Starting phenix.real_space_refine on Sat Mar 23 05:10:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpx_16789/03_2024/8cpx_16789_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpx_16789/03_2024/8cpx_16789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpx_16789/03_2024/8cpx_16789.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpx_16789/03_2024/8cpx_16789.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpx_16789/03_2024/8cpx_16789_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpx_16789/03_2024/8cpx_16789_updated.pdb" } resolution = 1.76 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 8333 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 GLU 61": "OE1" <-> "OE2" Residue "1 ASP 89": "OD1" <-> "OD2" Residue "1 GLU 116": "OE1" <-> "OE2" Residue "2 GLU 61": "OE1" <-> "OE2" Residue "2 GLU 116": "OE1" <-> "OE2" Residue "4 GLU 61": "OE1" <-> "OE2" Residue "4 GLU 116": "OE1" <-> "OE2" Residue "6 GLU 61": "OE1" <-> "OE2" Residue "6 GLU 116": "OE1" <-> "OE2" Residue "A GLU 61": "OE1" <-> "OE2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "E GLU 61": "OE1" <-> "OE2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "F GLU 61": "OE1" <-> "OE2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 116": "OE1" <-> "OE2" Residue "H GLU 61": "OE1" <-> "OE2" Residue "H GLU 116": "OE1" <-> "OE2" Residue "I GLU 61": "OE1" <-> "OE2" Residue "I GLU 116": "OE1" <-> "OE2" Residue "K GLU 61": "OE1" <-> "OE2" Residue "K GLU 116": "OE1" <-> "OE2" Residue "M GLU 61": "OE1" <-> "OE2" Residue "M GLU 116": "OE1" <-> "OE2" Residue "O GLU 61": "OE1" <-> "OE2" Residue "O GLU 116": "OE1" <-> "OE2" Residue "P GLU 61": "OE1" <-> "OE2" Residue "P GLU 116": "OE1" <-> "OE2" Residue "Q GLU 61": "OE1" <-> "OE2" Residue "Q GLU 116": "OE1" <-> "OE2" Residue "S GLU 61": "OE1" <-> "OE2" Residue "S GLU 116": "OE1" <-> "OE2" Residue "U GLU 61": "OE1" <-> "OE2" Residue "U GLU 116": "OE1" <-> "OE2" Residue "W GLU 61": "OE1" <-> "OE2" Residue "W GLU 116": "OE1" <-> "OE2" Residue "X GLU 61": "OE1" <-> "OE2" Residue "X GLU 116": "OE1" <-> "OE2" Residue "Y GLU 61": "OE1" <-> "OE2" Residue "Y GLU 116": "OE1" <-> "OE2" Residue "a GLU 61": "OE1" <-> "OE2" Residue "a GLU 116": "OE1" <-> "OE2" Residue "e GLU 61": "OE1" <-> "OE2" Residue "e GLU 116": "OE1" <-> "OE2" Residue "r GLU 61": "OE1" <-> "OE2" Residue "r GLU 116": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35827 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "2" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "4" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "6" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "E" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "F" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "G" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "H" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "I" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "K" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "M" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "O" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "P" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "Q" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "S" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "U" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "W" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "X" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "Y" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "a" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "e" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "r" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Time building chain proxies: 19.00, per 1000 atoms: 0.53 Number of scatterers: 35827 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 8333 8.00 N 5976 7.00 C 21312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.13 Conformation dependent library (CDL) restraints added in 5.5 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 72.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.57 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 76 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 76 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 76 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 76 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 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 '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 2423 hydrogen bonds defined for protein. 