Starting phenix.real_space_refine on Sat Dec 16 16:59:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpt_16785/12_2023/8cpt_16785_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpt_16785/12_2023/8cpt_16785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpt_16785/12_2023/8cpt_16785.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpt_16785/12_2023/8cpt_16785.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpt_16785/12_2023/8cpt_16785_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpt_16785/12_2023/8cpt_16785_updated.pdb" } resolution = 1.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mg 14 5.21 5 S 168 5.16 5 Na 24 4.78 5 C 21312 2.51 5 N 5976 2.21 5 O 8530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 ASP 91": "OD1" <-> "OD2" Residue "1 ASP 123": "OD1" <-> "OD2" Residue "4 ASP 91": "OD1" <-> "OD2" Residue "4 ASP 123": "OD1" <-> "OD2" Residue "6 GLU 116": "OE1" <-> "OE2" Residue "A GLU 64": "OE1" <-> "OE2" Residue "A ASP 91": "OD1" <-> "OD2" Residue "B ASP 91": "OD1" <-> "OD2" Residue "E GLU 64": "OE1" <-> "OE2" Residue "E ASP 91": "OD1" <-> "OD2" Residue "F GLU 64": "OE1" <-> "OE2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "G GLU 94": "OE1" <-> "OE2" Residue "G GLU 116": "OE1" <-> "OE2" Residue "G ASP 123": "OD1" <-> "OD2" Residue "H GLU 64": "OE1" <-> "OE2" Residue "H ASP 91": "OD1" <-> "OD2" Residue "I GLU 64": "OE1" <-> "OE2" Residue "M GLU 64": "OE1" <-> "OE2" Residue "M GLU 116": "OE1" <-> "OE2" Residue "M ASP 123": "OD1" <-> "OD2" Residue "O ASP 123": "OD1" <-> "OD2" Residue "P GLU 64": "OE1" <-> "OE2" Residue "P ASP 91": "OD1" <-> "OD2" Residue "Q ASP 91": "OD1" <-> "OD2" Residue "Q GLU 116": "OE1" <-> "OE2" Residue "Q ASP 123": "OD1" <-> "OD2" Residue "S GLU 64": "OE1" <-> "OE2" Residue "S GLU 94": "OE1" <-> "OE2" Residue "W GLU 64": "OE1" <-> "OE2" Residue "W GLU 116": "OE1" <-> "OE2" Residue "W ASP 123": "OD1" <-> "OD2" Residue "Y GLU 64": "OE1" <-> "OE2" Residue "Y GLU 94": "OE1" <-> "OE2" Residue "a GLU 64": "OE1" <-> "OE2" Residue "a GLU 94": "OE1" <-> "OE2" Residue "a GLU 116": "OE1" <-> "OE2" Residue "a ASP 123": "OD1" <-> "OD2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "e ASP 91": "OD1" <-> "OD2" Residue "r ASP 91": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 36024 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: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "2" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "4" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "6" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "A" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "B" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "E" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "F" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "G" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "H" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "I" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "K" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "M" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "O" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "P" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "Q" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "S" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "U" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "W" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "X" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "Y" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "a" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "e" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "r" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Time building chain proxies: 18.36, per 1000 atoms: 0.51 Number of scatterers: 36024 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 8530 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: 16.72 Conformation dependent library (CDL) restraints added in 5.6 seconds 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7968 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 144 helices and 0 sheets defined 72.