Starting phenix.real_space_refine on Sat Mar 23 06:00:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpt_16785/03_2024/8cpt_16785_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpt_16785/03_2024/8cpt_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_16785/03_2024/8cpt_16785.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpt_16785/03_2024/8cpt_16785.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpt_16785/03_2024/8cpt_16785_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpt_16785/03_2024/8cpt_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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 18.22, 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: 15.70 Conformation dependent library (CDL) restraints added in 6.0 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: 5.80 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: 11.54 Time building geometry restraints manager: 16.61 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: 1.270 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: 0.040 Extract box with map and model: 7.650 Check model and map are aligned: 0.500 Set scattering table: 0.320 Process input model: 94.330 Find NCS groups from input model: 3.090 Set up NCS constraints: 0.470 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:12.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.700 ------------------------------------------------------------------------------- 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 : 4.352 Fit side-chains REVERT: 1 124 LYS cc_start: 0.8253 (mmtt) cc_final: 0.8042 (mmtt) REVERT: 2 124 LYS cc_start: 0.8258 (mmtt) cc_final: 0.8047 (mmtt) REVERT: 4 124 LYS cc_start: 0.8249 (mmtt) cc_final: 0.8040 (mmtt) REVERT: 6 124 LYS cc_start: 0.8246 (mmtt) cc_final: 0.8027 (mmtt) REVERT: A 124 LYS cc_start: 0.8242 (mmtt) cc_final: 0.8033 (mmtt) REVERT: B 124 LYS cc_start: 0.8246 (mmtt) cc_final: 0.8036 (mmtt) REVERT: E 124 LYS cc_start: 0.8243 (mmtt) cc_final: 0.8033 (mmtt) REVERT: F 124 LYS cc_start: 0.8243 (mmtt) cc_final: 0.8034 (mmtt) REVERT: G 124 LYS cc_start: 0.8244 (mmtt) cc_final: 0.8025 (mmtt) REVERT: H 124 LYS cc_start: 0.8246 (mmtt) cc_final: 0.8034 (mmtt) REVERT: I 124 LYS cc_start: 0.8257 (mmtt) cc_final: 0.8040 (mmtt) REVERT: K 124 LYS cc_start: 0.8247 (mmtt) cc_final: 0.8037 (mmtt) REVERT: M 70 MET cc_start: 0.9008 (mtp) cc_final: 0.8703 (mtp) REVERT: M 124 LYS cc_start: 0.8250 (mmtt) cc_final: 0.8031 (mmtt) REVERT: O 124 LYS cc_start: 0.8249 (mmtt) cc_final: 0.8039 (mmtt) REVERT: P 124 LYS cc_start: 0.8255 (mmtt) cc_final: 0.8043 (mmtt) REVERT: Q 124 LYS cc_start: 0.8241 (mmtt) cc_final: 0.8023 (mmtt) REVERT: S 124 LYS cc_start: 0.8254 (mmtt) cc_final: 0.8042 (mmtt) REVERT: U 124 LYS cc_start: 0.8253 (mmtt) cc_final: 0.8043 (mmtt) REVERT: W 124 LYS cc_start: 0.8254 (mmtt) cc_final: 0.8032 (mmtt) REVERT: X 124 LYS cc_start: 0.8250 (mmtt) cc_final: 0.8040 (mmtt) REVERT: Y 124 LYS cc_start: 0.8249 (mmtt) cc_final: 0.8039 (mmtt) REVERT: a 124 LYS cc_start: 0.8250 (mmtt) cc_final: 0.8030 (mmtt) REVERT: e 124 LYS cc_start: 0.8245 (mmtt) cc_final: 0.8038 (mmtt) REVERT: r 124 LYS cc_start: 0.8249 (mmtt) cc_final: 0.8038 (mmtt) outliers start: 18 outliers final: 18 residues processed: 712 average time/residue: 2.3894 time to fit residues: 1912.2889 Evaluate side-chains 574 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 556 time to evaluate : 4.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 117 LEU 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: 10.0000 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: 0.8222 moved from start: 0.0786 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= 0.127 Angle : 0.488 5.228 46848 Z= 0.270 Chirality : 0.037 0.142 4920 Planarity : 0.003 0.021 6192 Dihedral : 5.074 45.595 4572 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.49 % Allowed : 4.87 % Favored : 94.64 % 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: 4.84 (0.13), residues: 4032 helix: 3.61 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.08 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP S 93 HIS 0.004 0.001 HIS X 128 PHE 0.018 0.002 PHE M 41 TYR 0.021 0.002 TYR Q 39 ARG 0.002 0.000 ARG S 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 617 time to evaluate : 4.292 Fit side-chains REVERT: M 70 MET cc_start: 0.9035 (mtp) cc_final: 0.8727 (mtp) outliers start: 18 outliers final: 0 residues processed: 635 average time/residue: 2.2491 time to fit residues: 1617.0009 Evaluate side-chains 665 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 665 time to evaluate : 4.017 ------------------------------------------------------------------------------- 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: 9.9990 chunk 114 optimal weight: 0.9990 chunk 308 optimal weight: 0.7980 chunk 252 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 371 optimal weight: 6.9990 chunk 400 optimal weight: 2.9990 chunk 330 optimal weight: 9.9990 chunk 368 optimal weight: 20.0000 chunk 126 optimal weight: 9.9990 chunk 297 optimal weight: 20.