7269 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: 12.39 Time building geometry restraints manager: 17.13 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: 11664 1.34 - 1.46: 6516 1.46 - 1.58: 16332 1.58 - 1.70: 0 1.70 - 1.82: 264 Bond restraints: 34776 Sorted by residual: bond pdb=" CB CSX U 90 " pdb=" SG CSX U 90 " ideal model delta sigma weight residual 1.831 1.759 0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" CB CSX r 90 " pdb=" SG CSX r 90 " ideal model delta sigma weight residual 1.831 1.759 0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" CB CSX A 90 " pdb=" SG CSX A 90 " ideal model delta sigma weight residual 1.831 1.759 0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" CB CSX W 90 " pdb=" SG CSX W 90 " ideal model delta sigma weight residual 1.831 1.759 0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" CB CSX Y 90 " pdb=" SG CSX Y 90 " ideal model delta sigma weight residual 1.831 1.759 0.072 2.00e-02 2.50e+03 1.30e+01 ... (remaining 34771 not shown) Histogram of bond angle deviations from ideal: 100.47 - 107.17: 855 107.17 - 113.87: 19495 113.87 - 120.58: 13933 120.58 - 127.28: 12229 127.28 - 133.99: 336 Bond angle restraints: 46848 Sorted by residual: angle pdb=" C TYR I 32 " pdb=" CA TYR I 32 " pdb=" CB TYR I 32 " ideal model delta sigma weight residual 110.85 117.16 -6.31 1.70e+00 3.46e-01 1.38e+01 angle pdb=" C TYR O 32 " pdb=" CA TYR O 32 " pdb=" CB TYR O 32 " ideal model delta sigma weight residual 110.85 117.14 -6.29 1.70e+00 3.46e-01 1.37e+01 angle pdb=" C TYR U 32 " pdb=" CA TYR U 32 " pdb=" CB TYR U 32 " ideal model delta sigma weight residual 110.85 117.13 -6.28 1.70e+00 3.46e-01 1.37e+01 angle pdb=" C TYR H 32 " pdb=" CA TYR H 32 " pdb=" CB TYR H 32 " ideal model delta sigma weight residual 110.85 117.13 -6.28 1.70e+00 3.46e-01 1.36e+01 angle pdb=" C TYR E 32 " pdb=" CA TYR E 32 " pdb=" CB TYR E 32 " ideal model delta sigma weight residual 110.85 117.12 -6.27 1.70e+00 3.46e-01 1.36e+01 ... (remaining 46843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.54: 18987 16.54 - 33.08: 1440 33.08 - 49.62: 327 49.62 - 66.17: 102 66.17 - 82.71: 144 Dihedral angle restraints: 21000 sinusoidal: 8688 harmonic: 12312 Sorted by residual: 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 180.00 163.06 16.94 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA VAL F 46 " pdb=" C VAL F 46 " pdb=" N ALA F 47 " pdb=" CA ALA F 47 " ideal model delta harmonic sigma weight residual 180.00 163.08 16.92 0 5.00e+00 4.00e-02 1.14e+01 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 180.00 163.09 16.91 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 20997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3646 0.049 - 0.098: 892 0.098 - 0.147: 244 0.147 - 0.196: 86 0.196 - 0.246: 52 Chirality restraints: 4920 Sorted by residual: chirality pdb=" CG LEU S 72 " pdb=" CB LEU S 72 " pdb=" CD1 LEU S 72 " pdb=" CD2 LEU S 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CG LEU B 72 " pdb=" CB LEU B 72 " pdb=" CD1 LEU B 72 " pdb=" CD2 LEU B 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CG LEU Y 72 " pdb=" CB LEU Y 72 " pdb=" CD1 LEU Y 72 " pdb=" CD2 LEU Y 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 4917 not shown) Planarity restraints: 6192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 32 " -0.050 2.00e-02 2.50e+03 4.74e-02 4.49e+01 pdb=" CG TYR F 32 " 0.117 2.00e-02 2.50e+03 pdb=" CD1 TYR F 32 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR F 32 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR F 32 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR F 32 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR F 32 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR F 32 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 32 " 0.051 2.00e-02 2.50e+03 4.74e-02 4.48e+01 pdb=" CG TYR E 32 " -0.116 2.00e-02 2.50e+03 pdb=" CD1 TYR E 32 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR E 32 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR E 32 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR E 32 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR E 32 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR E 32 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 6 32 " 0.050 2.00e-02 2.50e+03 4.72e-02 4.46e+01 pdb=" CG TYR 6 32 " -0.116 2.00e-02 2.50e+03 pdb=" CD1 TYR 6 32 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR 6 32 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR 6 32 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR 6 32 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR 6 32 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR 6 32 " 0.000 2.00e-02 2.50e+03 ... (remaining 6189 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 1255 2.63 - 3.20: 34928 3.20 - 3.77: 68427 3.77 - 4.33: 94756 4.33 - 4.90: 146988 Nonbonded interactions: 346354 Sorted by model distance: nonbonded pdb=" O HOH 1 301 " pdb=" O HOH 1 302 " model vdw 2.063 2.440 nonbonded pdb=" O HOH W 601 " pdb=" O HOH W 602 " model vdw 2.065 2.440 nonbonded pdb=" O HOH Q 601 " pdb=" O HOH Q 602 " model vdw 2.065 2.440 nonbonded pdb=" NZ LYS A 119 " pdb=" OD1 ASP A 123 " model vdw 2.182 2.520 nonbonded pdb=" NZ LYS P 119 " pdb=" OD1 ASP P 123 " model vdw 2.199 2.520 ... (remaining 346349 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 or resid 201)) selection = (chain '2' and (resid 4 through 176 or resid 201)) selection = (chain '4' and (resid 4 through 176 or resid 201)) selection = (chain '6' and (resid 4 through 176 or resid 201)) selection = (chain 'A' and (resid 4 through 176 or resid 500)) selection = (chain 'B' and (resid 4 through 176 or resid 500)) selection = chain 'E' selection = chain 'F' selection = (chain 'G' and (resid 4 through 176 or resid 201)) selection = (chain 'H' and (resid 4 through 176 or resid 201)) selection = chain 'I' selection = chain 'K' selection = (chain 'M' and (resid 4 through 176 or resid 201)) selection = (chain 'O' and (resid 4 through 176 or resid 500)) selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'e' selection = chain 'r' } 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: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.230 Check model and map are aligned: 0.510 Set scattering table: 0.290 Process input model: 92.590 Find NCS groups from input model: 4.300 Set up NCS constraints: 0.600 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:12.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 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 0.072 34776 Z= 0.324 Angle : 0.803 6.612 46848 Z= 0.453 Chirality : 0.056 0.246 4920 Planarity : 0.008 0.060 6192 Dihedral : 14.967 82.707 13032 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 2.18 (0.13), residues: 4032 helix: 1.63 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.93 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP H 93 HIS 0.011 0.004 HIS 1 151 PHE 0.028 0.005 PHE G 41 TYR 0.117 0.008 TYR F 32 ARG 0.021 0.004 ARG P 63 *********************** 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 732 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 732 time to evaluate : 4.309 Fit side-chains REVERT: 6 135 THR cc_start: 0.8317 (m) cc_final: 0.7976 (p) REVERT: G 135 THR cc_start: 0.8331 (m) cc_final: 0.7994 (p) REVERT: I 135 THR cc_start: 0.8241 (m) cc_final: 0.7962 (p) REVERT: M 135 THR cc_start: 0.8324 (m) cc_final: 0.7986 (p) REVERT: Q 135 THR cc_start: 0.8319 (m) cc_final: 0.7972 (p) REVERT: W 135 THR cc_start: 0.8324 (m) cc_final: 0.7980 (p) REVERT: a 135 THR cc_start: 0.8312 (m) cc_final: 0.7981 (p) outliers start: 0 outliers final: 0 residues processed: 732 average time/residue: 1.8035 time to fit residues: 1538.1396 Evaluate side-chains 513 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 513 time to evaluate : 4.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 6.9990 chunk 309 optimal weight: 10.0000 chunk 171 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 165 optimal weight: 9.9990 chunk 319 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 238 optimal weight: 0.7980 chunk 370 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 14 GLN 1 112 GLN 2 14 GLN 2 112 GLN 4 14 GLN 4 112 GLN 6 14 GLN A 14 GLN A 112 GLN B 14 GLN B 112 GLN E 14 GLN E 112 GLN F 14 GLN F 112 GLN G 14 GLN H 14 GLN H 112 GLN I 14 GLN I 112 GLN K 14 GLN K 112 GLN M 14 GLN O 14 GLN O 112 GLN P 14 GLN P 112 GLN Q 14 GLN S 14 GLN S 112 GLN U 14 GLN U 112 GLN W 14 GLN X 14 GLN X 112 GLN Y 14 GLN Y 112 GLN a 14 GLN e 14 GLN e 112 GLN r 14 GLN r 112 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.0728 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= 0.198 Angle : 0.627 6.340 46848 Z= 0.343 Chirality : 0.040 0.166 4920 Planarity : 0.004 0.045 6192 Dihedral : 4.375 19.503 4536 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 2.07 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.93 (0.13), residues: 4032 helix: 2.95 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.02 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP X 93 HIS 0.005 0.002 HIS 6 60 PHE 0.019 0.004 PHE W 41 TYR 0.054 0.005 TYR E 32 ARG 0.006 0.001 ARG r 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 610 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 586 time to evaluate : 4.674 Fit side-chains REVERT: 1 135 THR cc_start: 0.8165 (m) cc_final: 0.7927 (p) REVERT: 2 135 THR cc_start: 0.8174 (m) cc_final: 0.7922 (p) REVERT: 4 135 THR cc_start: 0.8180 (m) cc_final: 0.7924 (p) REVERT: A 135 THR cc_start: 0.8177 (m) cc_final: 0.7931 (p) REVERT: B 135 THR cc_start: 0.8177 (m) cc_final: 0.7929 (p) REVERT: E 135 THR cc_start: 0.8175 (m) cc_final: 0.7923 (p) REVERT: F 135 THR cc_start: 0.8174 (m) cc_final: 0.7927 (p) REVERT: H 135 THR cc_start: 0.8180 (m) cc_final: 0.7933 (p) REVERT: K 135 THR cc_start: 0.8180 (m) cc_final: 0.7930 (p) REVERT: O 135 THR cc_start: 0.8173 (m) cc_final: 0.7922 (p) REVERT: P 135 THR cc_start: 0.8164 (m) cc_final: 0.7921 (p) REVERT: S 135 THR cc_start: 0.8170 (m) cc_final: 0.7925 (p) REVERT: U 135 THR cc_start: 0.8166 (m) cc_final: 0.7927 (p) REVERT: X 135 THR cc_start: 0.8167 (m) cc_final: 0.7927 (p) REVERT: Y 135 THR cc_start: 0.8178 (m) cc_final: 0.7933 (p) REVERT: e 135 THR cc_start: 0.8181 (m) cc_final: 0.7936 (p) REVERT: r 135 THR cc_start: 0.8162 (m) cc_final: 0.7917 (p) outliers start: 24 outliers final: 24 residues processed: 609 average time/residue: 1.8793 time to fit residues: 1328.8673 Evaluate side-chains 580 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 556 time to evaluate : 4.