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.23 Creating SS restraints... Processing helix chain '1' and resid 14 through 41 Processing helix chain '1' and resid 49 through 76 Processing helix chain '1' and resid 96 through 123 Processing helix chain '1' and resid 127 through 136 Processing helix chain '1' and resid 138 through 158 Processing helix chain '1' and resid 164 through 173 Processing helix chain '2' and resid 14 through 41 Processing helix chain '2' and resid 49 through 76 Processing helix chain '2' and resid 96 through 123 Processing helix chain '2' and resid 127 through 136 Processing helix chain '2' and resid 138 through 158 Processing helix chain '2' and resid 164 through 173 Processing helix chain '4' and resid 14 through 41 Processing helix chain '4' and resid 49 through 76 Processing helix chain '4' and resid 96 through 123 Processing helix chain '4' and resid 127 through 136 Processing helix chain '4' and resid 138 through 158 Processing helix chain '4' and resid 164 through 173 Processing helix chain '6' and resid 14 through 41 Processing helix chain '6' and resid 49 through 75 Processing helix chain '6' and resid 96 through 123 Processing helix chain '6' and resid 127 through 136 Processing helix chain '6' and resid 138 through 158 Processing helix chain '6' and resid 164 through 173 Processing helix chain 'A' and resid 14 through 41 Processing helix chain 'A' and resid 49 through 76 Processing helix chain 'A' and resid 96 through 123 Processing helix chain 'A' and resid 127 through 136 Processing helix chain 'A' and resid 138 through 158 Processing helix chain 'A' and resid 164 through 173 Processing helix chain 'B' and resid 14 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 96 through 123 Processing helix chain 'B' and resid 127 through 136 Processing helix chain 'B' and resid 138 through 158 Processing helix chain 'B' and resid 164 through 173 Processing helix chain 'E' and resid 14 through 41 Processing helix chain 'E' and resid 49 through 76 Processing helix chain 'E' and resid 96 through 123 Processing helix chain 'E' and resid 127 through 136 Processing helix chain 'E' and resid 138 through 158 Processing helix chain 'E' and resid 164 through 173 Processing helix chain 'F' and resid 14 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 96 through 123 Processing helix chain 'F' and resid 127 through 136 Processing helix chain 'F' and resid 138 through 158 Processing helix chain 'F' and resid 164 through 173 Processing helix chain 'G' and resid 14 through 41 Processing helix chain 'G' and resid 49 through 75 Processing helix chain 'G' and resid 96 through 123 Processing helix chain 'G' and resid 127 through 136 Processing helix chain 'G' and resid 138 through 158 Processing helix chain 'G' and resid 164 through 173 Processing helix chain 'H' and resid 14 through 41 Processing helix chain 'H' and resid 49 through 76 Processing helix chain 'H' and resid 96 through 123 Processing helix chain 'H' and resid 127 through 136 Processing helix chain 'H' and resid 138 through 158 Processing helix chain 'H' and resid 164 through 173 Processing helix chain 'I' and resid 14 through 41 Processing helix chain 'I' and resid 49 through 76 Processing helix chain 'I' and resid 96 through 123 Processing helix chain 'I' and resid 127 through 136 Processing helix chain 'I' and resid 138 through 158 Processing helix chain 'I' and resid 164 through 173 Processing helix chain 'K' and resid 14 through 41 Processing helix chain 'K' and resid 49 through 76 Processing helix chain 'K' and resid 96 through 123 Processing helix chain 'K' and resid 127 through 136 Processing helix chain 'K' and resid 138 through 158 Processing helix chain 'K' and resid 164 through 173 Processing helix chain 'M' and resid 14 through 41 Processing helix chain 'M' and resid 49 through 75 Processing helix chain 'M' and resid 96 through 123 Processing helix chain 'M' and resid 127 through 136 Processing helix chain 'M' and resid 138 through 158 Processing helix chain 'M' and resid 164 through 173 Processing helix chain 'O' and resid 14 through 41 Processing helix chain 'O' and resid 49 through 76 Processing helix chain 'O' and resid 96 through 123 Processing helix chain 'O' and resid 127 through 136 Processing helix chain 'O' and resid 138 through 158 Processing helix chain 'O' and resid 164 through 173 Processing helix chain 'P' and resid 14 through 41 Processing helix chain 'P' and resid 49 through 76 Processing helix chain 'P' and resid 96 through 123 Processing helix chain 'P' and resid 127 through 136 Processing helix chain 'P' and resid 138 through 158 Processing helix chain 'P' and resid 164 through 173 Processing helix chain 'Q' and resid 14 through 41 Processing helix chain 'Q' and resid 49 through 75 Processing helix chain 'Q' and resid 96 through 123 Processing helix chain 'Q' and resid 127 through 136 Processing helix chain 'Q' and resid 138 through 158 Processing helix chain 'Q' and resid 164 through 173 Processing helix chain 'S' and resid 14 through 41 Processing helix chain 'S' and resid 49 through 76 Processing helix chain 'S' and resid 96 through 123 Processing helix chain 'S' and resid 127 through 136 Processing helix chain 'S' and resid 138 through 158 Processing helix chain 'S' and resid 164 through 173 Processing helix chain 'U' and resid 