Starting phenix.real_space_refine on Fri Mar 6 01:13:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ofh_12874/03_2026/7ofh_12874.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ofh_12874/03_2026/7ofh_12874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ofh_12874/03_2026/7ofh_12874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ofh_12874/03_2026/7ofh_12874.map" model { file = "/net/cci-nas-00/data/ceres_data/7ofh_12874/03_2026/7ofh_12874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ofh_12874/03_2026/7ofh_12874.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.007 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: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 17235 2.51 5 N 4455 2.21 5 O 5400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27135 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1742 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1742 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1742 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1742 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1742 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1742 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1742 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1742 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1742 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1742 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1742 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1742 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1742 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1742 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1742 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'CPS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'CPS:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'CPS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'CPS:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'CPS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'CPS:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'CPS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'CPS:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'CPS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'CPS:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'CPS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'CPS:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'CPS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'CPS:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'CPS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'CPS:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'CPS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'CPS:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'CPS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'CPS:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'CPS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'CPS:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'CPS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'CPS:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'CPS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'CPS:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'CPS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'CPS:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'CPS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'CPS:plan-1': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 5.79, per 1000 atoms: 0.21 Number of scatterers: 27135 At special positions: 0 Unit cell: (144.72, 144.72, 113.632, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 5400 8.00 N 4455 7.00 C 17235 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 - 3.00 Amino acid : True - 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: 2.19 Conformation dependent library (CDL) restraints added in 1.1 seconds 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6510 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 60 sheets defined 8.2% alpha, 44.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 158 through 167 removed outlier: 3.531A pdb=" N ASN A 162 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Proline residue: A 164 - end of helix Processing helix chain 'B' and resid 125 through 133 Processing helix chain 'B' and resid 158 through 167 removed outlier: 3.532A pdb=" N ASN B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) Proline residue: B 164 - end of helix Processing helix chain 'C' and resid 125 through 133 Processing helix chain 'C' and resid 158 through 167 removed outlier: 3.533A pdb=" N ASN C 162 " --> pdb=" O ASP C 158 " (cutoff:3.500A) Proline residue: C 164 - end of helix Processing helix chain 'D' and resid 125 through 133 Processing helix chain 'D' and resid 158 through 167 removed outlier: 3.531A pdb=" N ASN D 162 " --> pdb=" O ASP D 158 " (cutoff:3.500A) Proline residue: D 164 - end of helix Processing helix chain 'E' and resid 125 through 133 Processing helix chain 'E' and resid 158 through 167 removed outlier: 3.534A pdb=" N ASN E 162 " --> pdb=" O ASP E 158 " (cutoff:3.500A) Proline residue: E 164 - end of helix Processing helix chain 'F' and resid 125 through 133 Processing helix chain 'F' and resid 158 through 167 removed outlier: 3.533A pdb=" N ASN F 162 " --> pdb=" O ASP F 158 " (cutoff:3.500A) Proline residue: F 164 - end of helix Processing helix chain 'G' and resid 125 through 133 Processing helix chain 'G' and resid 158 through 167 removed outlier: 3.531A pdb=" N ASN G 162 " --> pdb=" O ASP G 158 " (cutoff:3.500A) Proline residue: G 164 - end of helix Processing helix chain 'H' and resid 125 through 133 Processing helix chain 'H' and resid 158 through 167 removed outlier: 3.530A pdb=" N ASN H 162 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Proline residue: H 164 - end of helix Processing helix chain 'I' and resid 125 through 133 Processing helix chain 'I' and resid 158 through 167 removed outlier: 3.530A pdb=" N ASN I 162 " --> pdb=" O ASP I 158 " (cutoff:3.500A) Proline residue: I 164 - end of helix Processing helix chain 'J' and resid 125 through 133 Processing helix chain 'J' and resid 158 through 167 removed outlier: 3.531A pdb=" N ASN J 162 " --> pdb=" O ASP J 158 " (cutoff:3.500A) Proline residue: J 164 - end of helix Processing helix chain 'K' and resid 125 through 133 Processing helix chain 'K' and resid 158 through 167 removed outlier: 3.531A pdb=" N ASN K 162 " --> pdb=" O ASP K 158 " (cutoff:3.500A) Proline residue: K 164 - end of helix Processing helix chain 'L' and resid 125 through 133 Processing helix chain 'L' and resid 158 through 167 removed outlier: 3.528A pdb=" N ASN L 162 " --> pdb=" O ASP L 158 " (cutoff:3.500A) Proline residue: L 164 - end of helix Processing helix chain 'M' and resid 125 through 133 Processing helix chain 'M' and resid 158 through 167 removed outlier: 3.529A pdb=" N ASN M 162 " --> pdb=" O ASP M 158 " (cutoff:3.500A) Proline residue: M 164 - end of helix Processing helix chain 'N' and resid 125 through 133 Processing helix chain 'N' and resid 158 through 167 removed outlier: 3.531A pdb=" N ASN N 162 " --> pdb=" O ASP N 158 " (cutoff:3.500A) Proline residue: N 164 - end of helix Processing helix chain 'O' and resid 125 through 133 Processing helix chain 'O' and resid 158 through 167 removed outlier: 3.531A pdb=" N ASN O 162 " --> pdb=" O ASP O 158 " (cutoff:3.500A) Proline residue: O 164 - end of helix Processing sheet with id=A, first strand: chain 'A' and resid 109 through 115 Processing sheet with id=B, first strand: chain 'A' and resid 253 through 257 removed outlier: 7.013A pdb=" N VAL A 397 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU A 352 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ALA A 399 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR A 350 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N ILE A 401 " --> pdb=" O GLY A 348 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N GLY A 348 " --> pdb=" O ILE A 401 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'A' and resid 183 through 186 Processing sheet with id=D, first strand: chain 'A' and resid 261 through 272 Processing sheet with id=E, first strand: chain 'B' and resid 109 through 115 Processing sheet with id=F, first strand: chain 'B' and resid 253 through 257 removed outlier: 7.004A pdb=" N VAL B 397 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU B 352 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ALA B 399 " --> pdb=" O THR B 350 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR B 350 " --> pdb=" O ALA B 399 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N ILE B 401 " --> pdb=" O GLY B 348 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLY B 348 " --> pdb=" O ILE B 401 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'B' and resid 183 through 186 Processing sheet with id=H, first strand: chain 'B' and resid 261 through 272 Processing sheet with id=I, first strand: chain 'C' and resid 109 through 115 Processing sheet with id=J, first strand: chain 'C' and resid 253 through 257 removed outlier: 6.993A pdb=" N VAL C 397 " --> pdb=" O LEU C 352 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU C 352 " --> pdb=" O VAL C 397 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ALA C 399 " --> pdb=" O THR C 350 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR C 350 " --> pdb=" O ALA C 399 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N ILE C 401 " --> pdb=" O GLY C 348 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N GLY C 348 " --> pdb=" O ILE C 401 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'C' and resid 183 through 186 Processing sheet with id=L, first strand: chain 'C' and resid 261 through 272 Processing sheet with id=M, first strand: chain 'D' and resid 109 through 115 Processing sheet with id=N, first strand: chain 'D' and resid 253 through 257 removed outlier: 7.004A pdb=" N VAL D 397 " --> pdb=" O LEU D 352 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU D 352 " --> pdb=" O VAL D 397 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ALA D 399 " --> pdb=" O THR D 350 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR D 350 " --> pdb=" O ALA D 399 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N ILE D 401 " --> pdb=" O GLY D 348 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLY D 348 " --> pdb=" O ILE D 401 " (cutoff:3.500A) Processing sheet with id=O, first strand: chain 'D' and resid 183 through 186 Processing sheet with id=P, first strand: chain 'D' and resid 261 through 272 Processing sheet with id=Q, first strand: chain 'E' and resid 109 through 115 Processing sheet with id=R, first strand: chain 'E' and resid 253 through 257 removed outlier: 6.992A pdb=" N VAL E 397 " --> pdb=" O LEU E 352 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU E 352 " --> pdb=" O VAL E 397 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ALA E 399 " --> pdb=" O THR E 350 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR E 350 " --> pdb=" O ALA E 399 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N ILE E 401 " --> pdb=" O GLY E 348 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N GLY E 348 " --> pdb=" O ILE E 401 " (cutoff:3.500A) Processing sheet with id=S, first strand: chain 'E' and resid 183 through 186 Processing sheet with id=T, first strand: chain 'E' and resid 261 through 272 Processing sheet with id=U, first strand: chain 'F' and resid 109 through 115 Processing sheet with id=V, first strand: chain 'F' and resid 253 through 257 removed outlier: 6.987A pdb=" N VAL F 397 " --> pdb=" O LEU F 352 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU F 352 " --> pdb=" O VAL F 397 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ALA F 399 " --> pdb=" O THR F 350 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR F 350 " --> pdb=" O ALA F 399 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N ILE F 401 " --> pdb=" O GLY F 348 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N GLY F 348 " --> pdb=" O ILE F 401 " (cutoff:3.500A) Processing sheet with id=W, first strand: chain 'F' and resid 183 through 186 Processing sheet with id=X, first strand: chain 'F' and resid 261 through 272 Processing sheet with id=Y, first strand: chain 'G' and resid 109 through 115 Processing sheet with id=Z, first strand: chain 'G' and resid 253 through 257 removed outlier: 7.004A pdb=" N VAL G 397 " --> pdb=" O LEU G 352 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU G 352 " --> pdb=" O VAL G 397 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ALA G 399 " --> pdb=" O THR G 350 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR G 350 " --> pdb=" O ALA G 399 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N ILE G 401 " --> pdb=" O GLY G 348 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N GLY G 348 " --> pdb=" O ILE G 401 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'G' and resid 183 through 186 Processing sheet with id=AB, first strand: chain 'G' and resid 261 through 272 Processing sheet with id=AC, first strand: chain 'H' and resid 109 