Starting phenix.real_space_refine on Sun Jul 5 08:56:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ofh_12874/07_2026/7ofh_12874.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ofh_12874/07_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_12874/07_2026/7ofh_12874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ofh_12874/07_2026/7ofh_12874.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ofh_12874/07_2026/7ofh_12874.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ofh_12874/07_2026/7ofh_12874.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ofh_12874/07_2026/7ofh_12874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ofh_12874/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 12 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: 12 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: 12 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: 12 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: 12 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: 12 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: 12 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: 12 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: 12 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: 12 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: 12 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: 12 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: 12 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: 12 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: 12 Planarities with less than four sites: {'CPS:plan-1': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 5.94, per 1000 atoms: 0.22 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: 2.84 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: 0.62 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: 4.41 Time building geometry restraints manager: 3.20 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: 14910 21.18 - 42.36: 997 42.36 - 63.54: 353 63.54 - 84.73: 30 84.73 - 105.91: 15 Dihedral angle restraints: 16305 sinusoidal: 6390 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 16302 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: 0.08 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.970 Find NCS groups from input model: 0.720 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: 0.000 Load rotamer database and sin/cos tables:9.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 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 : 16.726 105.907 9795 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/Z covalent geometry : bond 0.01044 / 0.68 (27420) covalent geometry : angle 1.59675 / 1.02 (37395) hydrogen bonds : bond 0.21186 / 14.21 ( 1065) hydrogen bonds : angle 9.01562 / 6.19 ( 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 : 0.789 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: 0.5299 time to fit residues: 616.1337 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 : 0.841 ------------------------------------------------------------------------------- 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... 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 = 0.150291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.120271 restraints weight = 27689.050| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.46 r_work: 0.3184 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 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= 0.139 Angle : 0.605 7.462 37395 Z= 0.309 Chirality : 0.048 0.226 4920 Planarity : 0.005 0.045 4530 Dihedral : 10.441 104.768 3818 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.67 % Allowed : 16.94 % Favored : 79.38 % 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: -1.85 (0.25), residues: 345 sheet: -1.67 (0.10), residues: 2235 loop : -1.06 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 126 TYR 0.016 0.002 TYR N 359 PHE 0.021 0.002 PHE H 194 HIS 0.002 0.001 HIS L 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (27420) covalent geometry : angle 0.60546 / 0.31 (37395) hydrogen bonds : bond 0.03068 / 2.05 ( 1065) hydrogen bonds : angle 6.05012 / 4.16 ( 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 672 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 559 time to evaluate : 1.094 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: 0.8594 (mtmt) REVERT: A 261 LYS cc_start: 0.9034 (mttp) cc_final: 0.8673 (mmmt) REVERT: A 388 ASN cc_start: 0.8211 (t0) cc_final: 0.7936 (t0) REVERT: B 364 GLN cc_start: 0.7118 (tt0) cc_final: 0.6676 (tm-30) REVERT: B 388 ASN cc_start: 0.8217 (t0) cc_final: 0.8016 (t0) REVERT: C 115 LYS cc_start: 0.8861 (mttt) cc_final: 0.8565 (mtmm) REVERT: D 261 LYS cc_start: 0.8897 (mttp) cc_final: 0.8572 (mmmt) REVERT: D 364 GLN cc_start: 0.7004 (tt0) cc_final: 0.6641 (tm-30) REVERT: E 115 LYS cc_start: 0.8828 (mttt) cc_final: 0.8596 (mtmt) REVERT: E 133 LYS cc_start: 0.7191 (tttt) cc_final: 0.6709 (tppt) REVERT: E 261 LYS cc_start: 0.9051 (mttp) cc_final: 0.8763 (mmmt) REVERT: E 392 THR cc_start: 0.8927 (t) cc_final: 0.8642 (m) REVERT: F 261 LYS cc_start: 0.8896 (mttp) cc_final: 0.8627 (mmmt) REVERT: F 307 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.8045 (mmt) REVERT: F 