14 through 41 Processing helix chain 'U' and resid 49 through 76 Processing helix chain 'U' and resid 96 through 123 Processing helix chain 'U' and resid 127 through 136 Processing helix chain 'U' and resid 138 through 158 Processing helix chain 'U' and resid 164 through 173 Processing helix chain 'W' and resid 14 through 41 Processing helix chain 'W' and resid 49 through 75 Processing helix chain 'W' and resid 96 through 123 Processing helix chain 'W' and resid 127 through 136 Processing helix chain 'W' and resid 138 through 158 Processing helix chain 'W' and resid 164 through 173 Processing helix chain 'X' and resid 14 through 41 Processing helix chain 'X' and resid 49 through 76 Processing helix chain 'X' and resid 96 through 123 Processing helix chain 'X' and resid 127 through 136 Processing helix chain 'X' and resid 138 through 158 Processing helix chain 'X' and resid 164 through 173 Processing helix chain 'Y' and resid 14 through 41 Processing helix chain 'Y' and resid 49 through 76 Processing helix chain 'Y' and resid 96 through 123 Processing helix chain 'Y' and resid 127 through 136 Processing helix chain 'Y' and resid 138 through 158 Processing helix chain 'Y' and resid 164 through 173 Processing helix chain 'a' and resid 14 through 41 Processing helix chain 'a' and resid 49 through 75 Processing helix chain 'a' and resid 96 through 123 Processing helix chain 'a' and resid 127 through 136 Processing helix chain 'a' and resid 138 through 158 Processing helix chain 'a' and resid 164 through 173 Processing helix chain 'e' and resid 14 through 41 Processing helix chain 'e' and resid 49 through 76 Processing helix chain 'e' and resid 96 through 123 Processing helix chain 'e' and resid 127 through 136 Processing helix chain 'e' and resid 138 through 158 Processing helix chain 'e' and resid 164 through 173 Processing helix chain 'r' and resid 14 through 41 Processing helix chain 'r' and resid 49 through 76 Processing helix chain 'r' and resid 96 through 123 Processing helix chain 'r' and resid 127 through 136 Processing helix chain 'r' and resid 138 through 158 Processing helix chain 'r' and resid 164 through 173 2418 hydrogen bonds defined for protein. 7254 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.19 Time building geometry restraints manager: 17.53 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: 11640 1.34 - 1.46: 5268 1.46 - 1.57: 17604 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 34776 Sorted by residual: bond pdb=" CB CSX X 90 " pdb=" SG CSX X 90 " ideal model delta sigma weight residual 1.831 1.757 0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" CB CSX M 90 " pdb=" SG CSX M 90 " ideal model delta sigma weight residual 1.831 1.757 0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" CB CSX B 90 " pdb=" SG CSX B 90 " ideal model delta sigma weight residual 1.831 1.757 0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" CB CSX S 90 " pdb=" SG CSX S 90 " ideal model delta sigma weight residual 1.831 1.757 0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" CB CSX F 90 " pdb=" SG CSX F 90 " ideal model delta sigma weight residual 1.831 1.757 0.074 2.00e-02 2.50e+03 1.35e+01 ... (remaining 34771 not shown) Histogram of bond angle deviations from ideal: 99.13 - 106.08: 413 106.08 - 113.03: 18795 113.03 - 119.98: 11999 119.98 - 126.93: 15250 126.93 - 133.88: 391 Bond angle restraints: 46848 Sorted by residual: angle pdb=" CA TYR H 39 " pdb=" CB TYR H 39 " pdb=" CG TYR H 39 " ideal model delta sigma weight residual 113.90 108.03 5.87 1.80e+00 3.09e-01 1.06e+01 angle pdb=" CA TYR B 39 " pdb=" CB TYR B 39 " pdb=" CG TYR B 39 " ideal model delta sigma weight residual 113.90 108.10 5.80 1.80e+00 3.09e-01 1.04e+01 angle pdb=" CA TYR A 39 " pdb=" CB TYR A 39 " pdb=" CG TYR A 39 " ideal model delta sigma weight residual 113.90 108.17 5.73 1.80e+00 3.09e-01 1.01e+01 angle pdb=" CA TYR 4 39 " pdb=" CB TYR 4 39 " pdb=" CG TYR 4 39 " ideal model delta sigma weight residual 113.90 108.17 5.73 1.80e+00 3.09e-01 1.01e+01 angle pdb=" CA TYR 1 39 " pdb=" CB TYR 1 39 " pdb=" CG TYR 1 39 " ideal model delta sigma weight residual 113.90 108.17 5.73 1.80e+00 3.09e-01 1.01e+01 ... (remaining 46843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 19073 17.90 - 35.79: 1436 35.79 - 53.69: 276 53.69 - 71.58: 119 71.58 - 89.48: 96 Dihedral angle restraints: 21000 sinusoidal: 8688 harmonic: 12312 Sorted by residual: dihedral pdb=" CA VAL A 46 " pdb=" C VAL A 46 " pdb=" N ALA A 47 " pdb=" CA ALA A 47 " ideal model delta harmonic sigma weight residual 180.00 162.84 17.16 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA VAL E 46 " pdb=" C VAL E 46 " pdb=" N ALA E 47 " pdb=" CA ALA E 47 " ideal model delta harmonic