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 119 LYS Chi-restraints excluded: chain 2 residue 119 LYS Chi-restraints excluded: chain 4 residue 119 LYS Chi-restraints excluded: chain 6 residue 119 LYS Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain H residue 119 LYS Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain K residue 119 LYS Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain O residue 119 LYS Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain Q residue 119 LYS Chi-restraints excluded: chain S residue 119 LYS Chi-restraints excluded: chain U residue 119 LYS Chi-restraints excluded: chain W residue 119 LYS Chi-restraints excluded: chain X residue 119 LYS Chi-restraints excluded: chain Y residue 119 LYS Chi-restraints excluded: chain a residue 119 LYS Chi-restraints excluded: chain e residue 119 LYS Chi-restraints excluded: chain r residue 119 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 308 optimal weight: 5.9990 chunk 252 optimal weight: 0.9980 chunk 102 optimal weight: 30.0000 chunk 371 optimal weight: 9.9990 chunk 400 optimal weight: 9.9990 chunk 330 optimal weight: 2.9990 chunk 368 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 297 optimal weight: 1.9990 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 14 GLN 1 112 GLN 2 14 GLN 2 112 GLN 4 14 GLN 4 112 GLN 6 14 GLN A 14 GLN A 112 GLN B 14 GLN B 112 GLN E 14 GLN E 112 GLN F 14 GLN F 112 GLN G 14 GLN H 14 GLN H 112 GLN I 14 GLN I 112 GLN K 14 GLN K 112 GLN M 14 GLN O 14 GLN O 112 GLN P 14 GLN P 112 GLN Q 14 GLN S 14 GLN S 112 GLN U 14 GLN U 112 GLN W 14 GLN X 14 GLN X 112 GLN Y 14 GLN Y 112 GLN a 14 GLN e 14 GLN e 112 GLN r 14 GLN r 112 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.0861 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= 0.232 Angle : 0.661 6.387 46848 Z= 0.360 Chirality : 0.041 0.163 4920 Planarity : 0.004 0.052 6192 Dihedral : 4.358 19.387 4536 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 2.73 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: 3.81 (0.13), residues: 4032 helix: 2.87 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.94 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP W 93 HIS 0.006 0.002 HIS Y 57 PHE 0.020 0.004 PHE 2 81 TYR 0.033 0.004 TYR A 32 ARG 0.008 0.001 ARG M 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 586 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 562 time to evaluate : 4.173 Fit side-chains REVERT: 1 135 THR cc_start: 0.8202 (m) cc_final: 0.7969 (p) REVERT: 2 135 THR cc_start: 0.8213 (m) cc_final: 0.7971 (p) REVERT: 4 135 THR cc_start: 0.8221 (m) cc_final: 0.7973 (p) REVERT: A 135 THR cc_start: 0.8217 (m) cc_final: 0.7976 (p) REVERT: B 135 THR cc_start: 0.8214 (m) cc_final: 0.7972 (p) REVERT: E 135 THR cc_start: 0.8209 (m) cc_final: 0.7966 (p) REVERT: F 135 THR cc_start: 0.8213 (m) cc_final: 0.7974 (p) REVERT: H 135 THR cc_start: 0.8216 (m) cc_final: 0.7975 (p) REVERT: K 135 THR cc_start: 0.8220 (m) cc_final: 0.7973 (p) REVERT: O 135 THR cc_start: 0.8224 (m) cc_final: 0.7979 (p) REVERT: P 135 THR cc_start: 0.8205 (m) cc_final: 0.7966 (p) REVERT: S 135 THR cc_start: 0.8214 (m) cc_final: 0.7972 (p) REVERT: U 135 THR cc_start: 0.8207 (m) cc_final: 0.7972 (p) REVERT: X 135 THR cc_start: 0.8207 (m) cc_final: 0.7972 (p) REVERT: Y 135 THR cc_start: 0.8217 (m) cc_final: 0.7975 (p) REVERT: e 135 THR cc_start: 0.8218 (m) cc_final: 0.7977 (p) REVERT: r 135 THR cc_start: 0.8214 (m) cc_final: 0.7974 (p) outliers start: 24 outliers final: 24 residues processed: 585 average time/residue: 1.9081 time to fit residues: 1292.2085 Evaluate side-chains 532 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 508 time to evaluate : 4.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 119 LYS Chi-restraints excluded: chain 2 residue 119 LYS Chi-restraints excluded: chain 4 residue 119 LYS Chi-restraints excluded: chain 6 residue 119 LYS Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain H residue 119 LYS Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain K residue 119 LYS Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain O residue 119 LYS Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain Q residue 119 LYS Chi-restraints excluded: chain S residue 119 LYS Chi-restraints excluded: chain U residue 119 LYS Chi-restraints excluded: chain W residue 119 LYS Chi-restraints excluded: chain X residue 119 LYS Chi-restraints excluded: chain Y residue 119 LYS Chi-restraints excluded: chain a residue 119 LYS Chi-restraints excluded: chain e residue 119 LYS Chi-restraints excluded: chain r residue 119 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 8.9990 chunk 279 optimal weight: 3.9990 chunk 192 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 177 optimal weight: 8.9990 chunk 249 