through 115 Processing sheet with id=AD, first strand: chain 'H' and resid 253 through 257 removed outlier: 7.006A pdb=" N VAL H 397 " --> pdb=" O LEU H 352 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU H 352 " --> pdb=" O VAL H 397 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ALA H 399 " --> pdb=" O THR H 350 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR H 350 " --> pdb=" O ALA H 399 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N ILE H 401 " --> pdb=" O GLY H 348 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N GLY H 348 " --> pdb=" O ILE H 401 " (cutoff:3.500A) Processing sheet with id=AE, first strand: chain 'H' and resid 183 through 186 Processing sheet with id=AF, first strand: chain 'H' and resid 261 through 272 Processing sheet with id=AG, first strand: chain 'I' and resid 109 through 115 Processing sheet with id=AH, first strand: chain 'I' and resid 253 through 257 removed outlier: 7.002A pdb=" N VAL I 397 " --> pdb=" O LEU I 352 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU I 352 " --> pdb=" O VAL I 397 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ALA I 399 " --> pdb=" O THR I 350 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR I 350 " --> pdb=" O ALA I 399 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N ILE I 401 " --> pdb=" O GLY I 348 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N GLY I 348 " --> pdb=" O ILE I 401 " (cutoff:3.500A) Processing sheet with id=AI, first strand: chain 'I' and resid 183 through 186 Processing sheet with id=AJ, first strand: chain 'I' and resid 261 through 272 Processing sheet with id=AK, first strand: chain 'J' and resid 109 through 115 Processing sheet with id=AL, first strand: chain 'J' and resid 253 through 257 removed outlier: 6.994A pdb=" N VAL J 397 " --> pdb=" O LEU J 352 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU J 352 " --> pdb=" O VAL J 397 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N ALA J 399 " --> pdb=" O THR J 350 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR J 350 " --> pdb=" O ALA J 399 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N ILE J 401 " --> pdb=" O GLY J 348 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N GLY J 348 " --> pdb=" O ILE J 401 " (cutoff:3.500A) Processing sheet with id=AM, first strand: chain 'J' and resid 183 through 186 Processing sheet with id=AN, first strand: chain 'J' and resid 261 through 272 Processing sheet with id=AO, first strand: chain 'K' and resid 109 through 115 Processing sheet with id=AP, first strand: chain 'K' and resid 253 through 257 removed outlier: 7.003A pdb=" N VAL K 397 " --> pdb=" O LEU K 352 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LEU K 352 " --> pdb=" O VAL K 397 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ALA K 399 " --> pdb=" O THR K 350 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR K 350 " --> pdb=" O ALA K 399 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N ILE K 401 " --> pdb=" O GLY K 348 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N GLY K 348 " --> pdb=" O ILE K 401 " (cutoff:3.500A) Processing sheet with id=AQ, first strand: chain 'K' and resid 183 through 186 Processing sheet with id=AR, first strand: chain 'K' and resid 261 through 272 Processing sheet with id=AS, first strand: chain 'L' and resid 109 through 115 Processing sheet with id=AT, first strand: chain 'L' and resid 253 through 257 removed outlier: 7.001A pdb=" N VAL L 397 " --> pdb=" O LEU L 352 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU L 352 " --> pdb=" O VAL L 397 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ALA L 399 " --> pdb=" O THR L 350 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR L 350 " --> pdb=" O ALA L 399 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N ILE L 401 " --> pdb=" O GLY L 348 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLY L 348 " --> pdb=" O ILE L 401 " (cutoff:3.500A) Processing sheet with id=AU, first strand: chain 'L' and resid 183 through 186 Processing sheet with id=AV, first strand: chain 'L' and resid 261 through 272 Processing sheet with id=AW, first strand: chain 'M' and resid 109 through 115 Processing sheet with id=AX, first strand: chain 'M' and resid 253 through 257 removed outlier: 7.005A pdb=" N VAL M 397 " --> pdb=" O LEU M 352 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU M 352 " --> pdb=" O VAL M 397 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ALA M 399 " --> pdb=" O THR M 350 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR M 350 " --> pdb=" O ALA M 399 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N ILE M 401 " --> pdb=" O GLY M 348 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N GLY M 348 " --> pdb=" O ILE M 401 " (cutoff:3.500A) Processing sheet with id=AY, first strand: chain 'M' and resid 183 through 186 Processing sheet with id=AZ, first strand: chain 'M' and resid 261 through 272 Processing sheet with id=BA, first strand: chain 'N' and resid 109 through 115 Processing sheet with id=BB, first strand: chain 'N' and resid 253 through 257 removed outlier: 7.004A pdb=" N VAL N 397 " --> pdb=" O LEU N 352 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU N 352 " --> pdb=" O VAL N 397 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ALA N 399 " --> pdb=" O THR N 350 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR N 350 " --> pdb=" O ALA N 399 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N ILE N 401 " --> pdb=" O GLY N 348 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N GLY N 348 " --> pdb=" O ILE N 401 " (cutoff:3.500A) Processing sheet with id=BC, first strand: chain 'N' and resid 183 through 186 Processing sheet with id=BD, first strand: chain 'N' and resid 261 through 272 Processing sheet with id=BE, first strand: chain 'O' and resid 109 through 115 Processing sheet with id=BF, first strand: chain 'O' and resid 253 through 257 removed outlier: 7.011A pdb=" N VAL O 397 " --> pdb=" O LEU O 352 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU O 352 " --> pdb=" O VAL O 397 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ALA O 399 " --> pdb=" O THR O 350 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR O 350 " --> pdb=" O ALA O 399 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ILE O 401 " --> pdb=" O GLY O 348 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N GLY O 348 " --> pdb=" O ILE O 401 " (cutoff:3.500A) Processing sheet with id=BG, first strand: chain 'O' and resid 183 through 186 Processing sheet with id=BH, first strand: chain 'O' and resid 261 through 272 1065 hydrogen bonds defined for protein. 3015 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: 4.68 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5066 1.32 - 1.44: 5815 1.44 - 1.56: 16359 1.56 - 1.68: 105 1.68 - 1.80: 75 Bond restraints: 27420 Sorted by residual: bond pdb=" CA SER B 154 " pdb=" CB SER B 154 " ideal model delta sigma weight residual 1.530 1.478 0.052 1.50e-02 4.44e+03 1.21e+01 bond pdb=" CA SER C 258 " pdb=" CB SER C 258 " ideal model delta sigma weight residual 1.530 1.476 0.055 1.57e-02 4.06e+03 1.21e+01 bond pdb=" CA SER L 154 " pdb=" CB SER L 154 " ideal model delta sigma weight residual 1.530 1.480 0.051 1.50e-02 4.44e+03 1.15e+01 bond pdb=" CA SER A 154 " pdb=" CB SER A 154 " ideal model delta sigma weight residual 1.530 1.480 0.050 1.50e-02 4.44e+03 1.11e+01 bond pdb=" CA SER D 301 " pdb=" CB SER D 301 " ideal model delta sigma weight residual 1.530 1.482 0.047 1.43e-02 4.89e+03 1.09e+01 ... (remaining 27415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 27333 1.59 - 3.19: 7915 3.19 - 4.78: 1765 4.78 - 6.37: 294 6.37 - 7.96: 88 Bond angle restraints: 37395 Sorted by residual: angle pdb=" N PRO D 156 " pdb=" CA PRO D 156 " pdb=" CB PRO D 156 " ideal model delta sigma weight residual 103.32 97.68 5.64 8.40e-01 1.42e+00 4.52e+01 angle pdb=" N PRO G 156 " pdb=" CA PRO G 156 " pdb=" CB PRO G 156 " ideal model delta sigma weight residual 103.32 97.82 5.50 8.40e-01 1.42e+00 4.29e+01 angle pdb=" N PRO A 156 " pdb=" CA PRO A 156 " pdb=" CB PRO A 156 " ideal model delta sigma weight residual 103.32 97.83 5.49 8.40e-01 1.42e+00 4.27e+01 angle pdb=" N PRO O 156 " pdb=" CA PRO O 156 " pdb=" CB PRO O 156 " ideal model delta sigma weight residual 103.32 97.85 5.47 8.40e-01 1.42e+00 4.23e+01 angle pdb=" N PRO F 156 " pdb=" CA PRO F 156 " pdb=" CB PRO F 156 " ideal model delta sigma weight residual 103.32 97.91 5.41 8.40e-01 1.42e+00 4.15e+01 ... (remaining 37390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.18: 16935 21.18 - 42.36: 1012 42.36 - 63.54: 353 63.54 - 84.73: 30 84.73 - 105.91: 15 Dihedral angle restraints: 18345 sinusoidal: 8430 harmonic: 9915 Sorted by residual: dihedral pdb=" C ARG M 293 " pdb=" N ARG M 293 " pdb=" CA ARG M 293 " pdb=" CB ARG M 293 " ideal model delta harmonic sigma weight residual -122.60 -110.31 -12.29 0 2.50e+00 1.60e-01 2.42e+01 dihedral pdb=" C ARG K 293 " pdb=" N ARG K 293 " pdb=" CA ARG K 293 " pdb=" CB ARG K 293 " ideal model delta harmonic sigma weight residual -122.60 -110.35 -12.25 0 2.50e+00 1.60e-01 2.40e+01 dihedral pdb=" C TYR F 359 " pdb=" N TYR F 359 " pdb=" CA TYR F 359 " pdb=" CB TYR F 359 " ideal model delta harmonic sigma weight residual -122.60 -110.44 -12.16 0 2.50e+00 1.60e-01 2.37e+01 ... (remaining 18342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2293 0.069 - 0.138: 1683 0.138 - 0.206: 756 0.206 - 0.275: 139 0.275 - 0.344: 49 Chirality restraints: 4920 Sorted by residual: chirality pdb=" C9 CPS K 501 " pdb=" C20 CPS K 501 " pdb=" C5 CPS K 501 " pdb=" C8 CPS K 501 " both_signs ideal model delta sigma weight residual False 2.63 2.29 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" C9 CPS J 501 " pdb=" C20 CPS J 501 " pdb=" C5 CPS J 501 " pdb=" C8 CPS J 501 " both_signs ideal model delta sigma weight residual False 2.63 2.29 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" C9 CPS H 501 " pdb=" C20 CPS H 501 " pdb=" C5 CPS H 501 " pdb=" C8 CPS H 501 " both_signs ideal model delta sigma weight residual False 2.63 2.29 0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 4917 not shown) Planarity restraints: 4530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C23 CPS I 501 " -0.008 2.00e-02 2.50e+03 4.01e-02 2.01e+01 pdb=" C24 CPS I 501 " -0.012 2.00e-02 2.50e+03 pdb=" C25 CPS I 501 " 0.046 2.00e-02 2.50e+03 pdb=" N1 CPS I 501 " -0.065 2.00e-02 2.50e+03 pdb=" O1 CPS I 501 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 CPS M 501 " -0.008 2.00e-02 2.50e+03 3.96e-02 1.96e+01 pdb=" C24 CPS M 501 " -0.011 2.00e-02 2.50e+03 pdb=" C25 CPS M 501 " 0.046 2.00e-02 2.50e+03 pdb=" N1 CPS M 501 " -0.065 2.00e-02 2.50e+03 pdb=" O1 CPS M 501 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 CPS G 501 " 0.008 2.00e-02 2.50e+03 3.94e-02 1.94e+01 pdb=" C24 CPS G 501 " 0.011 2.00e-02 2.50e+03 pdb=" C25 CPS G 501 " -0.045 2.00e-02 2.50e+03 pdb=" N1 CPS G 501 " 0.064 2.00e-02 2.50e+03 pdb=" O1 CPS G 501 " -0.038 2.00e-02 2.50e+03 ... (remaining 4527 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4565 2.77 - 3.30: 23096 3.30 - 3.83: 41167 3.83 - 4.37: 52267 4.37 - 4.90: 90832 Nonbonded interactions: 211927 Sorted by model distance: nonbonded pdb=" O SER E 385 " pdb=" OD1 ASP E 386 " model vdw 2.236 3.040 nonbonded pdb=" O SER M 385 " pdb=" OD1 ASP M 386 " model vdw 2.236 3.040 nonbonded pdb=" O SER B 385 " pdb=" OD1 ASP B 386 " model vdw 2.237 3.040 nonbonded pdb=" O SER I 385 " pdb=" OD1 ASP I 386 " model vdw 2.238 3.040 nonbonded pdb=" O SER A 385 " pdb=" OD1 ASP A 386 " model vdw 2.238 3.040 ... (remaining 211922 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 108 through 403 or (resid 501 through 502 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name \ C22 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 \ or name O2 or name O3 or name O4 )))) selection = (chain 'B' and (resid 108 through 403 or (resid 501 through 502 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name \ C22 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 \ or name O2 or name O3 or name O4 )))) selection = (chain 'C' and (resid 108 through 403 or (resid 501 through 502 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name \ C22 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 \ or name O2 or name O3 or name O4 )))) selection = (chain 'D' and (resid 108 through 403 or (resid 501 through 502 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name \ C22 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 \ or name O2 or name O3 or name O4 )))) selection = (chain 'E' and (resid 108 through 403 or (resid 501 through 502 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name \ C22 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 \ or name O2 or name O3 or name O4 )))) selection = (chain 'F' and (resid 108 through 403 or (resid 501 through 502 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name \ C22 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 \ or name O2 or name O3 or name O4 )))) selection = (chain 'G' and (resid 108 through 403 or (resid 