sigma weight residual 180.00 162.89 17.11 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA VAL M 46 " pdb=" C VAL M 46 " pdb=" N ALA M 47 " pdb=" CA ALA M 47 " ideal model delta harmonic sigma weight residual 180.00 162.89 17.11 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 20997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3523 0.047 - 0.094: 1050 0.094 - 0.141: 238 0.141 - 0.189: 67 0.189 - 0.236: 42 Chirality restraints: 4920 Sorted by residual: chirality pdb=" CA TYR r 137 " pdb=" N TYR r 137 " pdb=" C TYR r 137 " pdb=" CB TYR r 137 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA TYR A 137 " pdb=" N TYR A 137 " pdb=" C TYR A 137 " pdb=" CB TYR A 137 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA TYR F 137 " pdb=" N TYR F 137 " pdb=" C TYR F 137 " pdb=" CB TYR F 137 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 4917 not shown) Planarity restraints: 6192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR P 137 " 0.025 2.00e-02 2.50e+03 1.82e-02 6.59e+00 pdb=" CG TYR P 137 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR P 137 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR P 137 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR P 137 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR P 137 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR P 137 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR P 137 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR r 137 " -0.025 2.00e-02 2.50e+03 1.81e-02 6.57e+00 pdb=" CG TYR r 137 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR r 137 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR r 137 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR r 137 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR r 137 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR r 137 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR r 137 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 137 " -0.025 2.00e-02 2.50e+03 1.81e-02 6.56e+00 pdb=" CG TYR E 137 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR E 137 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR E 137 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR E 137 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR E 137 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR E 137 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR E 137 " -0.018 2.00e-02 2.50e+03 ... (remaining 6189 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 2284 2.71 - 3.25: 39364 3.25 - 3.80: 72565 3.80 - 4.35: 93381 4.35 - 4.90: 144621 Nonbonded interactions: 352215 Sorted by model distance: nonbonded pdb=" NH2 ARG S 63 " pdb=" O HOH S 601 " model vdw 2.157 2.520 nonbonded pdb=" OD1 ASP H 91 " pdb=" O HOH H 301 " model vdw 2.241 2.440 nonbonded pdb=" OD1 ASP B 91 " pdb=" O HOH B 601 " model vdw 2.241 2.440 nonbonded pdb=" OD1 ASP r 91 " pdb=" O HOH r 601 " model vdw 2.241 2.440 nonbonded pdb=" OD1 ASP 1 91 " pdb=" O HOH 1 301 " model vdw 2.241 2.440 ... (remaining 352210 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: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 7.900 Check model and map are aligned: 0.570 Set scattering table: 0.360 Process input model: 91.930 Find NCS groups from input model: 2.900 Set up NCS constraints: 0.480 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 : 0.004 0.074 34776 Z= 0.267 Angle : 0.719 5.874 46848 Z= 0.413 Chirality : 0.052 0.236 4920 Planarity : 0.007 0.060 6192 Dihedral : 15.650 89.477 13032 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.49 % Allowed : 5.04 % Favored : 94.47 % 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: 2.30 (0.13), residues: 4032 helix: 1.72 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.94 (0.28), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP r 93 HIS 0.011 0.002 HIS O 128 PHE 0.028 0.004 PHE W 41 TYR 0.036 0.005 TYR E 137 ARG 0.013 0.003 ARG K 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 694 time to evaluate : 4.210 Fit side-chains outliers start: 18 outliers final: 18 residues processed: 712 average time/residue: 2.3488 time to fit residues: 1892.5940 Evaluate side-chains 574 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 556 time to evaluate : 4.742 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 0 time to fit residues: 6.1593 ------------------------------------------------------------------------------- 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: 20.0000 chunk 309 optimal weight: 10.0000 chunk 171 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 208 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 319 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 194 optimal weight: 20.0000 chunk 238 optimal