optimal weight: 20.0000 chunk 372 optimal weight: 1.9990 chunk 394 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 353 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 14 GLN 2 14 GLN 4 14 GLN 6 14 GLN A 14 GLN B 14 GLN B 112 GLN E 14 GLN F 14 GLN G 14 GLN G 86 GLN H 14 GLN H 112 GLN I 14 GLN K 14 GLN K 112 GLN M 14 GLN O 14 GLN P 14 GLN Q 14 GLN S 14 GLN U 14 GLN W 14 GLN X 14 GLN X 86 GLN Y 14 GLN a 14 GLN e 14 GLN r 14 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 34776 Z= 0.159 Angle : 0.562 5.941 46848 Z= 0.306 Chirality : 0.038 0.152 4920 Planarity : 0.003 0.039 6192 Dihedral : 4.227 19.977 4536 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 2.40 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: 4.26 (0.13), residues: 4032 helix: 3.21 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.98 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 93 HIS 0.003 0.001 HIS B 57 PHE 0.014 0.003 PHE P 81 TYR 0.023 0.003 TYR Q 39 ARG 0.006 0.001 ARG r 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 613 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 589 time to evaluate : 4.567 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 613 average time/residue: 1.8333 time to fit residues: 1308.8786 Evaluate side-chains 574 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 550 time to evaluate : 4.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 119 LYS Chi-restraints excluded: chain 2 residue 119 LYS Chi-restraints excluded: chain 4 residue 119 LYS Chi-restraints excluded: chain 6 residue 119 LYS Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain H residue 119 LYS Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain K residue 119 LYS Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain O residue 119 LYS Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain Q residue 119 LYS Chi-restraints excluded: chain S residue 119 LYS Chi-restraints excluded: chain U residue 119 LYS Chi-restraints excluded: chain W residue 119 LYS Chi-restraints excluded: chain X residue 119 LYS Chi-restraints excluded: chain Y residue 119 LYS Chi-restraints excluded: chain a residue 119 LYS Chi-restraints excluded: chain e residue 119 LYS Chi-restraints excluded: chain r residue 119 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 3.9990 chunk 223 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 293 optimal weight: 0.6980 chunk 162 optimal weight: 9.9990 chunk 336 optimal weight: 6.9990 chunk 272 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 201 optimal weight: 5.9990 chunk 353 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 14 GLN 2 14 GLN 4 14 GLN 6 14 GLN A 14 GLN B 14 GLN E 14 GLN F 14 GLN F 86 GLN G 14 GLN H 14 GLN I 14 GLN K 14 GLN M 14 GLN O 14 GLN O 86 GLN P 14 GLN Q 14 GLN S 14 GLN U 14 GLN W 14 GLN X 14 GLN Y 14 GLN a 14 GLN e 14 GLN r 14 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.0997 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= 0.209 Angle : 0.620 5.819 46848 Z= 0.337 Chirality : 0.039 0.154 4920 Planarity : 0.004 0.044 6192 Dihedral : 4.322 21.942 4536 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 3.21 % Favored : 96.13 % 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: 3.96 (0.13), residues: 4032 helix: 3.01 (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 0.013 0.003 TRP Y 93 HIS 0.005 0.002 HIS 6 57 PHE 0.020 0.004 PHE r 81 TYR 0.030 0.003 TYR E 39 ARG 0.008 0.001 ARG U 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 598 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 574 time to evaluate : 3.969 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 598 average time/residue: 1.8499 time to fit residues: 1285.8587 Evaluate side-chains 581 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 557 time to evaluate : 4.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 119 LYS Chi-restraints excluded: chain 2 residue 119 LYS Chi-restraints excluded: chain 4 residue 119 LYS Chi-restraints excluded: chain 6 residue 119 LYS Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain H residue 119 LYS Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain K residue 119 LYS Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain O residue 119 LYS Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain Q residue 119 LYS Chi-restraints excluded: chain S residue 119 LYS Chi-restraints excluded: chain U residue 119 LYS Chi-restraints excluded: chain W residue 119 LYS Chi-restraints excluded: chain X residue 119 LYS Chi-restraints excluded: chain Y residue 119 LYS Chi-restraints excluded: chain a residue 119 LYS Chi-restraints excluded: chain e residue 119 LYS Chi-restraints excluded: chain r residue 119 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 2.9990 chunk 355 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 231 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 394 optimal weight: 5.9990 chunk 327 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 