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- 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: 0.8293 moved from start: 0.0730 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= 0.236 Angle : 0.642 5.973 46848 Z= 0.358 Chirality : 0.042 0.152 4920 Planarity : 0.004 0.030 6192 Dihedral : 4.468 20.905 4536 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.77 % Allowed : 4.11 % Favored : 94.12 % 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: 4.10 (0.13), residues: 4032 helix: 3.10 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.83 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 93 HIS 0.004 0.002 HIS O 128 PHE 0.027 0.004 PHE E 41 TYR 0.030 0.003 TYR Q 39 ARG 0.004 0.001 ARG S 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 764 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 699 time to evaluate : 3.873 Fit side-chains REVERT: M 70 MET cc_start: 0.9045 (mtp) cc_final: 0.8734 (mtp) outliers start: 65 outliers final: 45 residues processed: 720 average time/residue: 2.3047 time to fit residues: 1873.4788 Evaluate side-chains 667 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 622 time to evaluate : 4.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 14 GLN Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 2 residue 14 GLN Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 14 GLN Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 6 residue 14 GLN Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain G residue 14 GLN Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain I residue 14 GLN Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain M residue 14 GLN Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 14 GLN Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain Q residue 14 GLN Chi-restraints excluded: chain S residue 14 GLN Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 14 GLN Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain W residue 14 GLN Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain Y residue 14 GLN Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain a residue 14 GLN Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain e residue 14 GLN Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 14 GLN Chi-restraints excluded: chain r residue 117 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 4.9990 chunk 279 optimal weight: 4.9990 chunk 192 optimal weight: 5.9990 chunk 41 optimal weight: 0.3980 chunk 177 optimal weight: 0.6980 chunk 249 optimal weight: 20.0000 chunk 372 optimal weight: 0.6980 chunk 394 optimal weight: 9.9990 chunk 194 optimal weight: 3.9990 chunk 353 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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: 0.0940 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= 0.153 Angle : 0.529 5.490 46848 Z= 0.294 Chirality : 0.037 0.136 4920 Planarity : 0.003 0.021 6192 Dihedral : 4.401 21.740 4536 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.03 % Allowed : 5.07 % 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: 4.42 (0.13), residues: 4032 helix: 3.35 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.77 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP S 93 HIS 0.003 0.001 HIS O 128 PHE 0.020 0.003 PHE 1 41 TYR 0.023 0.002 TYR 2 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 665 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 627 time to evaluate : 4.689 Fit side-chains outliers start: 38 outliers final: 20 residues processed: 648 average time/residue: 2.2346 time to fit residues: 1641.2486 Evaluate side-chains 686 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 666 time to evaluate : 4.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 14 GLN Chi-restraints excluded: chain 6 residue 14 GLN Chi-restraints excluded: chain 6 residue 94 GLU Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain G residue 14 GLN Chi-restraints excluded: chain I residue 14 GLN Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain M residue 14 GLN Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 14 GLN Chi-restraints excluded: chain Q residue 14 GLN Chi-restraints excluded: chain S residue 14 GLN Chi-restraints excluded: chain W residue 14 GLN Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain a residue 14 GLN Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain e residue 14 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 1.9990 chunk 223 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 293 optimal weight: 4.9990 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: 7.9990 chunk 353 optimal weight: 20.0000 chunk 99 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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: 0.8284 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 34776 Z= 0.207 Angle : 0.598 5.839 46848 Z= 0.333 Chirality : 0.040 0.148 4920 Planarity : 0.004 0.024 6192 Dihedral : 4.477 21.795 4536 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.96 % Allowed : 5.28 % Favored : 92.76 % 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: 3.10 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.67 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP 6 93 HIS 0.004 0.001 HIS Q 57 PHE 0.024 0.003 PHE 4 41 TYR 0.027 0.003 TYR H 39 ARG 0.003 0.001 ARG S 43 *********************** 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 756 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 684 time to evaluate : 4.359 Fit side-chains outliers start: 72 outliers final: 49 residues processed: 708 average time/residue: 2.3165 time to fit residues: 1852.3170 Evaluate side-chains 654 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 605 time to evaluate : 4.