weight: 9.9990 chunk 370 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 2 109 ASN 4 109 ASN 6 109 ASN A 109 ASN B 109 ASN E 109 ASN F 109 ASN G 109 ASN H 109 ASN I 109 ASN K 109 ASN M 109 ASN O 109 ASN P 109 ASN Q 109 ASN S 109 ASN U 109 ASN W 109 ASN X 109 ASN Y 109 ASN a 109 ASN e 109 ASN r 109 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.0787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 34776 Z= 0.126 Angle : 0.488 5.225 46848 Z= 0.270 Chirality : 0.037 0.142 4920 Planarity : 0.003 0.021 6192 Dihedral : 4.208 21.138 4536 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.49 % Allowed : 5.53 % Favored : 93.98 % 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: 4.83 (0.13), residues: 4032 helix: 3.60 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.09 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP U 93 HIS 0.004 0.001 HIS P 128 PHE 0.018 0.002 PHE W 41 TYR 0.021 0.002 TYR Q 39 ARG 0.002 0.000 ARG 6 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 614 time to evaluate : 4.330 Fit side-chains outliers start: 18 outliers final: 18 residues processed: 632 average time/residue: 2.2488 time to fit residues: 1618.8719 Evaluate side-chains 683 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 665 time to evaluate : 4.272 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 0 time to fit residues: 5.6991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 chunk 308 optimal weight: 9.9990 chunk 252 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 371 optimal weight: 20.0000 chunk 400 optimal weight: 2.9990 chunk 330 optimal weight: 8.9990 chunk 368 optimal weight: 10.0000 chunk 126 optimal weight: 0.5980 chunk 297 optimal weight: 20.0000 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 2 109 ASN 4 109 ASN 6 109 ASN A 109 ASN B 109 ASN E 109 ASN F 109 ASN G 109 ASN H 109 ASN I 109 ASN I 136 HIS K 109 ASN M 109 ASN O 109 ASN P 109 ASN Q 109 ASN S 60 HIS S 109 ASN U 109 ASN W 109 ASN X 109 ASN Y 109 ASN a 109 ASN e 109 ASN r 109 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.0740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 34776 Z= 0.249 Angle : 0.655 6.050 46848 Z= 0.367 Chirality : 0.043 0.154 4920 Planarity : 0.004 0.031 6192 Dihedral : 4.489 20.871 4536 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.77 % Allowed : 4.74 % Favored : 93.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.98 (0.13), residues: 4032 helix: 3.02 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.80 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP 6 93 HIS 0.005 0.002 HIS G 65 PHE 0.027 0.004 PHE Y 41 TYR 0.031 0.004 TYR H 39 ARG 0.004 0.001 ARG 1 43 *********************** 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 762 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 697 time to evaluate : 4.859 Fit side-chains outliers start: 65 outliers final: 45 residues processed: 718 average time/residue: 2.2979 time to fit residues: 1875.4008 Evaluate side-chains 662 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 617 time to evaluate : 4.287 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 21 residues processed: 24 average time/residue: 1.7248 time to fit residues: 54.8909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 3.9990 chunk 279 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 41 optimal weight: 0.1980 chunk 177 optimal weight: 0.9990 chunk 249 optimal weight: 20.0000 chunk 372 optimal weight: 0.7980 chunk 394 optimal weight: 10.0000 chunk 194 optimal weight: 4.9990 chunk 353 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 2 109 ASN 4 109 ASN 6 109 ASN A 109 ASN B 109 ASN E 109 ASN F 109 ASN G 109 ASN H 109 ASN I 109 ASN K 109 ASN M 109 ASN O 109 ASN P 109 ASN Q 109 ASN S 60 HIS S 109 ASN U 109 ASN W 109 ASN X 109 ASN Y 109 ASN a 109 ASN e 109 ASN r 109 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.0961 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= 0.133 Angle : 0.493 5.316 46848 Z= 0.274 Chirality : 0.036 0.134 4920 Planarity : 0.003 0.020 6192 Dihedral : 4.354 21.294 4536 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.68 % Allowed : 5.42 % Favored : 93.90 % 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: 4.59 (0.13), residues: 4032 helix: 3.48 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.76 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP 6 93 HIS 0.003 0.001 HIS I 128 PHE 0.018 0.002 PHE 1 41 TYR 0.021 0.002 TYR H 39 ARG 0.003 0.000 ARG S 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 653 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 628 time to evaluate : 4.291 Fit side-chains outliers start: 25 outliers final: 25 residues processed: 649 average time/residue: 2.2307 time