to fit residues: 1142.3892 Evaluate side-chains 533 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 509 time to evaluate : 4.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 109 ASN Chi-restraints excluded: chain 2 residue 109 ASN Chi-restraints excluded: chain 4 residue 109 ASN Chi-restraints excluded: chain 6 residue 109 ASN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain Q residue 109 ASN Chi-restraints excluded: chain S residue 109 ASN Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain W residue 109 ASN Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain a residue 109 ASN Chi-restraints excluded: chain e residue 109 ASN Chi-restraints excluded: chain r residue 109 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 224 optimal weight: 5.9990 chunk 288 optimal weight: 9.9990 chunk 223 optimal weight: 1.9990 chunk 332 optimal weight: 2.9990 chunk 220 optimal weight: 20.0000 chunk 393 optimal weight: 10.0000 chunk 246 optimal weight: 9.9990 chunk 239 optimal weight: 2.9990 chunk 181 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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: 0.8010 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 34776 Z= 0.209 Angle : 0.625 6.829 46848 Z= 0.345 Chirality : 0.041 0.143 4920 Planarity : 0.004 0.043 6192 Dihedral : 4.410 17.513 4536 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.68 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: 4.08 (0.13), residues: 4032 helix: 3.17 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.54 (0.26), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP X 93 HIS 0.005 0.002 HIS 4 136 PHE 0.022 0.003 PHE 6 41 TYR 0.028 0.003 TYR 6 39 ARG 0.006 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 539 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 515 time to evaluate : 4.545 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 515 average time/residue: 1.8918 time to fit residues: 1129.9836 Evaluate side-chains 531 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 507 time to evaluate : 4.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 109 ASN Chi-restraints excluded: chain 2 residue 109 ASN Chi-restraints excluded: chain 4 residue 109 ASN Chi-restraints excluded: chain 6 residue 109 ASN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain Q residue 109 ASN Chi-restraints excluded: chain S residue 109 ASN Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain W residue 109 ASN Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain a residue 109 ASN Chi-restraints excluded: chain e residue 109 ASN Chi-restraints excluded: chain r residue 109 ASN 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: 7.9990 chunk 234 optimal weight: 20.0000 chunk 118 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 250 optimal weight: 0.8980 chunk 267 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 309 optimal weight: 10.0000 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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: 0.7983 moved from start: 0.0935 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= 0.137 Angle : 0.525 6.241 46848 Z= 0.289 Chirality : 0.037 0.137 4920 Planarity : 0.003 0.023 6192 Dihedral : 4.228 18.400 4536 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.08 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: 4.52 (0.13), residues: 4032 helix: 3.51 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.55 (0.27), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP X 93 HIS 0.003 0.001 HIS X 105 PHE 0.017 0.002 PHE 6 41 TYR 0.020 0.002 TYR 2 39 ARG 0.003 0.000 ARG K 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 576 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 552 time to evaluate : 4.151 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 552 average time/residue: 1.8061 time to fit residues: 1164.0474 Evaluate side-chains 551 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 527 time to evaluate : 4.