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 14 GLN Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 2 residue 14 GLN Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 14 GLN Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 6 residue 14 GLN Chi-restraints excluded: chain 6 residue 94 GLU Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain G residue 14 GLN Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain I residue 14 GLN Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain M residue 14 GLN Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 14 GLN Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain Q residue 14 GLN Chi-restraints excluded: chain S residue 14 GLN Chi-restraints excluded: chain S residue 94 GLU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 14 GLN Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain W residue 14 GLN Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain Y residue 14 GLN Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain a residue 14 GLN Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain e residue 14 GLN Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 14 GLN Chi-restraints excluded: chain r residue 117 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 10.0000 chunk 355 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 231 optimal weight: 20.0000 chunk 97 optimal weight: 7.9990 chunk 394 optimal weight: 10.0000 chunk 327 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 32 optimal weight: 0.0770 chunk 130 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 109 ASN 1 136 HIS 2 109 ASN 4 109 ASN 6 109 ASN A 109 ASN A 136 HIS 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 X 136 HIS Y 109 ASN a 109 ASN e 109 ASN e 136 HIS r 109 ASN r 136 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 34776 Z= 0.117 Angle : 0.469 5.132 46848 Z= 0.256 Chirality : 0.035 0.132 4920 Planarity : 0.003 0.019 6192 Dihedral : 4.280 21.459 4536 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.14 % Allowed : 6.45 % Favored : 92.40 % 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: 4.76 (0.13), residues: 4032 helix: 3.62 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.72 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP 6 93 HIS 0.002 0.001 HIS H 128 PHE 0.015 0.002 PHE 1 41 TYR 0.020 0.002 TYR H 39 ARG 0.001 0.000 ARG O 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 708 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 666 time to evaluate : 4.511 Fit side-chains outliers start: 42 outliers final: 20 residues processed: 690 average time/residue: 2.2679 time to fit residues: 1788.1633 Evaluate side-chains 634 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 614 time to evaluate : 4.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 14 GLN Chi-restraints excluded: chain 6 residue 14 GLN Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain G residue 14 GLN Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain I residue 14 GLN Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain M residue 14 GLN Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 14 GLN Chi-restraints excluded: chain Q residue 14 GLN Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 14 GLN Chi-restraints excluded: chain W residue 14 GLN Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain a residue 14 GLN Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain e residue 14 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 224 optimal weight: 30.0000 chunk 288 optimal weight: 3.9990 chunk 223 optimal weight: 3.9990 chunk 332 optimal weight: 0.7980 chunk 220 optimal weight: 8.9990 chunk 393 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 239 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 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 B 60 HIS B 109 ASN B 136 HIS E 60 HIS E 109 ASN F 60 HIS F 109 ASN G 60 HIS G 109 ASN G 136 HIS 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 M 136 HIS O 60 HIS O 109 ASN 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 W 60 HIS W 109 ASN X 60 HIS X 109 ASN Y 60 HIS Y 109 ASN a 60 HIS a 109 ASN a 136 HIS e 60 HIS e 109 ASN r 60 HIS r 109 ASN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1018 