to fit residues: 1651.8790 Evaluate side-chains 714 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 689 time to evaluate : 4.265 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 21 residues processed: 4 average time/residue: 1.9351 time to fit residues: 14.7316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 0.9980 chunk 223 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 293 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 336 optimal weight: 20.0000 chunk 272 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 201 optimal weight: 9.9990 chunk 353 optimal weight: 20.0000 chunk 99 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 2 109 ASN 4 109 ASN 6 109 ASN A 109 ASN B 109 ASN E 109 ASN F 109 ASN G 109 ASN H 109 ASN I 109 ASN K 109 ASN M 109 ASN O 109 ASN P 109 ASN Q 109 ASN S 60 HIS S 109 ASN U 109 ASN W 109 ASN X 109 ASN Y 109 ASN a 109 ASN e 109 ASN r 109 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.0872 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= 0.154 Angle : 0.522 5.420 46848 Z= 0.291 Chirality : 0.037 0.135 4920 Planarity : 0.003 0.021 6192 Dihedral : 4.388 21.993 4536 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.31 % Allowed : 6.10 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.44 (0.13), residues: 4032 helix: 3.38 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.70 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP 6 93 HIS 0.003 0.001 HIS 4 128 PHE 0.020 0.003 PHE H 41 TYR 0.024 0.002 TYR 4 39 ARG 0.002 0.000 ARG S 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 767 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 719 time to evaluate : 4.283 Fit side-chains outliers start: 48 outliers final: 21 residues processed: 743 average time/residue: 2.3073 time to fit residues: 1950.7271 Evaluate side-chains 625 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 604 time to evaluate : 4.494 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 21 residues processed: 0 time to fit residues: 5.6955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 9.9990 chunk 355 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 231 optimal weight: 20.0000 chunk 97 optimal weight: 8.9990 chunk 394 optimal weight: 9.9990 chunk 327 optimal weight: 20.0000 chunk 182 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 207 optimal weight: 9.9990 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 60 HIS 1 109 ASN 2 60 HIS 2 109 ASN 4 60 HIS 4 109 ASN 6 60 HIS 6 109 ASN A 60 HIS A 109 ASN B 60 HIS B 109 ASN E 60 HIS E 109 ASN F 60 HIS F 109 ASN G 60 HIS G 109 ASN H 60 HIS H 109 ASN H 136 HIS I 60 HIS I 109 ASN K 60 HIS K 109 ASN M 60 HIS M 109 ASN O 60 HIS O 109 ASN P 60 HIS P 109 ASN Q 60 HIS Q 109 ASN S 60 HIS S 109 ASN U 60 HIS U 109 ASN W 60 HIS W 109 ASN W 136 HIS X 60 HIS X 109 ASN Y 60 HIS Y 109 ASN Y 136 HIS a 60 HIS a 109 ASN e 60 HIS e 109 ASN r 60 HIS r 109 ASN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 34776 Z= 0.264 Angle : 0.659 6.161 46848 Z= 0.369 Chirality : 0.042 0.157 4920 Planarity : 0.004 0.029 6192 Dihedral : 4.534 21.748 4536 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.72 % Allowed : 6.40 % Favored : 91.88 % 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: 3.85 (0.13), residues: 4032 helix: 3.05 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.29 (0.25), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP 6 93 HIS 0.005 0.002 HIS 6 57 PHE 0.026 0.004 PHE X 41 TYR 0.030 0.004 TYR H 39 ARG 0.004 0.001 ARG S 43 *********************** 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 709 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 646 time to evaluate : 4.061 Fit side-chains outliers start: 63 outliers final: 52 residues processed: 670 average time/residue: 2.2115 time to fit residues: 1695.4193 Evaluate side-chains 674 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 622 time to evaluate : 4.277 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 24 residues processed: 28 average time/residue: 1.7910 time to fit residues: 64.4655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 224 optimal weight: 9.9990 chunk 288 optimal weight: 20.0000 chunk 223 optimal weight: 3.9990 chunk 332 optimal weight: 0.9980 chunk 220 optimal weight: 8.9990 chunk 393 optimal weight: 6.9990 chunk 246 optimal weight: 20.0000 chunk 239 optimal weight: 9.9990 chunk 181 optimal weight: 9.