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 109 ASN Chi-restraints excluded: chain 2 residue 109 ASN Chi-restraints excluded: chain 4 residue 109 ASN Chi-restraints excluded: chain 6 residue 109 ASN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain Q residue 109 ASN Chi-restraints excluded: chain S residue 109 ASN Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain W residue 109 ASN Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain a residue 109 ASN Chi-restraints excluded: chain e residue 109 ASN Chi-restraints excluded: chain r residue 109 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 3.9990 chunk 376 optimal weight: 10.0000 chunk 343 optimal weight: 3.9990 chunk 366 optimal weight: 4.9990 chunk 220 optimal weight: 20.0000 chunk 159 optimal weight: 0.8980 chunk 287 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 331 optimal weight: 2.9990 chunk 346 optimal weight: 0.9980 chunk 365 optimal weight: 0.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 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: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 34776 Z= 0.148 Angle : 0.545 6.617 46848 Z= 0.300 Chirality : 0.038 0.134 4920 Planarity : 0.003 0.023 6192 Dihedral : 4.226 18.396 4536 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 2.64 % Favored : 96.70 % 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: 4.54 (0.13), residues: 4032 helix: 3.52 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.58 (0.27), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP Q 93 HIS 0.007 0.001 HIS r 65 PHE 0.016 0.002 PHE G 41 TYR 0.022 0.002 TYR a 39 ARG 0.002 0.001 ARG e 156 *********************** 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 551 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 527 time to evaluate : 4.293 Fit side-chains REVERT: 1 70 MET cc_start: 0.8630 (mtp) cc_final: 0.8351 (mtp) REVERT: 4 70 MET cc_start: 0.8627 (mtp) cc_final: 0.8338 (mtp) REVERT: A 70 MET cc_start: 0.8637 (mtp) cc_final: 0.8353 (mtp) REVERT: B 70 MET cc_start: 0.8640 (mtp) cc_final: 0.8348 (mtp) REVERT: E 70 MET cc_start: 0.8638 (mtp) cc_final: 0.8353 (mtp) REVERT: F 70 MET cc_start: 0.8632 (mtp) cc_final: 0.8348 (mtp) REVERT: G 70 MET cc_start: 0.8632 (mtp) cc_final: 0.8357 (mtp) REVERT: H 70 MET cc_start: 0.8635 (mtp) cc_final: 0.8348 (mtp) REVERT: I 70 MET cc_start: 0.8621 (mtp) cc_final: 0.8342 (mtp) REVERT: K 70 MET cc_start: 0.8624 (mtp) cc_final: 0.8338 (mtp) REVERT: O 70 MET cc_start: 0.8625 (mtp) cc_final: 0.8342 (mtp) REVERT: P 70 MET cc_start: 0.8627 (mtp) cc_final: 0.8393 (mtp) REVERT: Q 70 MET cc_start: 0.8633 (mtp) cc_final: 0.8353 (mtp) REVERT: U 70 MET cc_start: 0.8625 (mtp) cc_final: 0.8339 (mtp) REVERT: X 70 MET cc_start: 0.8629 (mtp) cc_final: 0.8351 (mtp) REVERT: Y 70 MET cc_start: 0.8626 (mtp) cc_final: 0.8345 (mtp) REVERT: a 70 MET cc_start: 0.8637 (mtp) cc_final: 0.8361 (mtp) REVERT: e 70 MET cc_start: 0.8637 (mtp) cc_final: 0.8353 (mtp) REVERT: r 70 MET cc_start: 0.8630 (mtp) cc_final: 0.8350 (mtp) outliers start: 24 outliers final: 24 residues processed: 527 average time/residue: 1.8635 time to fit residues: 1139.2271 Evaluate side-chains 559 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 535 time to evaluate : 4.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 109 ASN Chi-restraints excluded: chain 2 residue 109 ASN Chi-restraints excluded: chain 4 residue 109 ASN Chi-restraints excluded: chain 6 residue 109 ASN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain Q residue 109 ASN Chi-restraints excluded: chain S residue 109 ASN Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain W residue 109 ASN Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain a residue 109 ASN Chi-restraints excluded: chain e residue 109 ASN Chi-restraints excluded: chain r residue 109 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 9.9990 chunk 387 optimal weight: 8.9990 chunk 236 optimal weight: 6.9990 chunk 183 optimal weight: 20.0000 chunk 269 optimal weight: 4.9990 chunk 406 optimal weight: 2.9990 chunk 374 optimal weight: 5.9990 chunk 323 optimal weight: 0.1980 chunk 33 optimal weight: 0.5980 chunk 250 optimal weight: 4.9990 chunk 198 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 