14 GLN 1 86 GLN 2 14 GLN 4 14 GLN 6 14 GLN A 14 GLN B 14 GLN E 14 GLN F 14 GLN G 14 GLN H 14 GLN I 14 GLN K 14 GLN M 14 GLN O 14 GLN P 14 GLN Q 14 GLN Q 86 GLN S 14 GLN U 14 GLN W 14 GLN X 14 GLN Y 14 GLN a 14 GLN a 86 GLN e 14 GLN e 86 GLN r 14 GLN r 86 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 34776 Z= 0.209 Angle : 0.619 5.807 46848 Z= 0.337 Chirality : 0.040 0.156 4920 Planarity : 0.004 0.060 6192 Dihedral : 4.302 21.638 4536 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 3.19 % Favored : 96.16 % 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: 3.94 (0.13), residues: 4032 helix: 3.00 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.81 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP Y 93 HIS 0.005 0.002 HIS Q 57 PHE 0.020 0.004 PHE W 81 TYR 0.028 0.003 TYR E 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 595 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 571 time to evaluate : 4.420 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 595 average time/residue: 1.8495 time to fit residues: 1281.3248 Evaluate side-chains 560 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 536 time to evaluate : 4.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 119 LYS Chi-restraints excluded: chain 2 residue 119 LYS Chi-restraints excluded: chain 4 residue 119 LYS Chi-restraints excluded: chain 6 residue 119 LYS Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain H residue 119 LYS Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain K residue 119 LYS Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain O residue 119 LYS Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain Q residue 119 LYS Chi-restraints excluded: chain S residue 119 LYS Chi-restraints excluded: chain U residue 119 LYS Chi-restraints excluded: chain W residue 119 LYS Chi-restraints excluded: chain X residue 119 LYS Chi-restraints excluded: chain Y residue 119 LYS Chi-restraints excluded: chain a residue 119 LYS Chi-restraints excluded: chain e residue 119 LYS Chi-restraints excluded: chain r residue 119 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 224 optimal weight: 6.9990 chunk 288 optimal weight: 9.9990 chunk 223 optimal weight: 9.9990 chunk 332 optimal weight: 0.9990 chunk 220 optimal weight: 30.0000 chunk 393 optimal weight: 8.9990 chunk 246 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 181 optimal weight: 20.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 14 GLN 2 14 GLN 2 86 GLN 4 14 GLN 4 86 GLN 6 14 GLN A 14 GLN A 136 HIS B 14 GLN E 14 GLN F 14 GLN F 136 HIS G 14 GLN H 14 GLN I 14 GLN I 86 GLN K 14 GLN M 14 GLN O 14 GLN P 14 GLN Q 14 GLN S 14 GLN U 14 GLN W 14 GLN W 86 GLN X 14 GLN Y 14 GLN Y 86 GLN a 14 GLN e 14 GLN r 14 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 34776 Z= 0.149 Angle : 0.539 5.513 46848 Z= 0.294 Chirality : 0.037 0.149 4920 Planarity : 0.003 0.040 6192 Dihedral : 4.189 21.618 4536 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.65 % Allowed : 3.21 % Favored : 96.13 % 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: 4.33 (0.13), residues: 4032 helix: 3.23 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.07 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP a 93 HIS 0.003 0.001 HIS G 57 PHE 0.013 0.003 PHE Y 81 TYR 0.022 0.002 TYR E 39 ARG 0.007 0.000 ARG U 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 637 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 613 time to evaluate : 4.237 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 637 average time/residue: 1.7367 time to fit residues: 1300.4445 Evaluate side-chains 602 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 578 time to evaluate : 4.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 119 LYS Chi-restraints excluded: chain 2 residue 119 LYS Chi-restraints excluded: chain 4 residue 119 LYS Chi-restraints excluded: chain 6 residue 119 LYS Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain H residue 119 LYS Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain K residue 119 LYS Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain O residue 119 LYS Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain Q residue 119 LYS Chi-restraints excluded: chain S residue 119 LYS Chi-restraints excluded: chain U residue 119 LYS Chi-restraints excluded: chain W residue 119 LYS Chi-restraints excluded: chain X residue 119 LYS Chi-restraints excluded: chain Y residue 119 LYS Chi-restraints excluded: chain a residue 119 LYS Chi-restraints excluded: chain e residue 119 LYS Chi-restraints excluded: chain r residue 119 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 10.0000 chunk 157 optimal weight: 4.9990 chunk 234 optimal weight: 0.9990 chunk 118 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 250 optimal weight: 0.7980 chunk 267 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 309 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 14 GLN 2 14 GLN 