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= 0.197 Angle : 0.578 5.656 46848 Z= 0.322 Chirality : 0.039 0.141 4920 Planarity : 0.004 0.023 6192 Dihedral : 4.458 22.228 4536 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.12 % Allowed : 6.43 % Favored : 92.46 % 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: 4.27 (0.13), residues: 4032 helix: 3.26 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.68 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP 6 93 HIS 0.004 0.001 HIS Q 57 PHE 0.022 0.003 PHE H 41 TYR 0.029 0.003 TYR H 39 ARG 0.003 0.001 ARG Y 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 726 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 685 time to evaluate : 4.313 Fit side-chains outliers start: 41 outliers final: 38 residues processed: 691 average time/residue: 2.2432 time to fit residues: 1759.3715 Evaluate side-chains 663 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 625 time to evaluate : 4.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 14 GLN Chi-restraints excluded: chain 1 residue 53 LYS Chi-restraints excluded: chain 2 residue 53 LYS Chi-restraints excluded: chain 4 residue 53 LYS Chi-restraints excluded: chain 6 residue 14 GLN Chi-restraints excluded: chain 6 residue 53 LYS Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain G residue 14 GLN Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain H residue 53 LYS Chi-restraints excluded: chain I residue 14 GLN Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain M residue 14 GLN Chi-restraints excluded: chain M residue 53 LYS Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 14 GLN Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain P residue 53 LYS Chi-restraints excluded: chain Q residue 14 GLN Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 14 GLN Chi-restraints excluded: chain U residue 53 LYS Chi-restraints excluded: chain W residue 14 GLN Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain X residue 53 LYS Chi-restraints excluded: chain a residue 14 GLN Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain e residue 14 GLN 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: 5.9990 chunk 234 optimal weight: 1.9990 chunk 118 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 250 optimal weight: 4.9990 chunk 267 optimal weight: 8.9990 chunk 194 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 309 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 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: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1009 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= 0.222 Angle : 0.608 5.924 46848 Z= 0.340 Chirality : 0.040 0.150 4920 Planarity : 0.004 0.027 6192 Dihedral : 4.510 22.066 4536 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.12 % Allowed : 5.56 % Favored : 92.32 % 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: 3.97 (0.13), residues: 4032 helix: 3.14 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.32 (0.26), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP Q 93 HIS 0.004 0.001 HIS 2 57 PHE 0.024 0.004 PHE E 41 TYR 0.028 0.003 TYR H 39 ARG 0.003 0.001 ARG 4 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 763 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 685 time to evaluate : 4.212 Fit side-chains outliers start: 78 outliers final: 78 residues processed: 691 average time/residue: 2.2449 time to fit residues: 1758.1421 Evaluate side-chains 703 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 625 time to evaluate : 4.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 14 GLN Chi-restraints excluded: chain 1 residue 53 LYS Chi-restraints excluded: chain 1 residue 94 GLU Chi-restraints excluded: chain 2 residue 14 GLN Chi-restraints excluded: chain 2 residue 53 LYS Chi-restraints excluded: chain 2 residue 94 GLU Chi-restraints excluded: chain 4 residue 14 GLN Chi-restraints excluded: chain 4 residue 53 LYS Chi-restraints excluded: chain 4 residue 94 GLU Chi-restraints excluded: chain 6 residue 14 GLN Chi-restraints excluded: chain 6 residue 53 LYS Chi-restraints excluded: chain 6 residue 94 GLU Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain G residue 14 GLN Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 53 LYS Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain I residue 14 GLN Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain I residue 94 GLU Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 94 GLU Chi-restraints excluded: chain M residue 14 GLN Chi-restraints excluded: chain M residue 53 LYS Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 14 GLN Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain P residue 53 LYS Chi-restraints excluded: chain P residue 94 GLU Chi-restraints excluded: chain Q residue 14 GLN Chi-restraints excluded: chain Q residue 53 LYS Chi-restraints excluded: chain Q residue 94 GLU Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 14 GLN Chi-restraints excluded: chain S residue 53 LYS Chi-restraints