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: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 34776 Z= 0.170 Angle : 0.580 6.876 46848 Z= 0.320 Chirality : 0.039 0.135 4920 Planarity : 0.003 0.024 6192 Dihedral : 4.272 18.035 4536 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 2.64 % Favored : 96.70 % 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: 4.40 (0.13), residues: 4032 helix: 3.41 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.61 (0.27), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP 6 93 HIS 0.009 0.001 HIS r 65 PHE 0.019 0.003 PHE G 41 TYR 0.024 0.002 TYR a 39 ARG 0.005 0.001 ARG I 156 ********************** 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 551 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 527 time to evaluate : 4.436 Fit side-chains REVERT: 1 70 MET cc_start: 0.8641 (mtp) cc_final: 0.8416 (mtp) REVERT: 4 70 MET cc_start: 0.8641 (mtp) cc_final: 0.8403 (mtp) REVERT: A 70 MET cc_start: 0.8649 (mtp) cc_final: 0.8419 (mtp) REVERT: B 70 MET cc_start: 0.8650 (mtp) cc_final: 0.8413 (mtp) REVERT: E 70 MET cc_start: 0.8648 (mtp) cc_final: 0.8414 (mtp) REVERT: F 70 MET cc_start: 0.8644 (mtp) cc_final: 0.8416 (mtp) REVERT: G 70 MET cc_start: 0.8645 (mtp) cc_final: 0.8366 (mtp) REVERT: H 70 MET cc_start: 0.8645 (mtp) cc_final: 0.8409 (mtp) REVERT: I 70 MET cc_start: 0.8634 (mtp) cc_final: 0.8405 (mtp) REVERT: K 70 MET cc_start: 0.8638 (mtp) cc_final: 0.8407 (mtp) REVERT: O 70 MET cc_start: 0.8637 (mtp) cc_final: 0.8410 (mtp) REVERT: P 70 MET cc_start: 0.8638 (mtp) cc_final: 0.8413 (mtp) REVERT: Q 70 MET cc_start: 0.8642 (mtp) cc_final: 0.8362 (mtp) REVERT: U 70 MET cc_start: 0.8637 (mtp) cc_final: 0.8406 (mtp) REVERT: X 70 MET cc_start: 0.8639 (mtp) cc_final: 0.8415 (mtp) REVERT: Y 70 MET cc_start: 0.8638 (mtp) cc_final: 0.8411 (mtp) REVERT: a 70 MET cc_start: 0.8648 (mtp) cc_final: 0.8372 (mtp) REVERT: e 70 MET cc_start: 0.8648 (mtp) cc_final: 0.8418 (mtp) REVERT: r 70 MET cc_start: 0.8642 (mtp) cc_final: 0.8412 (mtp) outliers start: 24 outliers final: 24 residues processed: 527 average time/residue: 1.8749 time to fit residues: 1146.6013 Evaluate side-chains 559 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 535 time to evaluate : 4.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 109 ASN Chi-restraints excluded: chain 2 residue 109 ASN Chi-restraints excluded: chain 4 residue 109 ASN Chi-restraints excluded: chain 6 residue 109 ASN Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain Q residue 109 ASN Chi-restraints excluded: chain S residue 109 ASN Chi-restraints excluded: chain U residue 109 ASN Chi-restraints excluded: chain W residue 109 ASN Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain Y residue 109 ASN Chi-restraints excluded: chain a residue 109 ASN Chi-restraints excluded: chain e residue 109 ASN Chi-restraints excluded: chain r residue 109 ASN 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: 4.9990 chunk 47 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 324 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 332 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.152726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.141002 restraints weight = 201037.656| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 3.77 r_work: 0.2764 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 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 : 0.003 0.018 34776 Z= 0.220 Angle : 0.644 7.253 46848 Z= 0.356 Chirality : 0.041 0.148 4920 Planarity : 0.004 0.027 6192 Dihedral : 4.341 17.204 4536 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 2.64 % Favored : 96.70 % 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: 4.15 (0.13), residues: 4032 helix: 3.22 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.61 (0.26), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP 6 93 HIS 0.007 0.002 HIS M 65 PHE 0.022 0.003 PHE G 41 TYR 0.029 0.003 TYR G 39 ARG 0.003 0.001 ARG Q 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16393.90 seconds wall clock time: 289 minutes 26.80 seconds (17366.80 seconds total)