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 60 HIS 1 109 ASN 2 60 HIS 2 109 ASN 4 60 HIS 4 109 ASN 6 60 HIS 6 109 ASN A 60 HIS A 109 ASN B 60 HIS B 109 ASN E 60 HIS E 109 ASN F 60 HIS F 109 ASN F 136 HIS G 60 HIS G 109 ASN H 60 HIS H 109 ASN I 60 HIS I 109 ASN K 60 HIS K 109 ASN M 60 HIS M 109 ASN O 60 HIS O 109 ASN P 60 HIS P 109 ASN P 136 HIS Q 60 HIS Q 109 ASN S 60 HIS S 109 ASN U 60 HIS U 109 ASN W 60 HIS W 109 ASN X 60 HIS X 109 ASN Y 60 HIS Y 109 ASN a 60 HIS a 109 ASN e 60 HIS e 109 ASN r 60 HIS r 109 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 34776 Z= 0.252 Angle : 0.643 6.131 46848 Z= 0.361 Chirality : 0.041 0.157 4920 Planarity : 0.004 0.029 6192 Dihedral : 4.554 21.516 4536 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.04 % Allowed : 6.24 % Favored : 91.72 % 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: 3.73 (0.13), residues: 4032 helix: 2.95 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.31 (0.25), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP 6 93 HIS 0.006 0.002 HIS e 57 PHE 0.026 0.004 PHE X 41 TYR 0.028 0.003 TYR H 39 ARG 0.004 0.001 ARG a 43 *********************** 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 721 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 646 time to evaluate : 4.690 Fit side-chains outliers start: 75 outliers final: 51 residues processed: 670 average time/residue: 2.1957 time to fit residues: 1682.7327 Evaluate side-chains 673 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 622 time to evaluate : 4.223 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 24 residues processed: 27 average time/residue: 2.0391 time to fit residues: 70.0355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 234 optimal weight: 20.0000 chunk 118 optimal weight: 20.0000 chunk 77 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 250 optimal weight: 0.9980 chunk 267 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 309 optimal weight: 9.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 60 HIS 1 109 ASN 1 136 HIS 2 60 HIS 2 109 ASN 2 136 HIS 4 60 HIS 4 109 ASN 4 136 HIS 6 60 HIS 6 109 ASN 6 136 HIS A 60 HIS A 109 ASN A 136 HIS B 60 HIS B 109 ASN B 136 HIS E 60 HIS E 109 ASN E 136 HIS F 60 HIS F 109 ASN G 60 HIS G 109 ASN G 136 HIS H 60 HIS H 109 ASN I 60 HIS I 109 ASN K 60 HIS K 109 ASN K 136 HIS M 60 HIS M 109 ASN M 136 HIS O 60 HIS O 109 ASN O 136 HIS P 60 HIS P 109 ASN Q 60 HIS Q 109 ASN Q 136 HIS S 60 HIS S 109 ASN S 136 HIS U 60 HIS U 109 ASN U 136 HIS W 60 HIS W 109 ASN X 60 HIS X 109 ASN X 136 HIS Y 60 HIS Y 109 ASN a 60 HIS a 109 ASN a 136 HIS e 60 HIS e 109 ASN e 136 HIS r 60 HIS r 109 ASN r 136 HIS Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1023 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= 0.193 Angle : 0.574 5.794 46848 Z= 0.321 Chirality : 0.039 0.147 4920 Planarity : 0.003 0.023 6192 Dihedral : 4.533 22.035 4536 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.87 % Allowed : 6.75 % Favored : 92.37 % 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: 4.06 (0.13), residues: 4032 helix: 3.14 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.52 (0.26), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP 6 93 HIS 0.004 0.001 HIS Q 57 PHE 0.024 0.003 PHE 4 41 TYR 0.025 0.003 TYR E 39 ARG 0.002 0.001 ARG e 43 *********************** 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 678 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 646 time to evaluate : 3.882 Fit side-chains outliers start: 32 outliers final: 32 residues processed: 670 average time/residue: 2.2439 time to fit residues: 1718.9310 Evaluate side-chains 654 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 622 time to evaluate : 4.513 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 24 residues processed: 8 average time/residue: 1.9410 time to fit residues: 24.0943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 0.0970 chunk 376 optimal weight: 0.8980 chunk 343 optimal weight: 10.0000 chunk 366 optimal weight: 5.9990 chunk 220 optimal weight: 8.9990 chunk 159 optimal weight: 0.8980 chunk 287 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 331 optimal weight: 6.9990 chunk 346 optimal weight: 0.9990 chunk 365 optimal weight: 5.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 60 HIS 1 109 ASN 2 60 HIS 2 109 ASN 4 60 HIS 4 109 ASN 6 60 HIS 6 109 ASN A 60 HIS A 109 ASN B 60 HIS B 109 ASN E 60 HIS E 109 ASN F 60 HIS F 109 ASN G 60 HIS G 109 ASN H 60 HIS H 109 ASN I 60 HIS I 109 ASN K 60 HIS K 109 ASN M 60 HIS M 109 ASN O 60 HIS O 109 ASN P 60 HIS P 109 ASN Q 60 HIS Q 109 ASN S 60 HIS S 109 ASN U 60 HIS U 109 ASN W 60 HIS W 109 ASN X 60 HIS X 109 ASN Y 60 HIS Y 109 ASN a 60 HIS a 109 ASN e 60 HIS e 109 ASN r 60 HIS r 109 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 34776 Z= 0.133 Angle : 0.494 5.377 46848 Z= 0.275 Chirality : 0.036 0.137 4920 Planarity : 0.003 0.020 6192 Dihedral : 4.411 21.841 4536 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.09 % Allowed : 6.54 % Favored : 92.