501 through 502 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name \ C22 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 \ or name O2 or name O3 or name O4 )))) selection = (chain 'H' and (resid 108 through 403 or (resid 501 through 502 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name \ C22 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 \ or name O2 or name O3 or name O4 )))) selection = (chain 'I' and (resid 108 through 403 or (resid 501 through 502 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name \ C22 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 \ or name O2 or name O3 or name O4 )))) selection = (chain 'J' and (resid 108 through 403 or (resid 501 through 502 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name \ C22 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 \ or name O2 or name O3 or name O4 )))) selection = (chain 'K' and (resid 108 through 403 or (resid 501 through 502 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name \ C22 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 \ or name O2 or name O3 or name O4 )))) selection = (chain 'L' and (resid 108 through 403 or (resid 501 through 502 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name \ C22 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 \ or name O2 or name O3 or name O4 )))) selection = (chain 'M' and (resid 108 through 403 or (resid 501 through 502 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name \ C22 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 \ or name O2 or name O3 or name O4 )))) selection = (chain 'N' and (resid 108 through 403 or (resid 501 through 502 and (name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name \ C22 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 \ or name O2 or name O3 or name O4 )))) selection = (chain 'O' and (resid 108 through 501 or (resid 502 and (name C1 or name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 \ or name C18 or name C19 or name C2 or name C20 or name C21 or name C22 or name \ C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name O2 \ or name O3 or name O4 )))) } 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: 1.070 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: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 23.230 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.050 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:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 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 : 0.010 0.063 27420 Z= 0.679 Angle : 1.597 7.963 37395 Z= 1.016 Chirality : 0.106 0.344 4920 Planarity : 0.007 0.040 4530 Dihedral : 15.397 105.907 11835 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.27 % Favored : 87.61 % Rotamer: Outliers : 3.90 % Allowed : 11.48 % Favored : 84.62 % Cbeta Deviations : 0.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.46 (0.12), residues: 3285 helix: -3.73 (0.17), residues: 270 sheet: -2.61 (0.09), residues: 2355 loop : -2.55 (0.18), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 293 TYR 0.048 0.014 TYR F 394 PHE 0.021 0.006 PHE N 166 HIS 0.004 0.002 HIS E 245 Details of bonding type rmsd covalent geometry : bond 0.01044 (27420) covalent geometry : angle 1.59675 (37395) hydrogen bonds : bond 0.21186 ( 1065) hydrogen bonds : angle 9.01562 ( 3015) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1026 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 906 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.9102 (mttt) cc_final: 0.8797 (mtmt) REVERT: A 122 LYS cc_start: 0.8874 (tttt) cc_final: 0.8660 (ptpp) REVERT: A 126 ARG cc_start: 0.8776 (mtt180) cc_final: 0.8493 (mmt180) REVERT: A 153 VAL cc_start: 0.8811 (OUTLIER) cc_final: 0.8522 (t) REVERT: A 156 PRO cc_start: 0.8806 (OUTLIER) cc_final: 0.8502 (Cg_exo) REVERT: A 180 GLU cc_start: 0.8324 (tt0) cc_final: 0.8079 (mt-10) REVERT: A 261 LYS cc_start: 0.9046 (mttp) cc_final: 0.8704 (mmmt) REVERT: B 115 LYS cc_start: 0.9021 (mttt) cc_final: 0.8716 (mtmm) REVERT: B 122 LYS cc_start: 0.8744 (tttt) cc_final: 0.8519 (ptpp) REVERT: B 153 VAL cc_start: 0.8784 (OUTLIER) cc_final: 0.8491 (t) REVERT: B 156 PRO cc_start: 0.8900 (OUTLIER) cc_final: 0.8622 (Cg_exo) REVERT: B 180 GLU cc_start: 0.8254 (tt0) cc_final: 0.7901 (mt-10) REVERT: B 346 ARG cc_start: 0.8290 (mtt180) cc_final: 0.8071 (ttm110) REVERT: C 115 LYS cc_start: 0.9086 (mttt) cc_final: 0.8785 (mtmm) REVERT: C 156 PRO cc_start: 0.8843 (OUTLIER) cc_final: 0.8535 (Cg_exo) REVERT: C 180 GLU cc_start: 0.8333 (tt0) cc_final: 0.8124 (mt-10) REVERT: C 360 LYS cc_start: 0.7863 (tttt) cc_final: 0.7644 (mtpp) REVERT: C 364 GLN cc_start: 0.7516 (tt0) cc_final: 0.6860 (tm-30) REVERT: C 390 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7834 (pt0) REVERT: D 126 ARG cc_start: 0.8557 (mtt180) cc_final: 0.8342 (mmt180) REVERT: D 133 LYS cc_start: 0.7553 (tttt) cc_final: 0.7278 (ttmm) REVERT: D 153 VAL cc_start: 0.8781 (OUTLIER) cc_final: 0.8563 (t) REVERT: D 180 GLU cc_start: 0.8172 (tt0) cc_final: 0.7774 (mt-10) REVERT: D 248 ILE cc_start: 0.9004 (mm) cc_final: 0.8700 (mm) REVERT: D 261 LYS cc_start: 0.9174 (mttp) cc_final: 0.8874 (mmmt) REVERT: D 400 THR cc_start: 0.8852 (m) cc_final: 0.8384 (p) REVERT: E 115 LYS cc_start: 0.9137 (mttt) cc_final: 0.8850 (mtmt) REVERT: E 133 LYS cc_start: 0.7460 (tttt) cc_final: 0.6865 (tppt) REVERT: E 261 LYS cc_start: 0.9213 (mttp) cc_final: 0.8972 (mmmt) REVERT: F 122 LYS cc_start: 0.8776 (tttt) cc_final: 0.8524 (ptpp) REVERT: F 180 GLU cc_start: 0.8150 (tt0) cc_final: 0.7891 (mt-10) REVERT: F 245 HIS cc_start: 0.8290 (t70) cc_final: 0.7988 (t70) REVERT: F 261 LYS cc_start: 0.9127 (mttp) cc_final: 0.8873 (mmmt) REVERT: F 400 THR cc_start: 0.8911 (m) cc_final: 0.8592 (p) REVERT: G 126 ARG cc_start: 0.8690 (mtt180) cc_final: 0.8405 (mmt180) REVERT: G 180 GLU cc_start: 0.8225 (tt0) cc_final: 0.7845 (mt-10) REVERT: G 346 ARG cc_start: 0.8494 (mtt180) cc_final: 0.8286 (ttm110) REVERT: G 400 THR cc_start: 0.8821 (m) cc_final: 0.8523 (p) REVERT: H 122 LYS cc_start: 0.8689 (tttt) cc_final: 0.8463 (ptpp) REVERT: H 133 LYS cc_start: 0.7775 (tttt) cc_final: 0.7464 (ttmm) REVERT: H 161 ASP cc_start: 0.8155 (m-30) cc_final: 0.7817 (m-30) REVERT: H 180 GLU cc_start: 0.8099 (tt0) cc_final: 0.7726 (mt-10) REVERT: H 300 MET cc_start: 0.9190 (ttp) cc_final: 0.8964 (ttm) REVERT: H 337 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8425 (mtm110) REVERT: H 390 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7779 (pt0) REVERT: H 400 THR cc_start: 0.8762 (m) cc_final: 0.8450 (p) REVERT: I 115 LYS cc_start: 0.8943 (mttt) cc_final: 0.8688 (mtmm) REVERT: I 122 LYS cc_start: 0.8795 (tttt) cc_final: 0.8552 (ptpp) REVERT: I 133 LYS cc_start: 0.7622 (tttt) cc_final: 0.7039 (tppt) REVERT: I 180 GLU cc_start: 0.8194 (tt0) cc_final: 0.7827 (mt-10) REVERT: I 400 THR cc_start: 0.8751 (m) cc_final: 0.8437 (p) REVERT: J 133 LYS cc_start: 0.7547 (tttt) cc_final: 0.7316 (ttmm) REVERT: J 141 ASN cc_start: 0.8503 (m-40) cc_final: 0.8125 (m-40) REVERT: J 180 GLU cc_start: 0.8272 (tt0) cc_final: 0.7801 (mt-10) REVERT: J 300 MET cc_start: 0.9174 (ttp) cc_final: 0.8891 (ttm) REVERT: J 337 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8426 (mtm110) REVERT: J 390 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7864 (pt0) REVERT: J 400 THR cc_start: 0.8765 (m) cc_final: 0.8428 (p) REVERT: K 115 LYS cc_start: 0.9139 (mttt) cc_final: 0.8849 (mtmm) REVERT: K 180 GLU cc_start: 0.8246 (tt0) cc_final: 0.7809 (mt-10) REVERT: K 346 ARG cc_start: 0.8390 (mtt180) cc_final: 0.8129 (ttm110) REVERT: K 400 THR cc_start: 0.8742 (m) cc_final: 0.8223 (p) REVERT: L 180 GLU cc_start: 0.8246 (tt0) cc_final: 0.7947 (mt-10) REVERT: L 238 ARG cc_start: 0.7497 (mtt90) cc_final: 0.7293 (mpt180) REVERT: L 346 ARG cc_start: 0.8289 (mtt180) cc_final: 0.8015 (ttm110) REVERT: M 115 LYS cc_start: 0.9138 (mttt) cc_final: 0.8872 (mtmm) REVERT: M 120 ARG cc_start: 0.8996 (mtm180) cc_final: 0.8687 (mtm-85) REVERT: M 141 ASN cc_start: 0.8625 (m-40) cc_final: 0.8424 (m-40) REVERT: M 156 PRO cc_start: 0.8793 (OUTLIER) cc_final: 0.8505 (Cg_exo) REVERT: M 238 ARG cc_start: 0.7382 (mtt90) cc_final: 0.7110 (mpt180) REVERT: M 248 ILE cc_start: 0.9025 (mm) cc_final: 0.8767 (mm) REVERT: M 300 MET cc_start: 0.9232 (ttp) cc_final: 0.8785 (ttm) REVERT: M 390 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7643 (pt0) REVERT: M 400 THR cc_start: 0.8572 (m) cc_final: 0.8001 (p) REVERT: N 115 LYS cc_start: 0.9101 (mttt) cc_final: 0.8900 (mtmt) REVERT: N 122 LYS cc_start: 0.8912 (tttt) cc_final: 0.8705 (ptpp) REVERT: N 126 ARG cc_start: 0.8651 (mtt180) cc_final: 0.8444 (mmt180) REVERT: N 180 GLU cc_start: 0.8223 (tt0) cc_final: 0.7938 (mt-10) REVERT: N 242 THR cc_start: 0.7946 (m) cc_final: 0.7588 (p) REVERT: N 300 MET cc_start: 0.9209 (ttp) cc_final: 0.8881 (ttm) REVERT: N 400 THR cc_start: 0.8811 (m) cc_final: 0.8231 (p) REVERT: O 122 LYS cc_start: 0.8860 (tttt) cc_final: 0.8607 (ptpp) REVERT: O 133 LYS cc_start: 0.7650 (tttt) cc_final: 0.7399 (ttmm) REVERT: O 180 GLU cc_start: 0.8323 (tt0) cc_final: 0.7846 (mt-10) REVERT: O 261 LYS cc_start: 0.8967 (mttp) cc_final: 0.8734 (mmtt) REVERT: O 300 MET cc_start: 0.9232 (ttp) cc_final: 0.8966 (ttp) REVERT: O 389 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7456 (tm-30) outliers start: 120 outliers final: 19 residues processed: 987 average time/residue: 0.5906 time to fit residues: 680.5581 Evaluate side-chains 627 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 599 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 156 PRO Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 156 PRO Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 156 PRO Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 156 PRO Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain E residue 156 PRO Chi-restraints excluded: chain F residue 156 PRO Chi-restraints excluded: chain F residue 365 ASP Chi-restraints excluded: chain G residue 156 PRO Chi-restraints excluded: chain H residue 156 PRO Chi-restraints excluded: chain H residue 332 VAL Chi-restraints excluded: chain H residue 337 ARG Chi-restraints excluded: chain H residue 365 ASP Chi-restraints excluded: chain I residue 156 PRO Chi-restraints excluded: chain J residue 156 PRO Chi-restraints excluded: chain J residue 337 ARG Chi-restraints excluded: chain K residue 156 PRO Chi-restraints excluded: chain L residue 156 PRO Chi-restraints excluded: chain M residue 156 PRO Chi-restraints excluded: chain N residue 156 PRO Chi-restraints excluded: chain N residue 332 VAL Chi-restraints excluded: chain N residue 388 ASN Chi-restraints excluded: chain O residue 156 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 361 ASN B 328 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN C 112 GLN C 187 GLN C 336 GLN C 361 ASN D 112 GLN D 328 GLN D 336 GLN D 361 ASN E 187 GLN E 328 GLN ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 GLN F 336 GLN F 361 ASN ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 361 ASN H 112 GLN H 187 GLN ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 349 GLN H 361 ASN I 328 GLN I 361 ASN J 328 GLN J 336 GLN J 361 ASN K 187 GLN K 336 GLN K 349 GLN L 112 GLN L 187 GLN L 328 GLN ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 349 GLN M 349 GLN M 361 ASN N 187 GLN ** N 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 361 ASN O 112 GLN O 328 GLN O 336 GLN O 361 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.150321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.120342 restraints weight = 27704.744| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.46 r_work: 0.3186 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 27420 Z= 0.138 Angle : 0.605 7.561 37395 Z= 0.309 Chirality : 0.048 0.239 4920 Planarity : 0.005 0.046 4530 Dihedral : 9.363 110.039 5858 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.74 % Allowed : 17.01 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.14), residues: 3285 helix: -1.86 (0.25), residues: 345 sheet: -1.67 (0.10), residues: 2235 loop : -1.08 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 126 TYR 0.016 0.002 TYR N 359 PHE 0.021 0.002 PHE H 194 HIS 0.001 0.001 HIS L 245 Details of bonding type rmsd covalent geometry : bond 0.00294 (27420) covalent geometry : angle 0.60461 (37395) hydrogen bonds : bond 0.03067 ( 1065) hydrogen bonds : angle 6.04164 ( 3015) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 561 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8876 (mttt) cc_final: 0.8595 (mtmt) REVERT: A 261 LYS cc_start: 0.9038 (mttp) cc_final: 0.8676 (mmmt) REVERT: A 388 ASN cc_start: 0.8212 (t0) cc_final: 0.7938 (t0) REVERT: B 364 GLN cc_start: 0.7120 (tt0) cc_final: 0.6671 (tm-30) REVERT: C 115 LYS cc_start: 0.8836 (mttt) cc_final: 0.8552 (mtmm) REVERT: D 261 LYS cc_start: 0.8895 (mttp) cc_final: 0.8570 (mmmt) REVERT: D 364 GLN cc_start: 0.7049 (tt0) cc_final: 0.6669 (tm-30) REVERT: E 115 LYS cc_start: 0.8830 (mttt) cc_final: 0.8599 (mtmt) REVERT: E 133 LYS cc_start: 0.7186 (tttt) cc_final: 0.6707 (tppt) REVERT: E 261 LYS cc_start: 0.9033 (mttp) cc_final: 0.8754 (mmmt) REVERT: E 392 THR cc_start: 0.8926 (t) cc_final: 0.8640 (m) REVERT: F 261 LYS cc_start: 0.8896 (mttp) cc_final: 0.8626 (mmmt) REVERT: F 307 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7991 (mmt) REVERT: F 364 GLN cc_start: 0.7268 (tt0) cc_final: 0.6611 (tm-30) REVERT: F 400 THR cc_start: 0.8856 (m) cc_final: 0.8391 (p) REVERT: G 261 LYS cc_start: 0.9016 (mmtm) cc_final: 0.8803 (mmtt) REVERT: G 321 ASP cc_start: 0.8590 (m-30) cc_final: 0.8370 (m-30) REVERT: G 346 ARG cc_start: 0.7768 (mtt180) cc_final: 0.7530 (ttm110) REVERT: H 133 LYS cc_start: 0.7509 (tttt) cc_final: 0.7223 (ttmm) REVERT: H 364 GLN cc_start: 0.7372 (tt0) cc_final: 0.6820 (tm-30) REVERT: H 389 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7363 (mt-10) REVERT: I 115 LYS cc_start: 0.8605 (mttt) cc_final: 0.8398 (mtmm) REVERT: I 126 ARG cc_start: 0.8148 (mmm-85) cc_final: 0.7885 (mmm-85) REVERT: I 133 LYS cc_start: 0.7301 (tttt) cc_final: 0.6800 (tppt) REVERT: I 261 LYS cc_start: 0.9057 (mmtm) cc_final: 0.8815 (mmtp) REVERT: I 389 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7447 (mt-10) REVERT: J 133 LYS cc_start: 0.7353 (tttt) cc_final: 0.6692 (tppt) REVERT: J 300 MET cc_start: 0.9344 (ttp) cc_final: 0.9062 (ttm) REVERT: K 115 LYS cc_start: 0.8766 (mttt) cc_final: 0.8463 (mtmm) REVERT: L 238 ARG cc_start: 0.6834 (mtt90) cc_final: 0.6492 (mpt180) REVERT: L 307 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7581 (mtt) REVERT: L 344 ASN cc_start: 0.8905 (OUTLIER) cc_final: 0.8638 (t0) REVERT: L 392 THR cc_start: 0.9042 (t) cc_final: 0.8838 (m) REVERT: M 115 LYS cc_start: 0.8802 (mttt) cc_final: 0.8507 (mtmm) REVERT: M 238 ARG cc_start: 0.6770 (mtt90) cc_final: 0.6524 (mpt180) REVERT: M 253 ARG cc_start: 0.8585 (mtp180) cc_final: 0.8210 (mtt90) REVERT: M 300 MET cc_start: 0.9316 (ttp) cc_final: 0.8776 (ttm) REVERT: M 360 LYS cc_start: 0.8003 (tttt) cc_final: 0.7787 (mptp) REVERT: N 300 MET cc_start: 0.9372 (ttp) cc_final: 0.9075 (ttm) REVERT: N 328 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8063 (tt0) REVERT: N 388 ASN cc_start: 0.8318 (OUTLIER) cc_final: 0.8009 (t0) REVERT: O 133 LYS cc_start: 0.7354 (tttt) cc_final: 0.6874 (tppt) REVERT: O 161 ASP cc_start: 0.7457 (m-30) cc_final: 0.7239 (m-30) REVERT: O 261 LYS cc_start: 0.8998 (mttp) cc_final: 0.8738 (mmtt) REVERT: O 292 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7721 (pp20) REVERT: O 389 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7383 (mt-10) outliers start: 115 outliers final: 38 residues processed: 638 average time/residue: 0.7192 time to fit residues: 521.9694 Evaluate side-chains 515 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 472 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 307 MET Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 307 MET Chi-restraints excluded: chain F residue 386 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 325 SER Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 301 SER Chi-restraints excluded: chain I residue 148 SER Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 386 ASP Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain J residue 171 ASP Chi-restraints excluded: chain J residue 325 SER Chi-restraints excluded: chain K residue 148 SER Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 148 SER Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 344 ASN Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 148 SER Chi-restraints excluded: chain M residue 256 THR Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 325 SER Chi-restraints excluded: chain M residue 386 ASP Chi-restraints excluded: chain N residue 148 SER Chi-restraints excluded: chain N residue 328 GLN Chi-restraints excluded: chain N residue 388 ASN Chi-restraints excluded: chain O residue 110 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 249 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 267 optimal weight: 2.9990 chunk 250 optimal weight: 8.9990 chunk 152 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 157 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 328 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN D 336 GLN E 328 GLN ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 GLN ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 328 GLN ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 328 GLN ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 328 GLN ** I 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 328 GLN J 336 GLN K 141 ASN K 328 GLN ** K 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 141 ASN M 328 GLN N 187 GLN ** N 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 336 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.144508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.113637 restraints weight = 27949.251| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.52 r_work: 0.3089 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 27420 Z= 0.259 Angle : 0.670 8.004 37395 Z= 0.341 Chirality : 0.050 0.217 4920 Planarity : 0.006 0.043 4530 Dihedral : 8.860 103.198 5792 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.65 % Allowed : 19.09 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.14), residues: 3285 helix: -1.00 (0.34), residues: 255 sheet: -1.08 (0.11), residues: 2175 loop : -0.47 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG N 337 TYR 0.020 0.004 TYR I 359 PHE 0.017 0.002 PHE H 194 HIS 0.004 0.001 HIS D 245 Details of bonding type rmsd covalent geometry : bond 0.00592 (27420) covalent geometry : angle 0.67025 (37395) hydrogen bonds : bond 0.03412 ( 1065) hydrogen bonds : angle 5.86337 ( 3015) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 449 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 LYS cc_start: 0.8966 (mttp) cc_final: 0.8533 (mmmt) REVERT: A 307 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7919 (mmt) REVERT: A 388 ASN cc_start: 0.8246 (t0) cc_final: 0.7977 (t0) REVERT: B 133 LYS cc_start: 0.7293 (tttt) cc_final: 0.6967 (tttp) REVERT: B 253 ARG cc_start: 0.8739 (mtp180) cc_final: 0.8217 (mtp85) REVERT: B 364 GLN cc_start: 0.7230 (tt0) cc_final: 0.6706 (tm-30) REVERT: C 115 LYS cc_start: 0.8851 (mttt) cc_final: 0.8510 (mtmm) REVERT: C 360 LYS cc_start: 0.7960 (tttt) cc_final: 0.7692 (mtpt) REVERT: C 364 GLN cc_start: 0.7091 (tt0) cc_final: 0.6600 (tm-30) REVERT: D 248 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8834 (mm) REVERT: D 364 GLN cc_start: 0.7045 (tt0) cc_final: 0.6580 (tm-30) REVERT: E 115 LYS cc_start: 0.8881 (mttt) cc_final: 0.8655 (mttt) REVERT: E 133 LYS cc_start: 0.7387 (tttt) cc_final: 0.6839 (tppt) REVERT: E 253 ARG cc_start: 0.8613 (mtm180) cc_final: 0.8281 (mtt90) REVERT: E 261 LYS cc_start: 0.8974 (mttp) cc_final: 0.8632 (mmmt) REVERT: E 319 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8687 (mtpt) REVERT: G 248 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8813 (mm) REVERT: G 346 ARG cc_start: 0.7955 (mtt180) cc_final: 0.7582 (ttm110) REVERT: G 360 LYS cc_start: 0.8012 (mtpt) cc_final: 0.7418 (mptp) REVERT: G 392 THR cc_start: 0.9175 (t) cc_final: 0.8899 (m) REVERT: H 133 LYS cc_start: 0.7404 (tttt) cc_final: 0.7182 (ttmm) REVERT: H 161 ASP cc_start: 0.7604 (m-30) cc_final: 0.7399 (m-30) REVERT: H 307 MET cc_start: 0.8157 (mmt) cc_final: 0.7911 (mmt) REVERT: H 364 GLN cc_start: 0.7414 (tt0) cc_final: 0.6722 (tm-30) REVERT: H 389 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7472 (mt-10) REVERT: I 115 LYS cc_start: 0.8745 (mttt) cc_final: 0.8443 (mtmm) REVERT: I 261 LYS cc_start: 0.9107 (mmtm) cc_final: 0.8788 (mmtp) REVERT: I 364 GLN cc_start: 0.7164 (tt0) cc_final: 0.6587 (tm-30) REVERT: I 389 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7558 (mt-10) REVERT: J 133 LYS cc_start: 0.7343 (tttt) cc_final: 0.6662 (tppt) REVERT: J 261 LYS cc_start: 0.8980 (mmmt) cc_final: 0.8657 (mmmt) REVERT: J 300 MET cc_start: 0.9266 (ttp) cc_final: 0.9005 (ttm) REVERT: K 115 LYS cc_start: 0.8772 (mttt) cc_final: 0.8408 (mtmm) REVERT: K 245 HIS cc_start: 0.7722 (t70) cc_final: 0.7465 (t70) REVERT: K 261 LYS cc_start: 0.8869 (mmmt) cc_final: 0.8663 (mmtt) REVERT: L 248 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8699 (mm) REVERT: L 344 ASN cc_start: 0.8906 (OUTLIER) cc_final: 0.8701 (t0) REVERT: M 115 LYS cc_start: 0.8713 (mttt) cc_final: 0.8411 (mttp) REVERT: M 253 ARG cc_start: 0.8659 (mtp180) cc_final: 0.8175 (mtt90) REVERT: M 300 MET cc_start: 0.9328 (ttp) cc_final: 0.8842 (ttm) REVERT: N 300 MET cc_start: 0.9333 (ttp) cc_final: 0.9101 (ttm) REVERT: N 307 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.6980 (mtm) REVERT: N 364 GLN cc_start: 0.7138 (tt0) cc_final: 0.6707 (tm-30) REVERT: N 388 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8168 (t0) REVERT: O 133 LYS cc_start: 0.7412 (tttt) cc_final: 0.6869 (tppt) REVERT: O 261 LYS cc_start: 0.8962 (mttp) cc_final: 0.8660 (mmtt) REVERT: O 292 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7785 (pp20) REVERT: O 358 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.7929 (m-30) REVERT: O 387 SER cc_start: 0.8016 (t) cc_final: 0.7782 (m) outliers start: 143 outliers final: 70 residues processed: 547 average time/residue: 0.7922 time to fit residues: 487.7097 Evaluate side-chains 525 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 446 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 307 MET Chi-restraints excluded: chain E residue 319 LYS Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 307 MET Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 386 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain G residue 301 SER Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 325 SER Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 301 SER Chi-restraints excluded: chain H residue 386 ASP Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain I residue 148 SER Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 301 SER Chi-restraints excluded: chain I residue 386 ASP Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain J residue 325 SER Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain K residue 148 SER Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain K residue 332 VAL Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 148 SER Chi-restraints excluded: chain L residue 180 GLU Chi-restraints excluded: chain L residue 248 ILE Chi-restraints excluded: chain L residue 301 SER Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 321 ASP Chi-restraints excluded: chain L residue 344 ASN Chi-restraints excluded: chain L residue 358 ASP Chi-restraints excluded: chain L residue 383 SER Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 148 SER Chi-restraints excluded: chain M residue 256 THR Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 325 SER Chi-restraints excluded: chain M residue 362 THR Chi-restraints excluded: chain M residue 386 ASP Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain N residue 148 SER Chi-restraints excluded: chain N residue 307 MET Chi-restraints excluded: chain N residue 362 THR Chi-restraints excluded: chain N residue 388 ASN Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 148 SER Chi-restraints excluded: chain O residue 161 ASP Chi-restraints excluded: chain O residue 344 ASN Chi-restraints excluded: chain O residue 358 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 338 optimal weight: 1.9990 chunk 179 optimal weight: 0.4980 chunk 288 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 212 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 289 optimal weight: 0.6980 chunk 308 optimal weight: 8.9990 chunk 236 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 187 GLN B 336 GLN C 336 GLN D 336 GLN ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 ASN F 336 GLN G 336 GLN ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 141 ASN J 336 GLN K 141 ASN K 336 GLN ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 141 ASN N 336 GLN O 336 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.147549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.116677 restraints weight = 27851.524| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.55 r_work: 0.3161 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 27420 Z= 0.121 Angle : 0.514 7.714 37395 Z= 0.262 Chirality : 0.046 0.208 4920 Planarity : 0.005 0.040 4530 Dihedral : 7.672 90.962 5792 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 4.03 % Allowed : 21.01 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.15), residues: 3285 helix: -0.77 (0.35), residues: 255 sheet: -0.72 (0.11), residues: 2265 loop : -0.26 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 337 TYR 0.016 0.002 TYR F 394 PHE 0.013 0.001 PHE J 194 HIS 0.001 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00263 (27420) covalent geometry : angle 0.51406 (37395) hydrogen bonds : bond 0.02620 ( 1065) hydrogen bonds : angle 5.44979 ( 3015) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 452 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LYS cc_start: 0.7556 (tttp) cc_final: 0.6795 (tppt) REVERT: A 261 LYS cc_start: 0.8985 (mttp) cc_final: 0.8531 (mmmt) REVERT: A 307 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7773 (mmt) REVERT: B 133 LYS cc_start: 0.7153 (tttt) cc_final: 0.6826 (tttp) REVERT: B 253 ARG cc_start: 0.8675 (mtp180) cc_final: 0.8180 (mtt90) REVERT: B 364 GLN cc_start: 0.7230 (tt0) cc_final: 0.6677 (tm-30) REVERT: C 248 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8648 (mm) REVERT: C 253 ARG cc_start: 0.8683 (mtm180) cc_final: 0.8301 (mtt90) REVERT: C 364 GLN cc_start: 0.7110 (tt0) cc_final: 0.6607 (tm-30) REVERT: D 364 GLN cc_start: 0.7043 (tt0) cc_final: 0.6590 (tm-30) REVERT: E 133 LYS cc_start: 0.7257 (tttt) cc_final: 0.6854 (tppt) REVERT: E 148 SER cc_start: 0.8518 (OUTLIER) cc_final: 0.8284 (m) REVERT: E 253 ARG cc_start: 0.8488 (mtm180) cc_final: 0.8245 (mtt90) REVERT: E 261 LYS cc_start: 0.8935 (mttp) cc_final: 0.8599 (mmmt) REVERT: E 389 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7229 (mt-10) REVERT: E 392 THR cc_start: 0.9088 (t) cc_final: 0.8824 (m) REVERT: F 261 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8778 (mmtt) REVERT: F 307 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7908 (mmt) REVERT: G 261 LYS cc_start: 0.8966 (mmtm) cc_final: 0.8726 (mmtt) REVERT: G 336 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8746 (tm-30) REVERT: G 360 LYS cc_start: 0.7812 (mtpt) cc_final: 0.7208 (mptp) REVERT: G 392 THR cc_start: 0.9163 (t) cc_final: 0.8870 (m) REVERT: H 133 LYS cc_start: 0.7435 (tttt) cc_final: 0.7192 (ttmm) REVERT: H 389 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7379 (mt-10) REVERT: I 115 LYS cc_start: 0.8616 (mttt) cc_final: 0.8345 (mtmm) REVERT: I 126 ARG cc_start: 0.8157 (mmm-85) cc_final: 0.7866 (mmm-85) REVERT: I 261 LYS cc_start: 0.9115 (mmtm) cc_final: 0.8798 (mmtp) REVERT: I 364 GLN cc_start: 0.7117 (tt0) cc_final: 0.6585 (tm-30) REVERT: I 389 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7441 (mt-10) REVERT: J 133 LYS cc_start: 0.7283 (tttt) cc_final: 0.6675 (tppt) REVERT: J 261 LYS cc_start: 0.9044 (mmmt) cc_final: 0.8727 (mmmt) REVERT: J 300 MET cc_start: 0.9308 (ttp) cc_final: 0.9010 (ttm) REVERT: K 115 LYS cc_start: 0.8785 (mttt) cc_final: 0.8441 (mtmm) REVERT: K 133 LYS cc_start: 0.7729 (ttpp) cc_final: 0.7292 (ttmm) REVERT: K 261 LYS cc_start: 0.8898 (mmmt) cc_final: 0.8686 (mmtt) REVERT: K 300 MET cc_start: 0.9272 (ttp) cc_final: 0.9021 (ttm) REVERT: L 133 LYS cc_start: 0.7493 (tttm) cc_final: 0.6902 (tppt) REVERT: L 307 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7549 (mtt) REVERT: L 364 GLN cc_start: 0.7163 (tt0) cc_final: 0.6589 (tm-30) REVERT: M 115 LYS cc_start: 0.8727 (mttt) cc_final: 0.8381 (mtmm) REVERT: M 180 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7952 (mt-10) REVERT: M 238 ARG cc_start: 0.6593 (mtt90) cc_final: 0.6353 (mpt180) REVERT: M 253 ARG cc_start: 0.8611 (mtp180) cc_final: 0.8159 (mtt90) REVERT: M 300 MET cc_start: 0.9298 (ttp) cc_final: 0.8794 (ttm) REVERT: M 358 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.8057 (m-30) REVERT: N 264 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8878 (tt) REVERT: N 300 MET cc_start: 0.9321 (ttp) cc_final: 0.9028 (ttm) REVERT: N 388 ASN cc_start: 0.8302 (OUTLIER) cc_final: 0.7979 (t0) REVERT: O 133 LYS cc_start: 0.7405 (tttt) cc_final: 0.6912 (tppt) REVERT: O 261 LYS cc_start: 0.8923 (mttp) cc_final: 0.8607 (mmtt) REVERT: O 292 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7727 (pp20) REVERT: O 300 MET cc_start: 0.9274 (ttp) cc_final: 0.8903 (ttp) outliers start: 124 outliers final: 53 residues processed: 543 average time/residue: 0.7943 time to fit residues: 485.4975 Evaluate side-chains 482 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 419 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 307 MET Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 141 ASN Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 261 LYS Chi-restraints excluded: chain F residue 307 MET Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 301 SER Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 336 GLN Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 301 SER Chi-restraints excluded: chain H residue 386 ASP Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 301 SER Chi-restraints excluded: chain I residue 386 ASP Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain K residue 148 SER Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 148 SER Chi-restraints excluded: chain L residue 180 GLU Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 148 SER Chi-restraints excluded: chain M residue 256 THR Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 325 SER Chi-restraints excluded: chain M residue 358 ASP Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain N residue 148 SER Chi-restraints excluded: chain N residue 264 ILE Chi-restraints excluded: chain N residue 388 ASN Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 148 SER Chi-restraints excluded: chain O residue 161 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 276 optimal weight: 0.9990 chunk 252 optimal weight: 7.9990 chunk 317 optimal weight: 0.0870 chunk 298 optimal weight: 3.9990 chunk 329 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 234 optimal weight: 0.0000 chunk 140 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 overall best weight: 1.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 112 GLN B 187 GLN B 336 GLN C 336 GLN D 336 GLN ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 ASN F 336 GLN G 336 GLN H 187 GLN ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 336 GLN J 141 ASN J 336 GLN K 141 ASN K 336 GLN L 165 GLN L 336 GLN M 141 ASN N 336 GLN O 336 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.148624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.117961 restraints weight = 27856.124| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.53 r_work: 0.3180 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 27420 Z= 0.106 Angle : 0.483 7.292 37395 Z= 0.247 Chirality : 0.046 0.203 4920 Planarity : 0.004 0.037 4530 Dihedral : 7.359 81.364 5792 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.16 % Allowed : 21.11 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.15), residues: 3285 helix: -0.44 (0.34), residues: 255 sheet: -0.55 (0.11), residues: 2235 loop : -0.14 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 253 TYR 0.016 0.002 TYR F 394 PHE 0.010 0.001 PHE J 194 HIS 0.001 0.000 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00231 (27420) covalent geometry : angle 0.48309 (37395) hydrogen bonds : bond 0.02448 ( 1065) hydrogen bonds : angle 5.25875 ( 3015) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 431 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LYS cc_start: 0.7519 (tttp) cc_final: 0.6807 (tppt) REVERT: A 261 LYS cc_start: 0.8971 (mttp) cc_final: 0.8540 (mmtt) REVERT: A 307 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7831 (mmt) REVERT: B 133 LYS cc_start: 0.7144 (tttt) cc_final: 0.6812 (tttp) REVERT: B 253 ARG cc_start: 0.8676 (mtp180) cc_final: 0.8196 (mtt90) REVERT: B 364 GLN cc_start: 0.7211 (tt0) cc_final: 0.6667 (tm-30) REVERT: C 115 LYS cc_start: 0.8793 (mttp) cc_final: 0.8448 (mtmm) REVERT: C 248 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8638 (mm) REVERT: C 253 ARG cc_start: 0.8681 (mtm180) cc_final: 0.8346 (mtt90) REVERT: C 319 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8731 (mtpt) REVERT: C 364 GLN cc_start: 0.7088 (tt0) cc_final: 0.6604 (tm-30) REVERT: D 261 LYS cc_start: 0.8846 (mttm) cc_final: 0.8608 (mtpp) REVERT: D 364 GLN cc_start: 0.7026 (tt0) cc_final: 0.6598 (tm-30) REVERT: E 133 LYS cc_start: 0.7232 (tttt) cc_final: 0.6839 (tppt) REVERT: E 253 ARG cc_start: 0.8469 (mtm180) cc_final: 0.8236 (mtt90) REVERT: E 261 LYS cc_start: 0.8952 (mttp) cc_final: 0.8613 (mmmt) REVERT: E 264 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8863 (tt) REVERT: E 389 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7237 (mt-10) REVERT: E 392 THR cc_start: 0.9045 (t) cc_final: 0.8766 (m) REVERT: F 115 LYS cc_start: 0.8697 (mttt) cc_final: 0.8467 (mtmt) REVERT: G 247 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7961 (tttm) REVERT: G 248 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8758 (mm) REVERT: G 261 LYS cc_start: 0.8949 (mmtm) cc_final: 0.8703 (mmtt) REVERT: G 307 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7570 (mtt) REVERT: G 336 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8693 (tm-30) REVERT: G 360 LYS cc_start: 0.7802 (mtpt) cc_final: 0.7198 (mptp) REVERT: G 392 THR cc_start: 0.9153 (t) cc_final: 0.8855 (m) REVERT: H 264 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8678 (tt) REVERT: H 389 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7376 (mt-10) REVERT: I 115 LYS cc_start: 0.8615 (mttt) cc_final: 0.8351 (mtmm) REVERT: I 248 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8370 (mm) REVERT: I 261 LYS cc_start: 0.9107 (mmtm) cc_final: 0.8801 (mmtp) REVERT: I 364 GLN cc_start: 0.7166 (tt0) cc_final: 0.6652 (tm-30) REVERT: I 389 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7475 (mt-10) REVERT: J 133 LYS cc_start: 0.7173 (tttt) cc_final: 0.6532 (tppt) REVERT: J 261 LYS cc_start: 0.9044 (mmmt) cc_final: 0.8739 (mmmt) REVERT: J 300 MET cc_start: 0.9273 (ttp) cc_final: 0.9003 (ttm) REVERT: K 115 LYS cc_start: 0.8790 (mttt) cc_final: 0.8452 (mtmm) REVERT: K 133 LYS cc_start: 0.7744 (ttpp) cc_final: 0.7337 (ttmm) REVERT: K 261 LYS cc_start: 0.8910 (mmmt) cc_final: 0.8686 (mmtt) REVERT: K 358 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.8086 (m-30) REVERT: L 133 LYS cc_start: 0.7498 (tttm) cc_final: 0.6909 (tppt) REVERT: L 307 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7592 (mtt) REVERT: L 364 GLN cc_start: 0.7175 (tt0) cc_final: 0.6616 (tm-30) REVERT: M 238 ARG cc_start: 0.6601 (mtt90) cc_final: 0.6340 (mpt180) REVERT: M 253 ARG cc_start: 0.8565 (mtp180) cc_final: 0.8148 (mtt90) REVERT: M 300 MET cc_start: 0.9269 (ttp) cc_final: 0.8738 (ttm) REVERT: M 319 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8410 (mtpt) REVERT: N 264 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8849 (tt) REVERT: N 300 MET cc_start: 0.9305 (ttp) cc_final: 0.9027 (ttm) REVERT: N 388 ASN cc_start: 0.8199 (OUTLIER) cc_final: 0.7888 (t0) REVERT: O 133 LYS cc_start: 0.7395 (tttt) cc_final: 0.6967 (tppt) REVERT: O 261 LYS cc_start: 0.8937 (mttp) cc_final: 0.8616 (mmtt) REVERT: O 292 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7717 (pp20) REVERT: O 300 MET cc_start: 0.9250 (ttp) cc_final: 0.8904 (ttp) outliers start: 128 outliers final: 50 residues processed: 531 average time/residue: 0.7774 time to fit residues: 465.7696 Evaluate side-chains 485 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 420 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 319 LYS Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 141 ASN Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 307 MET Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 247 LYS Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 336 GLN Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 301 SER Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 386 ASP Chi-restraints excluded: chain I residue 388 ASN Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain K residue 148 SER Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain K residue 358 ASP Chi-restraints excluded: chain K residue 383 SER Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 148 SER Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 148 SER Chi-restraints excluded: chain M residue 256 THR Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 319 LYS Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain N residue 148 SER Chi-restraints excluded: chain N residue 264 ILE Chi-restraints excluded: chain N residue 388 ASN Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 148 SER Chi-restraints excluded: chain O residue 161 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 234 optimal weight: 0.9990 chunk 226 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 237 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 54 optimal weight: 0.0770 chunk 286 optimal weight: 0.7980 chunk 204 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 112 GLN B 336 GLN C 336 GLN D 336 GLN ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 ASN F 336 GLN ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 141 ASN K 141 ASN K 336 GLN L 165 GLN L 336 GLN M 141 ASN N 141 ASN N 336 GLN O 336 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.147743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.117055 restraints weight = 27800.456| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.53 r_work: 0.3159 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 27420 Z= 0.122 Angle : 0.495 7.327 37395 Z= 0.253 Chirality : 0.046 0.193 4920 Planarity : 0.004 0.037 4530 Dihedral : 7.372 77.499 5792 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.64 % Allowed : 21.66 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.15), residues: 3285 helix: -0.13 (0.34), residues: 255 sheet: -0.41 (0.11), residues: 