364 GLN cc_start: 0.7270 (tt0) cc_final: 0.6619 (tm-30) REVERT: F 400 THR cc_start: 0.8856 (m) cc_final: 0.8387 (p) REVERT: G 261 LYS cc_start: 0.9022 (mmtm) cc_final: 0.8807 (mmtt) REVERT: G 321 ASP cc_start: 0.8595 (m-30) cc_final: 0.8376 (m-30) REVERT: G 346 ARG cc_start: 0.7767 (mtt180) cc_final: 0.7534 (ttm170) REVERT: H 133 LYS cc_start: 0.7509 (tttt) cc_final: 0.7220 (ttmm) REVERT: H 364 GLN cc_start: 0.7368 (tt0) cc_final: 0.6810 (tm-30) REVERT: H 389 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7353 (mt-10) REVERT: I 115 LYS cc_start: 0.8596 (mttt) cc_final: 0.8393 (mtmm) REVERT: I 126 ARG cc_start: 0.8149 (mmm-85) cc_final: 0.7883 (mmm-85) REVERT: I 133 LYS cc_start: 0.7304 (tttt) cc_final: 0.6800 (tppt) REVERT: I 261 LYS cc_start: 0.9040 (mmtm) cc_final: 0.8700 (mmtp) REVERT: I 389 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7461 (mt-10) REVERT: J 133 LYS cc_start: 0.7357 (tttt) cc_final: 0.6693 (tppt) REVERT: J 300 MET cc_start: 0.9348 (ttp) cc_final: 0.9065 (ttm) REVERT: K 115 LYS cc_start: 0.8765 (mttt) cc_final: 0.8463 (mtmm) REVERT: L 238 ARG cc_start: 0.6840 (mtt90) cc_final: 0.6498 (mpt180) REVERT: L 307 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7513 (mtt) REVERT: L 344 ASN cc_start: 0.8903 (OUTLIER) cc_final: 0.8638 (t0) REVERT: L 392 THR cc_start: 0.9044 (t) cc_final: 0.8840 (m) REVERT: M 115 LYS cc_start: 0.8795 (mttt) cc_final: 0.8500 (mtmm) REVERT: M 238 ARG cc_start: 0.6774 (mtt90) cc_final: 0.6528 (mpt180) REVERT: M 253 ARG cc_start: 0.8587 (mtp180) cc_final: 0.8212 (mtt90) REVERT: M 300 MET cc_start: 0.9321 (ttp) cc_final: 0.8783 (ttm) REVERT: M 360 LYS cc_start: 0.8003 (tttt) cc_final: 0.7788 (mptp) REVERT: N 300 MET cc_start: 0.9374 (ttp) cc_final: 0.9075 (ttm) REVERT: N 328 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8066 (tt0) REVERT: N 388 ASN cc_start: 0.8317 (OUTLIER) cc_final: 0.8015 (t0) REVERT: O 133 LYS cc_start: 0.7352 (tttt) cc_final: 0.6874 (tppt) REVERT: O 161 ASP cc_start: 0.7411 (m-30) cc_final: 0.7190 (m-30) REVERT: O 261 LYS cc_start: 0.9000 (mttp) cc_final: 0.8742 (mmtt) REVERT: O 292 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7718 (pp20) REVERT: O 389 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7378 (mt-10) outliers start: 113 outliers final: 36 residues processed: 634 average time/residue: 0.5249 time to fit residues: 379.7934 Evaluate side-chains 509 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 468 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 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 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 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 Chi-restraints excluded: chain O residue 386 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 249 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 267 optimal weight: 3.9990 chunk 250 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 157 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 328 GLN J 336 GLN K 141 ASN K 328 GLN ** K 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 311 ASN ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 344 ASN 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 = 0.3629 r_free = 0.3629 target = 0.145520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.115448 restraints weight = 27899.260| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.45 r_work: 0.3119 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 27420 Z= 0.192 Angle : 0.614 7.887 37395 Z= 0.312 Chirality : 0.048 0.204 4920 Planarity : 0.005 0.039 4530 Dihedral : 8.887 92.083 3752 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.26 % Allowed : 19.35 % Favored : 76.39 % 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 (0.15), residues: 3285 helix: -0.95 (0.35), residues: 255 sheet: -1.06 (0.11), residues: 2160 loop : -0.56 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 337 TYR 0.017 0.003 TYR N 359 PHE 0.017 0.002 PHE H 194 HIS 0.003 0.001 HIS L 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (27420) covalent geometry : angle 0.61376 / 0.31 (37395) hydrogen bonds : bond 0.03179 / 2.14 ( 1065) hydrogen bonds : angle 5.74912 / 3.97 ( 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 578 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 447 time to evaluate : 1.329 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: 0.8985 (mttp) cc_final: 0.8584 (mmmt) REVERT: A 307 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7841 (mmt) REVERT: A 364 GLN cc_start: 0.7127 (tt0) cc_final: 0.6823 (tm-30) REVERT: A 388 ASN cc_start: 0.8166 (t0) cc_final: 0.7961 (t0) REVERT: B 133 LYS cc_start: 0.7346 (tttt) cc_final: 0.7070 (tttp) REVERT: B 253 ARG cc_start: 0.8737 (mtp180) cc_final: 0.8284 (mtp85) REVERT: B 364 GLN cc_start: 0.7162 (tt0) cc_final: 0.6784 (tm-30) REVERT: C 364 GLN cc_start: 0.7057 (tt0) cc_final: 0.6709 (tm-30) REVERT: D 126 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7867 (mmt180) REVERT: D 261 LYS cc_start: 0.8923 (mttp) cc_final: 0.8562 (mmmt) REVERT: D 364 GLN cc_start: 0.6998 (tt0) cc_final: 0.6737 (tm-30) REVERT: E 133 LYS cc_start: 0.7350 (tttt) cc_final: 0.6924 (tppt) REVERT: E 261 LYS cc_start: 0.8953 (mttp) cc_final: 0.8649 (mmmt) REVERT: E 319 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8712 (mtpt) REVERT: G 364 GLN cc_start: 0.7287 (tt0) cc_final: 0.6741 (tm-30) REVERT: H 364 GLN cc_start: 0.7290 (tt0) cc_final: 0.6792 (tm-30) REVERT: I 115 LYS cc_start: 0.8637 (mttt) cc_final: 0.8418 (mtmm) REVERT: I 126 ARG cc_start: 0.8189 (mmm-85) cc_final: 0.7949 (mmm-85) REVERT: I 261 LYS cc_start: 0.9059 (mmtm) cc_final: 0.8805 (mmtp) REVERT: I 364 GLN cc_start: 0.7061 (tt0) cc_final: 0.6664 (tm-30) REVERT: I 389 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7509 (mt-10) REVERT: J 133 LYS cc_start: 0.7389 (tttt) cc_final: 0.6788 (tppt) REVERT: J 261 LYS cc_start: 0.9015 (mmmt) cc_final: 0.8702 (mmmt) REVERT: J 300 MET cc_start: 0.9288 (ttp) cc_final: 0.9008 (ttm) REVERT: K 115 LYS cc_start: 0.8789 (mttt) cc_final: 0.8485 (mtmm) REVERT: K 133 LYS cc_start: 0.7838 (ttpp) cc_final: 0.7392 (ttmm) REVERT: K 245 HIS cc_start: 0.7660 (t70) cc_final: 0.7438 (t70) REVERT: K 300 MET cc_start: 0.9273 (ttp) cc_final: 0.9004 (ttm) REVERT: L 248 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8687 (mm) REVERT: L 307 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7631 (mtt) REVERT: L 344 ASN cc_start: 0.8822 (OUTLIER) cc_final: 0.8558 (t0) REVERT: L 364 GLN cc_start: 0.7121 (tt0) cc_final: 0.6781 (tm-30) REVERT: M 115 LYS cc_start: 0.8738 (mttt) cc_final: 0.8423 (mtmm) REVERT: M 180 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7921 (mt-10) REVERT: M 238 ARG cc_start: 0.6646 (mtt90) cc_final: 0.6418 (mpt180) REVERT: M 253 ARG cc_start: 0.8579 (mtp180) cc_final: 0.8206 (mtt90) REVERT: M 300 MET cc_start: 0.9309 (ttp) cc_final: 0.8834 (ttm) REVERT: N 300 MET cc_start: 0.9338 (ttp) cc_final: 0.9057 (ttm) REVERT: N 388 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.8020 (t0) REVERT: O 133 LYS cc_start: 0.7403 (tttt) cc_final: 0.6930 (tppt) REVERT: O 261 LYS cc_start: 0.8965 (mttp) cc_final: 0.8679 (mmtt) REVERT: O 292 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7755 (pp20) REVERT: O 300 MET cc_start: 0.9254 (ttp) cc_final: 0.8993 (ttp) REVERT: O 358 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7783 (m-30) outliers start: 131 outliers final: 62 residues processed: 538 average time/residue: 0.7878 time to fit residues: 480.8087 Evaluate side-chains 505 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 434 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 307 MET Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain D residue 126 ARG 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 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 148 SER 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 319 LYS 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 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 344 ASN 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 180 GLU 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 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 358 ASP Chi-restraints excluded: chain O residue 386 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 338 optimal weight: 7.9990 chunk 179 optimal weight: 0.7980 chunk 288 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 175 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 289 optimal weight: 0.6980 chunk 308 optimal weight: 10.0000 chunk 236 optimal weight: 0.2980 chunk 12 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** I 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 141 ASN J 328 GLN J 336 GLN K 141 ASN K 336 GLN L 165 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.147724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.117826 restraints weight = 27829.722| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.45 r_work: 0.3136 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 27420 Z= 0.122 Angle : 0.510 7.374 37395 Z= 0.260 Chirality : 0.046 0.187 4920 Planarity : 0.005 0.040 4530 Dihedral : 7.747 83.089 3752 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.90 % Allowed : 21.04 % Favored : 75.06 % 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: -1.13 (0.15), residues: 3285 helix: -0.76 (0.35), residues: 255 sheet: -0.68 (0.11), residues: 2265 loop : -0.27 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 253 TYR 0.016 0.002 TYR L 394 PHE 0.012 0.001 PHE J 194 HIS 0.001 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (27420) covalent geometry : angle 0.51026 / 0.26 (37395) hydrogen bonds : bond 0.02599 / 1.74 ( 1065) hydrogen bonds : angle 5.39462 / 3.72 ( 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 547 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 427 time to evaluate : 1.071 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 133 LYS cc_start: 0.7623 (tttp) cc_final: 0.6876 (tppt) REVERT: A 261 LYS cc_start: 0.8989 (mttp) cc_final: 0.8571 (mmtt) REVERT: A 300 MET cc_start: 0.9310 (ttp) cc_final: 0.9030 (ttp) REVERT: A 307 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7757 (mmt) REVERT: B 133 LYS cc_start: 0.7262 (tttt) cc_final: 0.6946 (tttp) REVERT: B 248 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8556 (mm) REVERT: B 253 ARG cc_start: 0.8721 (mtp180) cc_final: 0.8293 (mtt90) REVERT: B 364 GLN cc_start: 0.7178 (tt0) cc_final: 