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.58 (0.13), residues: 4032 helix: 3.48 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.70 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP 6 93 HIS 0.002 0.001 HIS a 57 PHE 0.018 0.002 PHE 1 41 TYR 0.022 0.002 TYR H 39 ARG 0.001 0.000 ARG M 43 *********************** 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 686 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 646 time to evaluate : 3.945 Fit side-chains outliers start: 40 outliers final: 24 residues processed: 670 average time/residue: 2.2416 time to fit residues: 1722.0846 Evaluate side-chains 625 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 601 time to evaluate : 4.251 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 5.7762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 0.9980 chunk 387 optimal weight: 3.9990 chunk 236 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 269 optimal weight: 4.9990 chunk 406 optimal weight: 5.9990 chunk 374 optimal weight: 0.0570 chunk 323 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 chunk 250 optimal weight: 7.9990 chunk 198 optimal weight: 8.9990 overall best weight: 2.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 60 HIS 1 109 ASN 2 60 HIS 2 109 ASN 4 60 HIS 4 109 ASN 6 60 HIS 6 109 ASN A 60 HIS A 109 ASN B 60 HIS B 109 ASN E 60 HIS E 109 ASN F 60 HIS F 109 ASN G 60 HIS G 109 ASN H 60 HIS H 109 ASN I 60 HIS I 109 ASN K 60 HIS K 109 ASN M 60 HIS M 109 ASN O 60 HIS O 109 ASN P 60 HIS P 109 ASN Q 60 HIS Q 109 ASN S 60 HIS S 109 ASN U 60 HIS U 109 ASN W 60 HIS W 109 ASN X 60 HIS X 109 ASN Y 60 HIS Y 109 ASN a 60 HIS a 109 ASN e 60 HIS e 109 ASN r 60 HIS r 109 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 34776 Z= 0.155 Angle : 0.528 5.499 46848 Z= 0.294 Chirality : 0.037 0.136 4920 Planarity : 0.003 0.020 6192 Dihedral : 4.436 22.173 4536 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.95 % Allowed : 7.24 % Favored : 91.80 % 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: 4.48 (0.13), residues: 4032 helix: 3.46 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.57 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP 6 93 HIS 0.003 0.001 HIS S 57 PHE 0.020 0.003 PHE W 41 TYR 0.025 0.002 TYR r 39 ARG 0.002 0.000 ARG U 43 ********************** 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 680 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 645 time to evaluate : 4.483 Fit side-chains outliers start: 35 outliers final: 35 residues processed: 669 average time/residue: 2.2046 time to fit residues: 1686.2932 Evaluate side-chains 638 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 603 time to evaluate : 4.019 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 24 residues processed: 11 average time/residue: 2.0754 time to fit residues: 32.1767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 0.8980 chunk 344 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 chunk 298 optimal weight: 0.9980 chunk 47 optimal weight: 8.9990 chunk 89 optimal weight: 20.0000 chunk 324 optimal weight: 8.9990 chunk 135 optimal weight: 0.8980 chunk 332 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 60 HIS 1 109 ASN 2 60 HIS 2 109 ASN 4 60 HIS 4 109 ASN 6 60 HIS 6 109 ASN A 60 HIS A 109 ASN B 60 HIS B 109 ASN E 60 HIS E 109 ASN F 60 HIS F 109 ASN G 60 HIS G 109 ASN H 60 HIS H 109 ASN I 60 HIS I 109 ASN K 60 HIS K 109 ASN M 60 HIS M 109 ASN O 60 HIS O 109 ASN P 60 HIS P 109 ASN Q 60 HIS Q 109 ASN S 60 HIS S 109 ASN U 60 HIS U 109 ASN W 60 HIS W 109 ASN X 60 HIS X 109 ASN Y 60 HIS Y 109 ASN a 60 HIS a 109 ASN e 60 HIS e 109 ASN r 60 HIS r 109 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.142643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.138266 restraints weight = 18050.727| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 0.22 r_work: 0.3233 rms_B_bonded: 0.57 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 1.14 restraints_weight: 0.2500 r_work: 0.2905 rms_B_bonded: 3.15 restraints_weight: 0.1250 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 34776 Z= 0.178 Angle : 0.561 5.622 46848 Z= 0.313 Chirality : 0.038 0.142 4920 Planarity : 0.003 0.021 6192 Dihedral : 4.479 22.274 4536 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.65 % Allowed : 7.54 % Favored : 91.80 % 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: 4.32 (0.13), residues: 4032 helix: 3.34 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.53 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP 6 93 HIS 0.004 0.001 HIS S 57 PHE 0.022 0.003 PHE Q 41 TYR 0.027 0.003 TYR r 39 ARG 0.002 0.001 ARG U 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22582.27 seconds wall clock time: 397 minutes 59.03 seconds (23879.03 seconds total)