2235 loop : -0.12 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 126 TYR 0.017 0.002 TYR F 394 PHE 0.009 0.001 PHE J 194 HIS 0.002 0.001 HIS L 245 Details of bonding type rmsd covalent geometry : bond 0.00271 (27420) covalent geometry : angle 0.49475 (37395) hydrogen bonds : bond 0.02526 ( 1065) hydrogen bonds : angle 5.21524 ( 3015) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 422 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LYS cc_start: 0.7500 (tttp) cc_final: 0.6775 (tppt) REVERT: A 261 LYS cc_start: 0.8986 (mttp) cc_final: 0.8567 (mmmt) REVERT: A 307 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7736 (mmt) REVERT: B 133 LYS cc_start: 0.7122 (tttt) cc_final: 0.6794 (tttp) REVERT: B 253 ARG cc_start: 0.8692 (mtp180) cc_final: 0.8209 (mtt90) REVERT: B 294 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8821 (tt0) REVERT: B 364 GLN cc_start: 0.7211 (tt0) cc_final: 0.6669 (tm-30) REVERT: C 115 LYS cc_start: 0.8787 (mttp) cc_final: 0.8430 (mtmm) REVERT: C 122 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8353 (pttp) REVERT: C 248 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8663 (mm) REVERT: C 253 ARG cc_start: 0.8716 (mtm180) cc_final: 0.8374 (mtt90) REVERT: C 319 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8732 (mtpt) REVERT: C 364 GLN cc_start: 0.7203 (tt0) cc_final: 0.6660 (tm-30) REVERT: D 261 LYS cc_start: 0.8902 (mttm) cc_final: 0.8675 (mtpp) REVERT: D 364 GLN cc_start: 0.6975 (tt0) cc_final: 0.6534 (tm-30) REVERT: E 133 LYS cc_start: 0.7235 (tttt) cc_final: 0.6881 (tppt) REVERT: E 253 ARG cc_start: 0.8487 (mtm180) cc_final: 0.8238 (mtt90) REVERT: E 261 LYS cc_start: 0.8961 (mttp) cc_final: 0.8624 (mmmt) REVERT: E 264 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8866 (tt) REVERT: E 389 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7224 (mt-10) REVERT: E 392 THR cc_start: 0.9039 (t) cc_final: 0.8812 (m) REVERT: F 115 LYS cc_start: 0.8664 (mttt) cc_final: 0.8450 (mtmt) REVERT: F 264 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8665 (tt) REVERT: G 122 LYS cc_start: 0.8639 (pttm) cc_final: 0.8369 (pttm) REVERT: G 248 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8783 (mm) REVERT: G 253 ARG cc_start: 0.8585 (mtm180) cc_final: 0.8161 (mtt90) REVERT: G 261 LYS cc_start: 0.8980 (mmtm) cc_final: 0.8725 (mmtt) REVERT: G 360 LYS cc_start: 0.7776 (mtpt) cc_final: 0.7158 (mptp) REVERT: G 364 GLN cc_start: 0.7335 (tt0) cc_final: 0.6661 (tm-30) REVERT: G 392 THR cc_start: 0.9156 (t) cc_final: 0.8842 (m) REVERT: H 133 LYS cc_start: 0.7526 (ttmm) cc_final: 0.7073 (tppt) REVERT: H 389 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7397 (mt-10) REVERT: I 115 LYS cc_start: 0.8589 (mttt) cc_final: 0.8330 (mtmm) REVERT: I 240 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.7064 (tt) REVERT: I 248 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8422 (mm) REVERT: I 261 LYS cc_start: 0.9078 (mmtm) cc_final: 0.8766 (mmtp) REVERT: I 364 GLN cc_start: 0.7178 (tt0) cc_final: 0.6675 (tm-30) REVERT: I 389 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7474 (mt-10) REVERT: J 133 LYS cc_start: 0.7149 (tttt) cc_final: 0.6572 (tppt) REVERT: J 261 LYS cc_start: 0.9082 (mmmt) cc_final: 0.8763 (mmmt) REVERT: K 115 LYS cc_start: 0.8775 (mttt) cc_final: 0.8433 (mtmm) REVERT: K 133 LYS cc_start: 0.7785 (ttpp) cc_final: 0.7388 (ttmm) REVERT: K 261 LYS cc_start: 0.8841 (mmmt) cc_final: 0.8588 (mmtt) REVERT: K 300 MET cc_start: 0.9248 (ttp) cc_final: 0.9026 (ttm) REVERT: K 358 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.8064 (m-30) REVERT: L 133 LYS cc_start: 0.7544 (tttm) cc_final: 0.6979 (tppt) REVERT: L 307 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7527 (mtt) REVERT: L 364 GLN cc_start: 0.7217 (tt0) cc_final: 0.6646 (tm-30) REVERT: M 253 ARG cc_start: 0.8563 (mtp180) cc_final: 0.8119 (mtt90) REVERT: M 264 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8808 (tt) REVERT: M 300 MET cc_start: 0.9269 (ttp) cc_final: 0.8768 (ttm) REVERT: M 319 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8393 (mtpt) REVERT: M 388 ASN cc_start: 0.8286 (t0) cc_final: 0.8034 (m-40) REVERT: N 264 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8901 (tt) REVERT: N 300 MET cc_start: 0.9296 (ttp) cc_final: 0.8934 (ttm) REVERT: N 388 ASN cc_start: 0.8125 (OUTLIER) cc_final: 0.7792 (t0) REVERT: O 133 LYS cc_start: 0.7386 (tttt) cc_final: 0.6981 (tppt) REVERT: O 261 LYS cc_start: 0.8932 (mttp) cc_final: 0.8608 (mmtt) REVERT: O 264 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8743 (tt) REVERT: O 292 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7837 (pp20) REVERT: O 294 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8850 (tt0) REVERT: O 300 MET cc_start: 0.9247 (ttp) cc_final: 0.8824 (ttp) REVERT: O 358 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7781 (m-30) outliers start: 112 outliers final: 55 residues processed: 508 average time/residue: 0.7942 time to fit residues: 454.2988 Evaluate side-chains 478 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 404 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 319 LYS Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 141 ASN Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 307 MET Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 386 ASP Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 301 SER Chi-restraints excluded: chain I residue 386 ASP Chi-restraints excluded: chain I residue 388 ASN Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain K residue 148 SER Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain K residue 336 GLN Chi-restraints excluded: chain K residue 358 ASP Chi-restraints excluded: chain K residue 383 SER Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 148 SER Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 148 SER Chi-restraints excluded: chain M residue 256 THR Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 319 LYS Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain N residue 148 SER Chi-restraints excluded: chain N residue 264 ILE Chi-restraints excluded: chain N residue 388 ASN Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 148 SER Chi-restraints excluded: chain O residue 161 ASP Chi-restraints excluded: chain O residue 264 ILE Chi-restraints excluded: chain O residue 294 GLN Chi-restraints excluded: chain O residue 358 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 338 optimal weight: 0.0670 chunk 248 optimal weight: 0.6980 chunk 16 optimal weight: 8.9990 chunk 234 optimal weight: 10.0000 chunk 341 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 294 optimal weight: 5.9990 chunk 219 optimal weight: 6.9990 chunk 306 optimal weight: 1.9990 chunk 195 optimal weight: 10.0000 chunk 330 optimal weight: 4.9990 overall best weight: 2.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 141 ASN C 336 GLN D 336 GLN ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 ASN F 336 GLN ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 141 ASN K 141 ASN K 336 GLN L 328 GLN ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 141 ASN N 141 ASN N 336 GLN O 336 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.143783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.114046 restraints weight = 28225.334| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.44 r_work: 0.3081 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27420 Z= 0.187 Angle : 0.561 7.774 37395 Z= 0.286 Chirality : 0.047 0.178 4920 Planarity : 0.005 0.039 4530 Dihedral : 7.870 79.587 5792 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.20 % Allowed : 21.72 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.15), residues: 3285 helix: -0.04 (0.33), residues: 255 sheet: -0.30 (0.11), residues: 2160 loop : -0.19 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 293 TYR 0.020 0.003 TYR F 394 PHE 0.009 0.001 PHE F 194 HIS 0.003 0.001 HIS D 245 Details of bonding type rmsd covalent geometry : bond 0.00429 (27420) covalent geometry : angle 0.56089 (37395) hydrogen bonds : bond 0.02907 ( 1065) hydrogen bonds : angle 5.36544 ( 3015) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 424 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LYS cc_start: 0.7531 (tttp) cc_final: 0.6796 (tppt) REVERT: A 261 LYS cc_start: 0.8983 (mttp) cc_final: 0.8583 (mmmt) REVERT: A 300 MET cc_start: 0.9325 (ttp) cc_final: 0.9045 (ttp) REVERT: A 307 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7826 (mmt) REVERT: B 133 LYS cc_start: 0.7179 (tttt) cc_final: 0.6869 (tttp) REVERT: B 253 ARG cc_start: 0.8694 (mtp180) cc_final: 0.8241 (mtt90) REVERT: B 294 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8868 (tt0) REVERT: B 364 GLN cc_start: 0.7198 (tt0) cc_final: 0.6744 (tm-30) REVERT: C 122 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8367 (pttp) REVERT: C 248 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8709 (mm) REVERT: C 364 GLN cc_start: 0.7316 (tt0) cc_final: 0.6817 (tm-30) REVERT: D 248 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8806 (mm) REVERT: D 253 ARG cc_start: 0.8652 (mtm180) cc_final: 0.8309 (mtt90) REVERT: D 261 LYS cc_start: 0.9015 (mttm) cc_final: 0.8797 (mtpp) REVERT: D 364 GLN cc_start: 0.7053 (tt0) cc_final: 0.6566 (tm-30) REVERT: E 133 LYS cc_start: 0.7312 (tttt) cc_final: 0.6970 (tppt) REVERT: E 261 LYS cc_start: 0.8995 (mttp) cc_final: 0.8668 (mmmt) REVERT: E 319 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8710 (mtpt) REVERT: E 389 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7288 (mt-10) REVERT: F 261 LYS cc_start: 0.8993 (mmtt) cc_final: 0.8472 (mmmt) REVERT: F 264 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8806 (tt) REVERT: F 400 THR cc_start: 0.8754 (m) cc_final: 0.8193 (p) REVERT: G 122 LYS cc_start: 0.8783 (pttm) cc_final: 0.8533 (pttm) REVERT: G 248 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8792 (mm) REVERT: G 261 LYS cc_start: 0.9008 (mmtm) cc_final: 0.8750 (mmtt) REVERT: G 360 LYS cc_start: 0.7986 (mtpt) cc_final: 0.7402 (mptp) REVERT: G 364 GLN cc_start: 0.7427 (tt0) cc_final: 0.6772 (tm-30) REVERT: G 392 THR cc_start: 0.9176 (t) cc_final: 0.8866 (m) REVERT: H 133 LYS cc_start: 0.7624 (ttmm) cc_final: 0.7096 (tppt) REVERT: H 264 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8786 (tt) REVERT: H 364 GLN cc_start: 0.7334 (tt0) cc_final: 0.6653 (tm-30) REVERT: H 388 ASN cc_start: 0.8177 (t0) cc_final: 0.7870 (m-40) REVERT: H 389 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7500 (mt-10) REVERT: I 115 LYS cc_start: 0.8702 (mttt) cc_final: 0.8434 (mtmm) REVERT: I 248 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8512 (mm) REVERT: I 261 LYS cc_start: 0.9084 (mmtm) cc_final: 0.8760 (mmtp) REVERT: I 364 GLN cc_start: 0.7137 (tt0) cc_final: 0.6664 (tm-30) REVERT: J 133 LYS cc_start: 0.7195 (tttt) cc_final: 0.6685 (tppt) REVERT: J 253 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8247 (mtp85) REVERT: J 261 LYS cc_start: 0.9075 (mmmt) cc_final: 0.8744 (mmmt) REVERT: J 319 LYS cc_start: 0.9054 (mtpt) cc_final: 0.8794 (mtmt) REVERT: K 115 LYS cc_start: 0.8822 (mttt) cc_final: 0.8477 (mtmm) REVERT: K 133 LYS cc_start: 0.7817 (ttpp) cc_final: 0.7407 (ttmm) REVERT: K 261 LYS cc_start: 0.8852 (mmmt) cc_final: 0.8600 (mmtt) REVERT: L 133 LYS cc_start: 0.7557 (tttm) cc_final: 0.6975 (tppt) REVERT: L 364 GLN cc_start: 0.7322 (tt0) cc_final: 0.6752 (tm-30) REVERT: M 253 ARG cc_start: 0.8648 (mtp180) cc_final: 0.8193 (mtt90) REVERT: M 264 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8818 (tt) REVERT: M 300 MET cc_start: 0.9276 (ttp) cc_final: 0.8763 (ttm) REVERT: M 388 ASN cc_start: 0.8306 (t0) cc_final: 0.8079 (m-40) REVERT: N 126 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.7125 (mmp-170) REVERT: N 264 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8950 (tt) REVERT: N 300 MET cc_start: 0.9307 (ttp) cc_final: 0.9063 (ttm) REVERT: N 388 ASN cc_start: 0.8310 (OUTLIER) cc_final: 0.7971 (t0) REVERT: O 133 LYS cc_start: 0.7523 (tttt) cc_final: 0.7102 (tppt) REVERT: O 261 LYS cc_start: 0.8946 (mttp) cc_final: 0.8636 (mmtt) REVERT: O 264 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8811 (tt) REVERT: O 292 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7926 (pp20) REVERT: O 294 GLN cc_start: 0.9152 (OUTLIER) cc_final: 0.8950 (tt0) REVERT: O 300 MET cc_start: 0.9241 (ttp) cc_final: 0.8832 (ttp) REVERT: O 358 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7888 (m-30) REVERT: O 364 GLN cc_start: 0.7289 (tt0) cc_final: 0.6756 (tm-30) outliers start: 129 outliers final: 61 residues processed: 519 average time/residue: 0.7968 time to fit residues: 465.3269 Evaluate side-chains 494 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 415 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 319 LYS Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 307 MET Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 180 GLU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain G residue 301 SER Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 301 SER Chi-restraints excluded: chain H residue 386 ASP Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 