0.6751 (tm-30) REVERT: C 115 LYS cc_start: 0.8762 (mttp) cc_final: 0.8455 (mtmm) REVERT: C 248 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8612 (mm) REVERT: C 253 ARG cc_start: 0.8745 (mtm180) cc_final: 0.8416 (mtt90) REVERT: C 319 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8742 (mtpt) REVERT: C 364 GLN cc_start: 0.7121 (tt0) cc_final: 0.6675 (tm-30) REVERT: D 364 GLN cc_start: 0.7087 (tt0) cc_final: 0.6721 (tm-30) REVERT: E 133 LYS cc_start: 0.7279 (tttt) cc_final: 0.6906 (tppt) REVERT: E 148 SER cc_start: 0.8657 (OUTLIER) cc_final: 0.8446 (m) REVERT: E 261 LYS cc_start: 0.8961 (mttp) cc_final: 0.8662 (mmmt) REVERT: E 389 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7330 (mt-10) REVERT: E 392 THR cc_start: 0.9064 (t) cc_final: 0.8763 (m) REVERT: F 307 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7950 (mmt) REVERT: F 364 GLN cc_start: 0.7273 (tt0) cc_final: 0.6678 (tm-30) REVERT: G 248 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8752 (mm) REVERT: G 261 LYS cc_start: 0.9009 (mmtm) cc_final: 0.8794 (mmtt) REVERT: G 392 THR cc_start: 0.9083 (t) cc_final: 0.8856 (m) REVERT: H 133 LYS cc_start: 0.7776 (ttmm) cc_final: 0.7135 (tppt) REVERT: H 389 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7453 (mt-10) REVERT: I 115 LYS cc_start: 0.8619 (mttt) cc_final: 0.8413 (mtmm) REVERT: I 126 ARG cc_start: 0.8219 (mmm-85) cc_final: 0.8000 (mmm-85) REVERT: I 261 LYS cc_start: 0.9113 (mmtm) cc_final: 0.8859 (mmtp) REVERT: I 364 GLN cc_start: 0.7137 (tt0) cc_final: 0.6705 (tm-30) REVERT: I 389 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7529 (mt-10) REVERT: J 133 LYS cc_start: 0.7280 (tttt) cc_final: 0.6657 (tppt) REVERT: J 253 ARG cc_start: 0.8621 (mtm-85) cc_final: 0.8417 (mtm-85) REVERT: J 261 LYS cc_start: 0.9110 (mmmt) cc_final: 0.8828 (mmmt) REVERT: J 300 MET cc_start: 0.9316 (ttp) cc_final: 0.9019 (ttm) REVERT: J 319 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8800 (mtpt) REVERT: K 115 LYS cc_start: 0.8827 (mttt) cc_final: 0.8513 (mtmm) REVERT: K 133 LYS cc_start: 0.7810 (ttpp) cc_final: 0.7400 (ttmm) REVERT: K 300 MET cc_start: 0.9264 (ttp) cc_final: 0.9055 (ttm) REVERT: L 133 LYS cc_start: 0.7622 (tttm) cc_final: 0.7006 (tppt) REVERT: L 364 GLN cc_start: 0.7201 (tt0) cc_final: 0.6749 (tm-30) REVERT: M 115 LYS cc_start: 0.8799 (mttt) cc_final: 0.8481 (mtmm) REVERT: M 238 ARG cc_start: 0.6668 (mtt90) cc_final: 0.6456 (mpt180) REVERT: M 253 ARG cc_start: 0.8606 (mtp180) cc_final: 0.8255 (mtt90) REVERT: M 300 MET cc_start: 0.9298 (ttp) cc_final: 0.8786 (ttm) REVERT: M 319 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8406 (mtpt) REVERT: M 358 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.8027 (m-30) REVERT: N 264 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8922 (tt) REVERT: N 300 MET cc_start: 0.9337 (ttp) cc_final: 0.9048 (ttm) REVERT: N 388 ASN cc_start: 0.8269 (OUTLIER) cc_final: 0.7959 (t0) REVERT: O 133 LYS cc_start: 0.7440 (tttt) cc_final: 0.7003 (tppt) REVERT: O 261 LYS cc_start: 0.8948 (mttp) cc_final: 0.8659 (mmtt) REVERT: O 292 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7764 (pp20) REVERT: O 300 MET cc_start: 0.9240 (ttp) cc_final: 0.8911 (ttp) outliers start: 120 outliers final: 55 residues processed: 519 average time/residue: 0.8082 time to fit residues: 474.7022 Evaluate side-chains 479 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 412 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 248 ILE 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 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 392 THR 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 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 307 MET Chi-restraints excluded: chain F residue 319 LYS Chi-restraints excluded: chain F residue 386 ASP 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 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 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 319 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 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 180 GLU Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 321 ASP 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 325 SER Chi-restraints excluded: chain M residue 358 ASP 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 264 ILE Chi-restraints excluded: chain N residue 294 GLN 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: 5.9990 chunk 252 optimal weight: 7.9990 chunk 317 optimal weight: 6.9990 chunk 298 optimal weight: 1.9990 chunk 329 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 234 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 183 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN E 165 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 187 GLN H 328 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 ** both conformations clash, **PLEASE CHECK MANUALLY** L 165 GLN L 311 ASN ** 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 = 0.3580 r_free = 0.3580 target = 0.141570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.111933 restraints weight = 28820.812| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.47 r_work: 0.3068 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 27420 