excluded: chain S residue 94 GLU Chi-restraints excluded: chain U residue 14 GLN Chi-restraints excluded: chain U residue 53 LYS Chi-restraints excluded: chain U residue 94 GLU Chi-restraints excluded: chain W residue 14 GLN Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain X residue 53 LYS Chi-restraints excluded: chain X residue 94 GLU Chi-restraints excluded: chain Y residue 14 GLN Chi-restraints excluded: chain Y residue 53 LYS Chi-restraints excluded: chain Y residue 94 GLU Chi-restraints excluded: chain a residue 14 GLN Chi-restraints excluded: chain a residue 53 LYS Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain e residue 14 GLN Chi-restraints excluded: chain e residue 53 LYS Chi-restraints excluded: chain e residue 94 GLU Chi-restraints excluded: chain r residue 14 GLN Chi-restraints excluded: chain r residue 53 LYS Chi-restraints excluded: chain r residue 94 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 4.9990 chunk 376 optimal weight: 0.9980 chunk 343 optimal weight: 9.9990 chunk 366 optimal weight: 4.9990 chunk 220 optimal weight: 8.9990 chunk 159 optimal weight: 0.7980 chunk 287 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 331 optimal weight: 6.9990 chunk 346 optimal weight: 0.7980 chunk 365 optimal weight: 0.4980 overall best weight: 1.4182 ------------------------------------------------------------------------------- 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 O 136 HIS 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: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1077 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= 0.126 Angle : 0.484 5.286 46848 Z= 0.268 Chirality : 0.036 0.137 4920 Planarity : 0.003 0.019 6192 Dihedral : 4.370 21.677 4536 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.34 % Allowed : 5.83 % Favored : 91.83 % 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: 4.57 (0.13), residues: 4032 helix: 3.48 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.71 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP 6 93 HIS 0.003 0.001 HIS U 136 PHE 0.017 0.002 PHE Q 41 TYR 0.022 0.002 TYR H 39 ARG 0.001 0.000 ARG G 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 753 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 667 time to evaluate : 3.965 Fit side-chains outliers start: 86 outliers final: 86 residues processed: 691 average time/residue: 2.2320 time to fit residues: 1747.8504 Evaluate side-chains 710 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 624 time to evaluate : 4.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 14 GLN Chi-restraints excluded: chain 1 residue 53 LYS Chi-restraints excluded: chain 1 residue 94 GLU Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 2 residue 53 LYS Chi-restraints excluded: chain 2 residue 94 GLU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 53 LYS Chi-restraints excluded: chain 4 residue 94 GLU Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 6 residue 14 GLN Chi-restraints excluded: chain 6 residue 53 LYS Chi-restraints excluded: chain 6 residue 94 GLU Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain G residue 14 GLN Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain H residue 53 LYS Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain I residue 14 GLN Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain I residue 94 GLU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 94 GLU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain M residue 14 GLN Chi-restraints excluded: chain M residue 53 LYS Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 14 GLN Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain P residue 53 LYS Chi-restraints excluded: chain P residue 94 GLU Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain Q residue 14 GLN Chi-restraints excluded: chain Q residue 53 LYS Chi-restraints excluded: chain Q residue 94 GLU Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 14 GLN Chi-restraints excluded: chain S residue 53 LYS Chi-restraints excluded: chain S residue 94 GLU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 53 LYS Chi-restraints excluded: chain U residue 94 GLU Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain W residue 14 GLN Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain X residue 53 LYS Chi-restraints excluded: chain X residue 94 GLU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain Y residue 53 LYS Chi-restraints excluded: chain Y residue 94 GLU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain a residue 14 GLN Chi-restraints excluded: chain a residue 53 LYS Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain e residue 14 GLN Chi-restraints excluded: chain e residue 53 LYS Chi-restraints excluded: chain e residue 94 GLU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 53 LYS Chi-restraints excluded: chain r residue 94 GLU Chi-restraints excluded: chain r residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 0.9990 chunk 387 optimal weight: 20.0000 chunk 236 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 269 optimal weight: 10.0000 chunk 406 optimal weight: 8.9990 chunk 374 optimal weight: 0.8980 chunk 323 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 250 optimal weight: 4.9990 chunk 198 optimal weight: 20.