301 SER Chi-restraints excluded: chain I residue 386 ASP Chi-restraints excluded: chain I residue 388 ASN Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain J residue 253 ARG Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain K residue 148 SER Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain K residue 383 SER Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 148 SER Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 321 ASP Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 148 SER Chi-restraints excluded: chain M residue 256 THR Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 325 SER Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain N residue 126 ARG Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain N residue 148 SER Chi-restraints excluded: chain N residue 264 ILE Chi-restraints excluded: chain N residue 388 ASN Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 148 SER Chi-restraints excluded: chain O residue 161 ASP Chi-restraints excluded: chain O residue 264 ILE Chi-restraints excluded: chain O residue 294 GLN Chi-restraints excluded: chain O residue 358 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 127 optimal weight: 6.9990 chunk 187 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 245 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 143 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 176 optimal weight: 5.9990 chunk 315 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 141 ASN C 336 GLN D 336 GLN ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 ASN ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 141 ASN K 141 ASN K 336 GLN ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 141 ASN N 141 ASN N 336 GLN O 336 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.144945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.115601 restraints weight = 28428.432| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.43 r_work: 0.3103 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27420 Z= 0.141 Angle : 0.511 7.055 37395 Z= 0.261 Chirality : 0.046 0.187 4920 Planarity : 0.004 0.037 4530 Dihedral : 7.475 77.228 5792 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.58 % Allowed : 22.31 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.15), residues: 3285 helix: 0.12 (0.34), residues: 255 sheet: -0.31 (0.11), residues: 2235 loop : 0.04 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 126 TYR 0.018 0.002 TYR F 394 PHE 0.008 0.001 PHE L 194 HIS 0.002 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00317 (27420) covalent geometry : angle 0.51109 (37395) hydrogen bonds : bond 0.02623 ( 1065) hydrogen bonds : angle 5.23462 ( 3015) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 421 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8794 (mtpp) cc_final: 0.8572 (mtmt) REVERT: A 133 LYS cc_start: 0.7511 (tttp) cc_final: 0.6817 (tppt) REVERT: A 253 ARG cc_start: 0.8538 (mtp180) cc_final: 0.8118 (mtt90) REVERT: A 261 LYS cc_start: 0.8982 (mttp) cc_final: 0.8776 (mttm) REVERT: A 300 MET cc_start: 0.9327 (ttp) cc_final: 0.9060 (ttp) REVERT: A 307 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7796 (mmt) REVERT: B 133 LYS cc_start: 0.7125 (tttt) cc_final: 0.6683 (tppt) REVERT: B 253 ARG cc_start: 0.8672 (mtp180) cc_final: 0.8240 (mtt90) REVERT: B 294 GLN cc_start: 0.9125 (OUTLIER) cc_final: 0.8846 (tt0) REVERT: B 364 GLN cc_start: 0.7209 (tt0) cc_final: 0.6747 (tm-30) REVERT: C 122 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8451 (pttp) REVERT: C 248 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8680 (mm) REVERT: C 253 ARG cc_start: 0.8653 (mtm180) cc_final: 0.8375 (mtt90) REVERT: C 364 GLN cc_start: 0.7289 (tt0) cc_final: 0.6780 (tm-30) REVERT: D 253 ARG cc_start: 0.8639 (mtm180) cc_final: 0.8337 (mtt90) REVERT: D 261 LYS cc_start: 0.8882 (mttm) cc_final: 0.8651 (mtpp) REVERT: D 364 GLN cc_start: 0.7097 (tt0) cc_final: 0.6590 (tm-30) REVERT: E 133 LYS cc_start: 0.7250 (tttt) cc_final: 0.6953 (tppt) REVERT: E 261 LYS cc_start: 0.8966 (mttp) cc_final: 0.8646 (mmmt) REVERT: E 264 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8900 (tt) REVERT: E 319 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8765 (mtpt) REVERT: E 389 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7341 (mt-10) REVERT: E 392 THR cc_start: 0.9081 (t) cc_final: 0.8843 (m) REVERT: F 253 ARG cc_start: 0.8593 (mtm180) cc_final: 0.8344 (mtt90) REVERT: F 261 LYS cc_start: 0.8981 (mmtt) cc_final: 0.8371 (mmmt) REVERT: F 264 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8780 (tt) REVERT: G 122 LYS cc_start: 0.8687 (pttm) cc_final: 0.8434 (pttm) REVERT: G 248 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8754 (mm) REVERT: G 261 LYS cc_start: 0.9009 (mmtm) cc_final: 0.8768 (mmtt) REVERT: G 364 GLN cc_start: 0.7428 (tt0) cc_final: 0.6764 (tm-30) REVERT: G 392 THR cc_start: 0.9162 (t) cc_final: 0.8852 (m) REVERT: H 133 LYS cc_start: 0.7653 (ttmm) cc_final: 0.7114 (tppt) REVERT: H 364 GLN cc_start: 0.7342 (tt0) cc_final: 0.6616 (tm-30) REVERT: H 389 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7494 (mt-10) REVERT: I 115 LYS cc_start: 0.8666 (mttt) cc_final: 0.8385 (mtmm) REVERT: I 248 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8486 (mm) REVERT: I 261 LYS cc_start: 0.9081 (mmtm) cc_final: 0.8771 (mmtp) REVERT: J 133 LYS cc_start: 0.7253 (tttt) cc_final: 0.6749 (tppt) REVERT: J 253 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8292 (mtp85) REVERT: J 261 LYS cc_start: 0.9063 (mmmt) cc_final: 0.8746 (mmmt) REVERT: K 115 LYS cc_start: 0.8837 (mttt) cc_final: 0.8509 (mtmm) REVERT: K 133 LYS cc_start: 0.7806 (ttpp) cc_final: 0.7421 (ttmm) REVERT: K 300 MET cc_start: 0.9245 (ttp) cc_final: 0.9027 (ttm) REVERT: L 133 LYS cc_start: 0.7543 (tttm) cc_final: 0.6968 (tppt) REVERT: L 248 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8694 (mm) REVERT: L 307 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7487 (mtt) REVERT: L 364 GLN cc_start: 0.7324 (tt0) cc_final: 0.6720 (tm-30) REVERT: M 253 ARG cc_start: 0.8609 (mtp180) cc_final: 0.8214 (mtt90) REVERT: M 300 MET cc_start: 0.9282 (ttp) cc_final: 0.8804 (ttm) REVERT: N 126 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.7135 (mmp-170) REVERT: N 264 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8910 (tt) REVERT: N 300 MET cc_start: 0.9310 (ttp) cc_final: 0.9033 (ttm) REVERT: N 388 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.7977 (t0) REVERT: O 133 LYS cc_start: 0.7429 (tttt) cc_final: 0.7062 (tppt) REVERT: O 261 LYS cc_start: 0.8943 (mttp) cc_final: 0.8740 (mmtt) REVERT: O 264 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8775 (tt) REVERT: O 292 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7822 (pp20) REVERT: O 300 MET cc_start: 0.9231 (ttp) cc_final: 0.8809 (ttp) REVERT: O 358 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.7889 (m-30) outliers start: 110 outliers final: 62 residues processed: 500 average time/residue: 0.8135 time to fit residues: 457.7892 Evaluate side-chains 489 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 410 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 319 LYS Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 307 MET Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain G residue 301 SER Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 301 SER Chi-restraints excluded: chain H residue 386 ASP Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 301 SER Chi-restraints excluded: chain I residue 386 ASP Chi-restraints excluded: chain I residue 388 ASN Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain J residue 253 ARG Chi-restraints excluded: chain J residue 325 SER Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain K residue 148 SER Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain K residue 383 SER Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 148 SER Chi-restraints excluded: chain L residue 248 ILE Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 321 ASP Chi-restraints excluded: chain L residue 383 SER Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 148 SER Chi-restraints excluded: chain M residue 256 THR Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 325 SER Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain N residue 126 ARG Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain N residue 148 SER Chi-restraints excluded: chain N residue 171 ASP Chi-restraints excluded: chain N residue 264 ILE Chi-restraints excluded: chain N residue 388 ASN Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 148 SER Chi-restraints excluded: chain O residue 161 ASP Chi-restraints excluded: chain O residue 264 ILE Chi-restraints excluded: chain O residue 294 GLN Chi-restraints excluded: chain O residue 358 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 271 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 chunk 291 optimal weight: 7.9990 chunk 308 optimal weight: 10.0000 chunk 266 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 241 optimal weight: 9.9990 chunk 205 optimal weight: 9.9990 chunk 198 optimal weight: 5.9990 chunk 77 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: A 336 GLN C 336 GLN D 336 GLN ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 ASN ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 141 ASN K 141 ASN ** K 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 141 ASN N 141 ASN N 336 GLN O 336 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.141978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.112770 restraints weight = 28728.726| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.42 r_work: 0.3094 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 27420 Z= 0.245 Angle : 0.620 7.463 37395 Z= 0.315 Chirality : 0.048 0.167 4920 Planarity : 0.005 0.042 4530 Dihedral : 8.369 84.016 5792 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.58 % Allowed : 22.50 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.15), residues: 3285 helix: 0.07 (0.34), residues: 255 sheet: -0.37 (0.11), residues: 2130 loop : -0.11 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 293 TYR 0.022 0.003 TYR F 394 PHE 0.010 0.001 PHE A 194 HIS 0.004 0.002 HIS D 245 Details of bonding type rmsd covalent geometry : bond 0.00568 (27420) covalent geometry : angle 0.61997 (37395) hydrogen bonds : bond 0.03170 ( 1065) hydrogen bonds : angle 5.48619 ( 3015) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 428 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.8376 (mtp180) cc_final: 0.8028 (mtp85) REVERT: A 133 LYS cc_start: 0.7709 (tttp) cc_final: 0.6938 (tppt) REVERT: A 261 LYS cc_start: 0.8993 (mttp) cc_final: 0.8607 (mmmt) REVERT: A 307 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7933 (mmt) REVERT: B 133 LYS cc_start: 0.7280 (tttt) cc_final: 0.6961 (tttp) REVERT: B 253 ARG cc_start: 0.8726 (mtp180) cc_final: 0.8259 (mtp85) REVERT: B 294 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8792 (tt0) REVERT: C 122 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8379 (pttp) REVERT: C 248 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8747 (mm) REVERT: C 364 GLN cc_start: 0.7404 (tt0) cc_final: 0.6871 (tm-30) REVERT: D 253 ARG cc_start: 0.8657 (mtm180) cc_final: 0.8377 (mtt90) REVERT: D 261 LYS cc_start: 0.8997 (mttm) cc_final: 0.8781 (mtpp) REVERT: E 126 ARG cc_start: 0.8270 (mtp180) cc_final: 0.7904 (mtp85) REVERT: E 133 LYS cc_start: 0.7330 (tttt) cc_final: 0.6996 (tppt) REVERT: E 261 LYS cc_start: 0.8995 (mttp) cc_final: 0.8686 (mmmt) REVERT: E 264 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8935 (tt) REVERT: E 307 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7064 (mtt) REVERT: E 389 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7323 (mt-10) REVERT: E 392 THR cc_start: 0.9071 (t) cc_final: 0.8831 (m) REVERT: F 261 LYS cc_start: 0.8992 (mmtt) cc_final: 0.8703 (mmtm) REVERT: F 264 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8837 (tt) REVERT: F 400 THR cc_start: 0.8742 (m) cc_final: 0.8209 (p) REVERT: G 122 LYS cc_start: 0.8877 (pttm) cc_final: 0.8652 (pttm) REVERT: G 248 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8789 (mm) REVERT: G 253 ARG cc_start: 0.8791 (mtm180) cc_final: 0.8395 (mtt90) REVERT: G 261 LYS cc_start: 0.9043 (mmtm) cc_final: 0.8820 (mmmt) REVERT: G 392 THR cc_start: 0.9195 (t) cc_final: 0.8885 (m) REVERT: H 248 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8665 (mm) REVERT: H 264 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8794 (tt) REVERT: H 346 ARG cc_start: 0.7741 (mtm180) cc_final: 0.7443 (ttp-170) REVERT: H 364 GLN cc_start: 0.7340 (tt0) cc_final: 0.6617 (tm-30) REVERT: H 388 ASN cc_start: 0.8104 (t0) cc_final: 0.7868 (m-40) REVERT: H 389 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7483 (mt-10) REVERT: I 115 LYS cc_start: 0.8798 (mttt) cc_final: 0.8501 (mtmm) REVERT: I 248 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8555 (mm) REVERT: I 261 LYS cc_start: 0.9085 (mmtm) cc_final: 0.8765 (mmtp) REVERT: J 133 LYS cc_start: 0.7282 (tttt) cc_final: 0.6770 (tppt) REVERT: J 253 