Z= 0.222 Angle : 0.605 7.280 37395 Z= 0.307 Chirality : 0.048 0.157 4920 Planarity : 0.005 0.041 4530 Dihedral : 8.298 84.935 3752 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.78 % Allowed : 20.49 % 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: -1.01 (0.15), residues: 3285 helix: -0.51 (0.35), residues: 255 sheet: -0.64 (0.11), residues: 2130 loop : -0.26 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 293 TYR 0.018 0.003 TYR F 394 PHE 0.011 0.002 PHE L 194 HIS 0.003 0.001 HIS D 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 (27420) covalent geometry : angle 0.60471 / 0.31 (37395) hydrogen bonds : bond 0.03118 / 2.10 ( 1065) hydrogen bonds : angle 5.57528 / 3.85 ( 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 595 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 448 time to evaluate : 0.936 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: 0.7690 (tttp) cc_final: 0.6937 (tppt) REVERT: A 261 LYS cc_start: 0.9003 (mttp) cc_final: 0.8600 (mmmt) REVERT: A 307 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7868 (mmt) REVERT: B 133 LYS cc_start: 0.7297 (tttt) cc_final: 0.6988 (tttp) REVERT: B 248 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8688 (mm) REVERT: B 253 ARG cc_start: 0.8733 (mtp180) cc_final: 0.8261 (mtp85) REVERT: B 364 GLN cc_start: 0.7207 (tt0) cc_final: 0.6698 (tm-30) REVERT: C 122 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8525 (pttp) REVERT: C 248 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8724 (mm) REVERT: C 364 GLN cc_start: 0.7298 (tt0) cc_final: 0.6808 (tm-30) REVERT: D 182 LEU cc_start: 0.8569 (tt) cc_final: 0.8279 (tm) REVERT: D 360 LYS cc_start: 0.7583 (mttt) cc_final: 0.7353 (mptp) REVERT: D 364 GLN cc_start: 0.6988 (tt0) cc_final: 0.6575 (tm-30) REVERT: E 133 LYS cc_start: 0.7348 (tttt) cc_final: 0.6942 (tppt) REVERT: E 261 LYS cc_start: 0.8999 (mttp) cc_final: 0.8681 (mmmt) REVERT: E 389 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7269 (mt-10) REVERT: F 264 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8836 (tt) REVERT: F 315 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8195 (t70) REVERT: G 248 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8762 (mm) REVERT: G 261 LYS cc_start: 0.9012 (mmtm) cc_final: 0.8752 (mmtt) REVERT: G 360 LYS cc_start: 0.7974 (mtpt) cc_final: 0.7376 (mptp) REVERT: G 364 GLN cc_start: 0.7300 (tt0) cc_final: 0.6690 (tm-30) REVERT: G 392 THR cc_start: 0.9149 (t) cc_final: 0.8893 (m) REVERT: H 133 LYS cc_start: 0.7697 (ttmm) cc_final: 0.7129 (tppt) REVERT: H 364 GLN cc_start: 0.7303 (tt0) cc_final: 0.6713 (tm-30) REVERT: H 389 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7532 (mt-10) REVERT: I 115 LYS cc_start: 0.8624 (mttt) cc_final: 0.8404 (mtmm) REVERT: I 126 ARG cc_start: 0.8223 (mmm-85) cc_final: 0.7930 (mmm-85) REVERT: I 248 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8495 (mm) REVERT: I 261 LYS cc_start: 0.9111 (mmtm) cc_final: 0.8786 (mmtp) REVERT: I 364 GLN cc_start: 0.7255 (tt0) cc_final: 0.6698 (tm-30) REVERT: J 133 LYS cc_start: 0.7336 (tttt) cc_final: 0.6777 (tppt) REVERT: J 261 LYS cc_start: 0.9082 (mmmt) cc_final: 0.8742 (mmmt) REVERT: J 300 MET cc_start: 0.9255 (ttp) cc_final: 0.8993 (ttm) REVERT: K 115 LYS cc_start: 0.8804 (mttt) cc_final: 0.8463 (mtmm) REVERT: K 133 LYS cc_start: 0.7821 (ttpp) cc_final: 0.7359 (ttmm) REVERT: K 261 LYS cc_start: 0.8955 (mmtp) cc_final: 0.8627 (mptm) REVERT: K 300 MET cc_start: 0.9276 (ttp) cc_final: 0.9040 (ttm) REVERT: K 346 ARG cc_start: 0.7829 (mtt180) cc_final: 0.7574 (ttm110) REVERT: L 126 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.8059 (mtp180) REVERT: L 240 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7165 (tt) REVERT: L 248 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8753 (mm) REVERT: L 364 GLN cc_start: 0.7242 (tt0) cc_final: 0.6706 (tm-30) REVERT: M 115 LYS cc_start: 0.8712 (mttt) cc_final: 0.8411 (mtmt) REVERT: M 253 ARG cc_start: 0.8615 (mtp180) cc_final: 0.8206 (mtt90) REVERT: M 300 MET cc_start: 0.9301 (ttp) cc_final: 0.8825 (ttm) REVERT: M 358 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.8044 (m-30) REVERT: N 126 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7211 (mmp-170) REVERT: N 264 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8937 (tt) REVERT: N 300 MET cc_start: 0.9337 (ttp) cc_final: 0.9087 (ttm) REVERT: N 388 ASN cc_start: 0.8431 (OUTLIER) cc_final: 0.8060 (t0) REVERT: O 133 LYS cc_start: 0.7460 (tttt) cc_final: 0.7013 (tppt) REVERT: O 261 LYS cc_start: 0.8940 (mttp) cc_final: 0.8642 (mmtt) REVERT: O 292 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7886 (pp20) REVERT: O 300 MET cc_start: 0.9262 (ttp) cc_final: 0.8901 (ttp) REVERT: O 358 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.7993 (m-30) REVERT: O 364 GLN cc_start: 0.7237 (tt0) cc_final: 0.6647 (tm-30) outliers start: 147 outliers final: 67 residues processed: 557 average time/residue: 0.7380 time to fit residues: 466.2624 Evaluate side-chains 512 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 429 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 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 248 ILE 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 