4 14 GLN 6 14 GLN A 14 GLN B 14 GLN E 14 GLN F 14 GLN G 14 GLN H 14 GLN I 14 GLN K 14 GLN M 14 GLN O 14 GLN P 14 GLN Q 14 GLN S 14 GLN U 14 GLN W 14 GLN X 14 GLN Y 14 GLN a 14 GLN e 14 GLN r 14 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 34776 Z= 0.138 Angle : 0.521 5.433 46848 Z= 0.284 Chirality : 0.037 0.145 4920 Planarity : 0.004 0.045 6192 Dihedral : 4.166 21.702 4536 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.03 % Allowed : 2.91 % Favored : 96.05 % 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: 4.51 (0.13), residues: 4032 helix: 3.37 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.04 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP a 93 HIS 0.003 0.001 HIS E 57 PHE 0.012 0.003 PHE X 81 TYR 0.021 0.002 TYR I 39 ARG 0.007 0.000 ARG U 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 640 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 602 time to evaluate : 4.631 Fit side-chains REVERT: 1 86 GLN cc_start: 0.7127 (mm-40) cc_final: 0.6879 (pm20) REVERT: 2 86 GLN cc_start: 0.7041 (mm-40) cc_final: 0.6754 (pm20) REVERT: Q 86 GLN cc_start: 0.7121 (mm-40) cc_final: 0.6895 (pm20) REVERT: W 86 GLN cc_start: 0.7032 (mm-40) cc_final: 0.6723 (pm20) REVERT: a 86 GLN cc_start: 0.7135 (mm-40) cc_final: 0.6914 (pm20) REVERT: e 86 GLN cc_start: 0.7060 (mm-40) cc_final: 0.6761 (pm20) outliers start: 38 outliers final: 32 residues processed: 626 average time/residue: 1.7791 time to fit residues: 1306.6707 Evaluate side-chains 615 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 583 time to evaluate : 4.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 119 LYS Chi-restraints excluded: chain 2 residue 94 GLU Chi-restraints excluded: chain 2 residue 119 LYS Chi-restraints excluded: chain 4 residue 119 LYS Chi-restraints excluded: chain 6 residue 94 GLU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain H residue 119 LYS Chi-restraints excluded: chain I residue 94 GLU Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain K residue 94 GLU Chi-restraints excluded: chain K residue 119 LYS Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 119 LYS Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain S residue 94 GLU Chi-restraints excluded: chain S residue 119 LYS Chi-restraints excluded: chain U residue 94 GLU Chi-restraints excluded: chain U residue 119 LYS Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain X residue 94 GLU Chi-restraints excluded: chain X residue 119 LYS Chi-restraints excluded: chain Y residue 94 GLU Chi-restraints excluded: chain Y residue 119 LYS Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain e residue 119 LYS Chi-restraints excluded: chain r residue 119 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 7.9990 chunk 376 optimal weight: 8.9990 chunk 343 optimal weight: 10.0000 chunk 366 optimal weight: 0.7980 chunk 220 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 287 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 331 optimal weight: 2.9990 chunk 346 optimal weight: 0.7980 chunk 365 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 14 GLN 2 14 GLN 2 136 HIS 4 14 GLN 4 136 HIS 6 14 GLN A 14 GLN B 14 GLN B 136 HIS E 14 GLN E 136 HIS F 14 GLN G 14 GLN H 14 GLN H 136 HIS I 14 GLN I 136 HIS K 14 GLN K 136 HIS M 14 GLN O 14 GLN O 136 HIS P 14 GLN P 136 HIS Q 14 GLN S 14 GLN S 136 HIS U 14 GLN U 136 HIS W 14 GLN X 14 GLN Y 14 GLN Y 136 HIS a 14 GLN e 14 GLN e 136 HIS r 14 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 34776 Z= 0.156 Angle : 0.550 5.510 46848 Z= 0.299 Chirality : 0.037 0.146 4920 Planarity : 0.004 0.046 6192 Dihedral : 4.192 21.953 4536 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.87 % Allowed : 2.94 % Favored : 96.19 % 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: 4.38 (0.13), residues: 4032 helix: 3.28 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.01 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP I 93 HIS 0.004 0.001 HIS E 57 PHE 0.014 0.003 PHE 1 81 TYR 0.024 0.002 TYR r 39 ARG 0.012 0.001 ARG K 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 597 time to evaluate : 4.139 Fit side-chains outliers start: 32 outliers final: 32 residues processed: 615 average time/residue: 1.7430 time to fit residues: 1255.4446 Evaluate side-chains 603 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 571 time to evaluate : 4.