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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: 0.8273 moved from start: 0.1009 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= 0.191 Angle : 0.573 5.691 46848 Z= 0.320 Chirality : 0.039 0.143 4920 Planarity : 0.003 0.022 6192 Dihedral : 4.489 22.346 4536 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.12 % Allowed : 6.75 % Favored : 91.12 % 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: 4.19 (0.13), residues: 4032 helix: 3.24 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.51 (0.26), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP Q 93 HIS 0.004 0.001 HIS K 57 PHE 0.022 0.003 PHE 4 41 TYR 0.029 0.003 TYR H 39 ARG 0.002 0.001 ARG 1 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 744 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 666 time to evaluate : 4.668 Fit side-chains outliers start: 78 outliers final: 78 residues processed: 690 average time/residue: 2.2298 time to fit residues: 1744.4859 Evaluate side-chains 690 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 612 time to evaluate : 4.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 14 GLN Chi-restraints excluded: chain 1 residue 53 LYS Chi-restraints excluded: chain 1 residue 94 GLU Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 2 residue 53 LYS Chi-restraints excluded: chain 2 residue 94 GLU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 94 GLU Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 6 residue 14 GLN Chi-restraints excluded: chain 6 residue 53 LYS Chi-restraints excluded: chain 6 residue 94 GLU Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain G residue 14 GLN Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain I residue 14 GLN Chi-restraints excluded: chain I residue 94 GLU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 94 GLU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain M residue 14 GLN Chi-restraints excluded: chain M residue 53 LYS Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 14 GLN Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain P residue 53 LYS Chi-restraints excluded: chain P residue 94 GLU Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain Q residue 14 GLN Chi-restraints excluded: chain Q residue 53 LYS Chi-restraints excluded: chain Q residue 94 GLU Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 14 GLN Chi-restraints excluded: chain S residue 53 LYS Chi-restraints excluded: chain S residue 94 GLU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 94 GLU Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain W residue 14 GLN Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain X residue 53 LYS Chi-restraints excluded: chain X residue 94 GLU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain Y residue 53 LYS Chi-restraints excluded: chain Y residue 94 GLU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain a residue 14 GLN Chi-restraints excluded: chain a residue 53 LYS Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain e residue 14 GLN Chi-restraints excluded: chain e residue 53 LYS Chi-restraints excluded: chain e residue 94 GLU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 53 LYS Chi-restraints excluded: chain r residue 94 GLU Chi-restraints excluded: chain r residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 0.9990 chunk 344 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 298 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 324 optimal weight: 5.9990 chunk 135 optimal weight: 20.0000 chunk 332 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 = 0.3401 r_free = 0.3401 target = 0.142165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.137797 restraints weight = 18087.482| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 0.22 r_work: 0.3226 rms_B_bonded: 0.57 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 1.14 restraints_weight: 0.2500 r_work: 0.2896 rms_B_bonded: 3.21 restraints_weight: 0.1250 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 34776 Z= 0.191 Angle : 0.575 5.683 46848 Z= 0.321 Chirality : 0.039 0.146 4920 Planarity : 0.003 0.022 6192 Dihedral : 4.499 22.231 4536 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.31 % Allowed : 6.56 % Favored : 91.12 % 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: 4.13 (0.13), residues: 4032 helix: 3.20 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.51 (0.26), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP 6 93 HIS 0.004 0.001 HIS K 57 PHE 0.023 0.003 PHE 4 41 TYR 0.028 0.003 TYR H 39 ARG 0.002 0.001 ARG 6 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22503.35 seconds wall clock time: 395 minutes 5.66 seconds (23705.66 seconds total)