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8247 (mtp85) REVERT: J 261 LYS cc_start: 0.9055 (mmmt) cc_final: 0.8757 (mmmt) REVERT: K 115 LYS cc_start: 0.8832 (mttt) cc_final: 0.8497 (mtmm) REVERT: K 133 LYS cc_start: 0.7855 (ttpp) cc_final: 0.7410 (ttmm) REVERT: K 300 MET cc_start: 0.9246 (ttp) cc_final: 0.9030 (ttm) REVERT: K 346 ARG cc_start: 0.7812 (mtt180) cc_final: 0.7565 (ttm110) REVERT: L 133 LYS cc_start: 0.7566 (tttm) cc_final: 0.6995 (tppt) REVERT: L 248 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8757 (mm) REVERT: M 253 ARG cc_start: 0.8663 (mtp180) cc_final: 0.8234 (mtt90) REVERT: M 264 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8897 (tt) REVERT: M 300 MET cc_start: 0.9259 (ttp) cc_final: 0.8734 (ttm) REVERT: M 346 ARG cc_start: 0.7574 (mtm110) cc_final: 0.7311 (ttm110) REVERT: N 126 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.7153 (mmp-170) REVERT: N 264 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8967 (tt) REVERT: N 300 MET cc_start: 0.9299 (ttp) cc_final: 0.8946 (ttm) REVERT: N 358 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.8006 (m-30) REVERT: N 388 ASN cc_start: 0.8446 (OUTLIER) cc_final: 0.8130 (t0) REVERT: O 133 LYS cc_start: 0.7574 (tttt) cc_final: 0.7137 (tppt) REVERT: O 261 LYS cc_start: 0.8906 (mttp) cc_final: 0.8610 (mmtt) REVERT: O 264 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8868 (tt) REVERT: O 292 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7843 (pp20) REVERT: O 300 MET cc_start: 0.9236 (ttp) cc_final: 0.8742 (ttp) outliers start: 110 outliers final: 63 residues processed: 508 average time/residue: 0.8195 time to fit residues: 467.5051 Evaluate side-chains 494 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 412 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 307 MET Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 307 MET Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain G residue 301 SER Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 301 SER Chi-restraints excluded: chain H residue 386 ASP Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 301 SER Chi-restraints excluded: chain I residue 386 ASP Chi-restraints excluded: chain I residue 388 ASN Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain J residue 253 ARG Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain K residue 148 SER Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain K residue 383 SER Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 148 SER Chi-restraints excluded: chain L residue 248 ILE Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 321 ASP Chi-restraints excluded: chain L residue 383 SER Chi-restraints excluded: chain L residue 392 THR Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 148 SER Chi-restraints excluded: chain M residue 256 THR Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 325 SER Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain N residue 126 ARG Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain N residue 148 SER Chi-restraints excluded: chain N residue 264 ILE Chi-restraints excluded: chain N residue 358 ASP Chi-restraints excluded: chain N residue 388 ASN Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 148 SER Chi-restraints excluded: chain O residue 161 ASP Chi-restraints excluded: chain O residue 264 ILE Chi-restraints excluded: chain O residue 294 GLN Chi-restraints excluded: chain O residue 344 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 238 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 chunk 325 optimal weight: 4.9990 chunk 289 optimal weight: 1.9990 chunk 205 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 158 optimal weight: 0.5980 chunk 226 optimal weight: 4.9990 chunk 237 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 141 ASN C 336 GLN D 336 GLN ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 ASN ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 141 ASN K 141 ASN ** K 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 141 ASN M 243 ASN N 141 ASN N 336 GLN O 336 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.144188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.114877 restraints weight = 28537.640| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.44 r_work: 0.3100 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 27420 Z= 0.142 Angle : 0.521 7.569 37395 Z= 0.266 Chirality : 0.046 0.183 4920 Planarity : 0.005 0.039 4530 Dihedral : 7.627 83.531 5792 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.67 % Allowed : 23.58 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.15), residues: 3285 helix: 0.26 (0.34), residues: 255 sheet: -0.28 (0.11), residues: 2235 loop : 0.07 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 126 TYR 0.019 0.002 TYR L 394 PHE 0.008 0.001 PHE B 194 HIS 0.002 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00319 (27420) covalent geometry : angle 0.52111 (37395) hydrogen bonds : bond 0.02651 ( 1065) hydrogen bonds : angle 5.27281 ( 3015) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 415 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 ARG cc_start: 0.8341 (mtp180) cc_final: 0.8024 (mtp85) REVERT: A 133 LYS cc_start: 0.7532 (tttp) cc_final: 0.6863 (tppt) REVERT: A 253 ARG cc_start: 0.8542 (mtp180) cc_final: 0.8131 (mtt90) REVERT: A 261 LYS cc_start: 0.8972 (mttp) cc_final: 0.8568 (mmtt) REVERT: A 307 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7789 (mmt) REVERT: B 133 LYS cc_start: 0.7217 (tttt) cc_final: 0.6763 (tppt) REVERT: B 253 ARG cc_start: 0.8671 (mtp180) cc_final: 0.8236 (mtt90) REVERT: B 294 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8834 (tt0) REVERT: B 364 GLN cc_start: 0.7219 (tt0) cc_final: 0.6729 (tm-30) REVERT: C 122 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8457 (pttp) REVERT: C 248 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8751 (mm) REVERT: C 364 GLN cc_start: 0.7350 (tt0) cc_final: 0.6804 (tm-30) REVERT: D 180 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7696 (mt-10) REVERT: D 253 ARG cc_start: 0.8642 (mtm180) cc_final: 0.8330 (mtt90) REVERT: D 261 LYS cc_start: 0.8858 (mttm) cc_final: 0.8627 (mtpp) REVERT: D 294 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8767 (tt0) REVERT: D 364 GLN cc_start: 0.7191 (tt0) cc_final: 0.6622 (tm-30) REVERT: E 126 ARG cc_start: 0.8262 (mtp180) cc_final: 0.7889 (mtp85) REVERT: E 133 LYS cc_start: 0.7325 (tttt) cc_final: 0.6979 (tppt) REVERT: E 261 LYS cc_start: 0.8982 (mttp) cc_final: 0.8668 (mmmt) REVERT: E 264 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8917 (tt) REVERT: E 389 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7337 (mt-10) REVERT: E 392 THR cc_start: 0.9090 (t) cc_final: 0.8872 (m) REVERT: F 261 LYS cc_start: 0.8976 (mmtt) cc_final: 0.8380 (mmmt) REVERT: F 264 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8777 (tt) REVERT: F 307 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7761 (mmt) REVERT: G 122 LYS cc_start: 0.8692 (pttm) cc_final: 0.8443 (pttm) REVERT: G 248 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8751 (mm) REVERT: G 253 ARG cc_start: 0.8691 (mtm180) cc_final: 0.8363 (mtt90) REVERT: G 261 LYS cc_start: 0.9001 (mmtm) cc_final: 0.8759 (mmtt) REVERT: G 364 GLN cc_start: 0.7412 (tt0) cc_final: 0.6781 (tm-30) REVERT: G 392 THR cc_start: 0.9181 (t) cc_final: 0.8875 (m) REVERT: H 300 MET cc_start: 0.9224 (ttp) cc_final: 0.8830 (ttp) REVERT: H 364 GLN cc_start: 0.7315 (tt0) cc_final: 0.6538 (tm-30) REVERT: H 388 ASN cc_start: 0.8147 (t0) cc_final: 0.7894 (m-40) REVERT: H 389 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7419 (mt-10) REVERT: I 115 LYS cc_start: 0.8655 (mttt) cc_final: 0.8365 (mtmm) REVERT: I 248 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8495 (mm) REVERT: I 261 LYS cc_start: 0.9077 (mmtm) cc_final: 0.8771 (mmtp) REVERT: J 126 ARG cc_start: 0.8151 (mtp-110) cc_final: 0.7870 (mtm180) REVERT: J 133 LYS cc_start: 0.7304 (tttt) cc_final: 0.6766 (tppt) REVERT: J 253 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8317 (mtm-85) REVERT: J 261 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8750 (mmmt) REVERT: K 115 LYS cc_start: 0.8822 (mttt) cc_final: 0.8497 (mtmm) REVERT: K 133 LYS cc_start: 0.7789 (ttpp) cc_final: 0.7387 (ttmm) REVERT: K 300 MET cc_start: 0.9247 (ttp) cc_final: 0.9044 (ttm) REVERT: L 133 LYS cc_start: 0.7558 (tttm) cc_final: 0.7022 (tppt) REVERT: L 238 ARG cc_start: 0.6643 (mtt90) cc_final: 0.6335 (mpt180) REVERT: L 248 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8699 (mm) REVERT: L 307 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7482 (mtt) REVERT: M 253 ARG cc_start: 0.8617 (mtp180) cc_final: 0.8193 (mtt90) REVERT: M 264 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8822 (tt) REVERT: M 300 MET cc_start: 0.9265 (ttp) cc_final: 0.8758 (ttm) REVERT: M 346 ARG cc_start: 0.7541 (mtm110) cc_final: 0.7293 (ttm110) REVERT: N 126 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.7136 (mmp-170) REVERT: N 264 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8931 (tt) REVERT: N 300 MET cc_start: 0.9297 (ttp) cc_final: 0.8934 (ttm) REVERT: N 388 ASN cc_start: 0.8328 (OUTLIER) cc_final: 0.7973 (t0) REVERT: O 133 LYS cc_start: 0.7437 (tttt) cc_final: 0.7053 (tppt) REVERT: O 261 LYS cc_start: 0.8905 (mttp) cc_final: 0.8595 (mmtt) REVERT: O 264 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8788 (tt) REVERT: O 292 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7825 (pp20) REVERT: O 300 MET cc_start: 0.9227 (ttp) cc_final: 0.8802 (ttp) outliers start: 82 outliers final: 53 residues processed: 475 average time/residue: 0.8465 time to fit residues: 449.9212 Evaluate side-chains 477 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 405 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 294 GLN Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 307 MET Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain G residue 301 SER Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 301 SER Chi-restraints excluded: chain H residue 386 ASP Chi-restraints excluded: chain H residue 392 THR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 301 SER Chi-restraints excluded: chain I residue 386 ASP Chi-restraints excluded: chain I residue 388 ASN Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain J residue 253 ARG Chi-restraints excluded: chain J residue 261 LYS Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain K residue 148 SER Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 148 SER Chi-restraints excluded: chain L residue 248 ILE Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 321 ASP Chi-restraints excluded: chain L residue 383 SER Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 148 SER Chi-restraints excluded: chain M residue 256 THR Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 325 SER Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain N residue 126 ARG Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain N residue 148 SER Chi-restraints excluded: chain N residue 264 ILE Chi-restraints excluded: chain N residue 388 ASN Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 148 SER Chi-restraints excluded: chain O residue 161 ASP Chi-restraints excluded: chain O residue 264 ILE Chi-restraints excluded: chain O residue 294 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 319 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 309 optimal weight: 2.9990 chunk 282 optimal weight: 9.9990 chunk 247 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 225 optimal weight: 0.9980 chunk 133 optimal weight: 0.3980 chunk 180 optimal weight: 8.9990 chunk 315 optimal weight: 0.0470 chunk 101 optimal weight: 9.9990 overall best weight: 1.4882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 141 ASN C 336 GLN D 336 GLN ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 ASN ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 141 ASN K 141 ASN ** K 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 141 ASN N 141 ASN N 336 GLN O 336 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.144998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.115764 restraints weight = 28296.121| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.44 r_work: 0.3112 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27420 Z= 0.130 Angle : 0.509 7.529 37395 Z= 0.259 Chirality : 0.046 0.186 4920 Planarity : 0.004 0.037 4530 Dihedral : 7.435 80.624 5792 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.83 % Allowed : 23.64 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.15), residues: 3285 helix: 0.38 (0.34), residues: 255 sheet: -0.23 (0.11), residues: 2235 loop : 0.12 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 126 TYR 0.019 0.002 TYR L 394 PHE 0.008 0.001 PHE A 194 HIS 0.002 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00292 (27420) covalent geometry : angle 0.50853 (37395) hydrogen bonds : bond 0.02589 ( 1065) hydrogen bonds : angle 5.20025 ( 3015) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10575.40 seconds wall clock time: 180 minutes 6.15 seconds (10806.15 seconds total)