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 119 LYS Chi-restraints excluded: chain 2 residue 94 GLU Chi-restraints excluded: chain 2 residue 119 LYS Chi-restraints excluded: chain 4 residue 119 LYS Chi-restraints excluded: chain 6 residue 94 GLU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain H residue 119 LYS Chi-restraints excluded: chain I residue 94 GLU Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain K residue 94 GLU Chi-restraints excluded: chain K residue 119 LYS Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 119 LYS Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain S residue 94 GLU Chi-restraints excluded: chain S residue 119 LYS Chi-restraints excluded: chain U residue 94 GLU Chi-restraints excluded: chain U residue 119 LYS Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain X residue 94 GLU Chi-restraints excluded: chain X residue 119 LYS Chi-restraints excluded: chain Y residue 94 GLU Chi-restraints excluded: chain Y residue 119 LYS Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain e residue 119 LYS Chi-restraints excluded: chain r residue 119 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 6.9990 chunk 387 optimal weight: 4.9990 chunk 236 optimal weight: 0.7980 chunk 183 optimal weight: 5.9990 chunk 269 optimal weight: 3.9990 chunk 406 optimal weight: 6.9990 chunk 374 optimal weight: 10.0000 chunk 323 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 250 optimal weight: 0.5980 chunk 198 optimal weight: 9.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 14 GLN 2 14 GLN 4 14 GLN 6 14 GLN A 14 GLN B 14 GLN E 14 GLN F 14 GLN G 14 GLN H 14 GLN I 14 GLN K 14 GLN M 14 GLN O 14 GLN P 14 GLN Q 14 GLN S 14 GLN U 14 GLN W 14 GLN X 14 GLN Y 14 GLN a 14 GLN e 14 GLN r 14 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 34776 Z= 0.172 Angle : 0.571 5.604 46848 Z= 0.311 Chirality : 0.038 0.149 4920 Planarity : 0.004 0.043 6192 Dihedral : 4.217 21.979 4536 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.14 % Allowed : 2.81 % Favored : 96.05 % 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: 4.25 (0.13), residues: 4032 helix: 3.19 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.00 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP W 93 HIS 0.005 0.001 HIS I 57 PHE 0.016 0.003 PHE 6 81 TYR 0.026 0.003 TYR r 39 ARG 0.012 0.001 ARG K 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 579 time to evaluate : 4.618 Fit side-chains outliers start: 42 outliers final: 42 residues processed: 597 average time/residue: 1.7873 time to fit residues: 1246.9043 Evaluate side-chains 598 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 556 time to evaluate : 4.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 94 GLU Chi-restraints excluded: chain 1 residue 119 LYS Chi-restraints excluded: chain 2 residue 94 GLU Chi-restraints excluded: chain 2 residue 119 LYS Chi-restraints excluded: chain 4 residue 94 GLU Chi-restraints excluded: chain 4 residue 119 LYS Chi-restraints excluded: chain 6 residue 94 GLU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 119 LYS Chi-restraints excluded: chain I residue 94 GLU Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain K residue 94 GLU Chi-restraints excluded: chain K residue 119 LYS Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 119 LYS Chi-restraints excluded: chain P residue 94 GLU Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain Q residue 94 GLU Chi-restraints excluded: chain S residue 94 GLU Chi-restraints excluded: chain S residue 119 LYS Chi-restraints excluded: chain U residue 94 GLU Chi-restraints excluded: chain U residue 119 LYS Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain X residue 94 GLU Chi-restraints excluded: chain X residue 119 LYS Chi-restraints excluded: chain Y residue 94 GLU Chi-restraints excluded: chain Y residue 119 LYS Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain e residue 94 GLU Chi-restraints excluded: chain e residue 119 LYS Chi-restraints excluded: chain r residue 94 GLU Chi-restraints excluded: chain r residue 119 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 5.9990 chunk 344 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 298 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 324 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 332 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 14 GLN 2 14 GLN 4 14 GLN 6 14 GLN A 14 GLN B 14 GLN E 14 GLN F 14 GLN G 14 GLN H 14 GLN I 14 GLN K 14 GLN M 14 GLN O 14 GLN P 14 GLN Q 14 GLN S 14 GLN U 14 GLN W 14 GLN X 14 GLN Y 14 GLN a 14 GLN e 14 GLN r 14 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.151362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.139576 restraints weight = 199561.352| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.78 r_work: 0.2794 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1119 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= 0.219 Angle : 0.634 5.881 46848 Z= 0.345 Chirality : 0.040 0.155 4920 Planarity : 0.004 0.042 6192 Dihedral : 4.261 22.177 4536 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.31 % Allowed : 2.67 % Favored : 96.02 % 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: 2.96 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.96 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP S 93 HIS 0.007 0.002 HIS W 57 PHE 0.021 0.004 PHE 6 81 TYR 0.032 0.003 TYR K 39 ARG 0.017 0.001 ARG K 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17774.40 seconds wall clock time: 313 minutes 11.43 seconds (18791.43 seconds total)