148 SER 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 E residue 110 VAL 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 133 LYS 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 315 ASP Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 386 ASP 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 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 319 LYS 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 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 126 ARG Chi-restraints excluded: chain L residue 148 SER Chi-restraints excluded: chain L residue 240 LEU 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 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 386 ASP 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 294 GLN 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 358 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 234 optimal weight: 0.8980 chunk 226 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 237 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 286 optimal weight: 0.9980 chunk 204 optimal weight: 0.7980 chunk 14 optimal weight: 0.2980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 GLN B 141 ASN 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 J 141 ASN K 141 ASN K 336 GLN L 336 GLN M 141 ASN M 243 ASN N 141 ASN N 336 GLN O 336 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.145811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.116403 restraints weight = 28415.712| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.45 r_work: 0.3149 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 27420 Z= 0.105 Angle : 0.484 7.439 37395 Z= 0.248 Chirality : 0.045 0.176 4920 Planarity : 0.004 0.039 4530 Dihedral : 7.645 80.244 3752 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.71 % Allowed : 22.08 % Favored : 74.21 % 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: -0.70 (0.15), residues: 3285 helix: -0.13 (0.34), residues: 255 sheet: -0.45 (0.11), residues: 2235 loop : -0.03 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 253 TYR 0.016 0.002 TYR F 394 PHE 0.009 0.001 PHE J 194 HIS 0.001 0.000 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (27420) covalent geometry : angle 0.48391 / 0.25 (37395) hydrogen bonds : bond 0.02439 / 1.64 ( 1065) hydrogen bonds : angle 5.24000 / 3.62 ( 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 547 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 433 time to evaluate : 1.085 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: 0.7515 (tttp) cc_final: 0.6887 (tppt) REVERT: A 307 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7710 (mmt) REVERT: B 133 LYS cc_start: 0.7124 (tttt) cc_final: 0.6659 (tppt) REVERT: B 253 ARG cc_start: 0.8663 (mtp180) cc_final: 0.8255 (mtt90) REVERT: B 364 GLN cc_start: 0.7134 (tt0) cc_final: 0.6753 (tm-30) REVERT: C 115 LYS cc_start: 0.8769 (mttp) cc_final: 0.8433 (mtmm) REVERT: C 253 ARG cc_start: 0.8622 (mtm180) cc_final: 0.8338 (mtt90) REVERT: C 364 GLN cc_start: 0.7253 (tt0) cc_final: 0.6842 (tm-30) REVERT: D 182 LEU cc_start: 0.8460 (tt) cc_final: 0.8218 (tm) REVERT: D 364 GLN cc_start: 0.6915 (tt0) cc_final: 0.6617 (tm-30) REVERT: E 126 ARG cc_start: 0.8337 (mtp180) cc_final: 0.7894 (mtp-110) REVERT: E 133 LYS cc_start: 0.7189 (tttt) cc_final: 0.6921 (tppt) REVERT: E 261 LYS cc_start: 0.8963 (mttp) cc_final: 0.8650 (mmmt) REVERT: E 389 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7327 (mt-10) REVERT: E 392 THR cc_start: 0.9075 (t) cc_final: 0.8850 (m) REVERT: F 141 ASN cc_start: 0.8359 (m-40) cc_final: 0.8134 (m110) REVERT: F 307 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7856 (mmt) REVERT: G 122 LYS cc_start: 0.8648 (pttm) cc_final: 0.8355 (pttm) REVERT: G 248 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8691 (mm) REVERT: G 253 ARG cc_start: 0.8574 (mtm180) cc_final: 0.8180 (mtt90) REVERT: G 261 LYS cc_start: 0.8952 (mmtm) cc_final: 0.8733 (mmtt) REVERT: G 336 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8804 (tm-30) REVERT: G 360 LYS cc_start: 0.7784 (mtpt) cc_final: 0.7255 (mptp) REVERT: G 392 THR cc_start: 0.9122 (t) cc_final: 0.8862 (m) REVERT: H 133 LYS cc_start: 0.7644 (ttmm) cc_final: 0.7052 (tppt) REVERT: I 115 LYS cc_start: 0.8583 (mttt) cc_final: 0.8377 (mtmm) REVERT: I 248 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8420 (mm) REVERT: I 261 LYS cc_start: 0.9099 (mmtm) cc_final: 0.8804 (mmtp) REVERT: J 133 LYS cc_start: 0.7137 (tttt) cc_final: 0.6735 (tppt) REVERT: J 261 LYS cc_start: 0.9004 (mmmt) cc_final: 0.8703 (mmmt) REVERT: J 300 MET cc_start: 0.9244 (ttp) cc_final: 0.8965 (ttm) REVERT: K 115 LYS cc_start: 0.8790 (mttt) cc_final: 0.8482 (mtmm) REVERT: K 133 LYS cc_start: 0.7795 (ttpp) cc_final: 0.7422 (ttmm) REVERT: K 300 MET cc_start: 0.9238 (ttp) cc_final: 0.9012 (ttm) REVERT: L 133 LYS cc_start: 0.7556 (tttm) cc_final: 0.6987 (tppt) REVERT: L 307 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7567 (mtt) REVERT: L 364 GLN cc_start: 0.7231 (tt0) cc_final: 0.6760 (tm-30) REVERT: M 253 ARG cc_start: 0.8540 (mtp180) cc_final: 0.8175 (mtt90) REVERT: M 300 MET cc_start: 0.9265 (ttp) cc_final: 0.8762 (ttm) REVERT: M 319 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8384 (mtpt) REVERT: N 264 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8893 (tt) REVERT: N 300 MET cc_start: 0.9303 (ttp) cc_final: 0.9029 (ttm) REVERT: N 358 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.8004 (m-30) REVERT: N 388 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.7950 (t0) REVERT: O 133 LYS cc_start: 0.7343 (tttt) cc_final: 0.7042 (tppt) REVERT: O 261 LYS cc_start: 0.8927 (mttp) cc_final: 0.8626 (mmtt) REVERT: O 292 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7821 (pp20) REVERT: O 300 MET cc_start: 0.9251 (ttp) cc_final: 0.8875 (ttp) REVERT: O 358 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.7971 (m-30) outliers start: 114 outliers final: 50 residues processed: 521 average time/residue: 0.7576 time to fit residues: 447.3386 Evaluate side-chains 471 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 410 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 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 392 THR 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 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 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 G residue 336 GLN Chi-restraints excluded: chain G residue 386 ASP Chi-restraints excluded: chain H residue 115 LYS Chi-restraints excluded: chain H residue 256 THR 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 301 SER Chi-restraints excluded: chain I residue 386 ASP 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 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 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 319 LYS Chi-restraints excluded: chain M residue 325 SER 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 171 ASP 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 358 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 338 optimal weight: 0.4980 chunk 248 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 234 optimal weight: 1.9990 chunk 341 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 294 optimal weight: 2.9990 chunk 219 optimal weight: 6.9990 chunk 306 optimal weight: 2.9990 chunk 195 optimal weight: 8.9990 chunk 330 optimal weight: 0.0870 overall best weight: 1.5164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 GLN B 141 ASN B 187 GLN B 336 GLN C 336 GLN D 336 GLN ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN G 336 GLN H 187 GLN ** 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.145195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.115828 restraints weight = 28197.591| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.43 r_work: 0.3115 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 27420 Z= 0.129 Angle : 0.506 7.413 37395 Z= 0.257 Chirality : 0.045 0.165 4920 Planarity : 0.004 0.037 4530 Dihedral : 7.610 77.207 3752 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.90 % Allowed : 22.11 % Favored : 73.98 % 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: 0.06 (0.34), residues: 255 sheet: -0.36 (0.11), residues: 2130 loop : -0.13 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 126 TYR 0.019 0.002 TYR L 394 PHE 0.008 0.001 PHE I 194 HIS 0.002 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (27420) covalent geometry : angle 0.50584 / 0.26 (37395) hydrogen bonds : bond 0.02576 / 1.73 ( 1065) hydrogen bonds : angle 5.21369 / 3.60 ( 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 541 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 421 time to evaluate : 1.234 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: 0.8806 (mtpp) cc_final: 0.8586 (mtmt) REVERT: A 133 LYS cc_start: 0.7560 (tttp) cc_final: 0.6885 (tppt) REVERT: A 307 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7747 (mmt) REVERT: B 133 LYS cc_start: 0.7198 (tttt) cc_final: 0.6882 (tttp) REVERT: B 253 ARG cc_start: 0.8673 (mtp180) cc_final: 0.8246 (mtt90) REVERT: B 364 GLN cc_start: 0.7157 (tt0) cc_final: 0.6715 (tm-30) REVERT: C 115 LYS cc_start: 0.8793 (mttp) cc_final: 0.8437 (mtmm) REVERT: C 253 ARG cc_start: 0.8677 (mtm180) cc_final: 0.8374 (mtt90) REVERT: C 364 GLN cc_start: 0.7313 (tt0) cc_final: 0.6803 (tm-30) REVERT: D 248 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8775 (mm) REVERT: D 253 ARG cc_start: 0.8602 (mtm180) cc_final: 0.8306 (mtt90) REVERT: D 294 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8747 (tt0) REVERT: D 364 GLN cc_start: 0.7046 (tt0) cc_final: 0.6579 (tm-30) REVERT: E 133 LYS cc_start: 0.7221 (tttt) cc_final: 0.6931 (tppt) REVERT: E 261 LYS cc_start: 0.8941 (mttp) cc_final: 0.8635 (mmmt) REVERT: E 264 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8892 (tt) REVERT: E 389 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7346 (mt-10) REVERT: E 392 THR cc_start: 0.9069 (t) cc_final: 0.8831 (m) REVERT: F 115 LYS cc_start: 0.8847 (mtmt) cc_final: 0.8571 (mttt) REVERT: F 141 ASN cc_start: 0.8346 (m-40) cc_final: 0.8136 (m110) REVERT: F 264 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8738 (tt) REVERT: G 122 LYS cc_start: 0.8672 (pttm) cc_final: 0.8377 (pttm) REVERT: G 248 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8750 (mm) REVERT: G 253 ARG cc_start: 0.8643 (mtm180) cc_final: 0.8299 (mtt90) REVERT: G 261 LYS cc_start: 0.9002 (mmtm) cc_final: 0.8764 (mmtt) REVERT: G 336 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8759 (tm-30) REVERT: G 360 LYS cc_start: 0.7891 (mtpt) cc_final: 0.7349 (mptp) REVERT: G 364 GLN cc_start: 0.7374 (tt0) cc_final: 0.6748 (tm-30) REVERT: G 392 THR cc_start: 0.9139 (t) cc_final: 0.8862 (m) REVERT: H 133 LYS cc_start: 0.7644 (ttmm) cc_final: 0.7026 (tppt) REVERT: H 364 GLN cc_start: 0.7388 (tt0) cc_final: 0.6657 (tm-30) REVERT: H 388 ASN cc_start: 0.8095 (t0) cc_final: 0.7817 (m-40) REVERT: I 115 LYS cc_start: 0.8606 (mttt) cc_final: 0.8390 (mtmm) REVERT: I 248 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8467 (mm) REVERT: I 261 LYS cc_start: 0.9098 (mmtm) cc_final: 0.8784 (mmtp) REVERT: I 364 GLN cc_start: 0.7172 (tt0) cc_final: 0.6675 (tm-30) REVERT: J 133 LYS cc_start: 0.7221 (tttt) cc_final: 0.6713 (tppt) REVERT: J 261 LYS cc_start: 0.9047 (mmmt) cc_final: 0.8739 (mmmt) REVERT: K 115 LYS cc_start: 0.8809 (mttt) cc_final: 0.8485 (mtmm) REVERT: K 133 LYS cc_start: 0.7795 (ttpp) cc_final: 0.7416 (ttmm) REVERT: K 300 MET cc_start: 0.9235 (ttp) cc_final: 0.9025 (ttm) REVERT: L 133 LYS cc_start: 0.7532 (tttm) cc_final: 0.6955 (tppt) REVERT: L 248 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8680 (mm) REVERT: L 307 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7515 (mtt) REVERT: L 364 GLN cc_start: 0.7286 (tt0) cc_final: 0.6712 (tm-30) REVERT: M 253 ARG cc_start: 0.8600 (mtp180) cc_final: 0.8210 (mtt90) REVERT: M 300 MET cc_start: 0.9276 (ttp) cc_final: 0.8789 (ttm) REVERT: M 319 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8385 (mtpt) REVERT: M 388 ASN cc_start: 0.8332 (t0) cc_final: 0.8089 (m-40) REVERT: N 264 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8935 (tt) REVERT: N 300 MET cc_start: 0.9290 (ttp) cc_final: 0.8952 (ttm) REVERT: N 358 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7928 (m-30) REVERT: N 388 ASN cc_start: 0.8318 (OUTLIER) cc_final: 0.8032 (t0) REVERT: O 133 LYS cc_start: 0.7373 (tttt) cc_final: 0.7037 (tppt) REVERT: O 292 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7856 (pp20) REVERT: O 300 MET cc_start: 0.9244 (ttp) cc_final: 0.8876 (ttp) REVERT: O 358 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.8039 (m-30) outliers start: 120 outliers final: 62 residues processed: 514 average time/residue: 0.7360 time to fit residues: 428.6294 Evaluate side-chains 484 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 406 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 158 ASP 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 126 ARG 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 129 GLU Chi-restraints excluded: chain C residue 148 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 294 GLN 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 264 ILE Chi-restraints excluded: chain E residue 307 MET 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 F residue 383 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 G residue 336 GLN Chi-restraints excluded: chain G residue 386 ASP Chi-restraints excluded: chain H residue 115 LYS 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 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 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 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 319 LYS Chi-restraints excluded: chain M residue 325 SER Chi-restraints excluded: chain M residue 383 SER 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 264 ILE Chi-restraints excluded: chain N residue 294 GLN 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 292 GLU Chi-restraints excluded: chain O residue 344 ASN 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: 5.9990 chunk 151 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 245 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 143 optimal weight: 1.9990 chunk 47 optimal weight: 0.0970 chunk 176 optimal weight: 7.9990 chunk 315 optimal weight: 0.0040 overall best weight: 1.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 GLN B 336 GLN C 336 GLN D 336 GLN ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 336 GLN ** 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 = 0.3611 r_free = 0.3611 target = 0.144674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.115376 restraints weight = 28540.519| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.43 r_work: 0.3104 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27420 Z= 0.145 Angle : 0.518 7.394 37395 Z= 0.264 Chirality : 0.046 0.163 4920 Planarity : 0.005 0.037 4530 Dihedral : 7.716 78.681 3752 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.71 % Allowed : 21.82 % Favored : 74.47 % 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: -0.52 (0.15), residues: 3285 helix: 0.19 (0.34), residues: 255 sheet: -0.32 (0.11), residues: 2130 loop : -0.10 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 126 TYR 0.020 0.002 TYR F 394 PHE 0.008 0.001 PHE I 194 HIS 0.002 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (27420) covalent geometry : angle 0.51759 / 0.26 (37395) hydrogen bonds : bond 0.02662 / 1.78 ( 1065) hydrogen bonds : angle 5.23263 / 3.62 ( 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 536 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 422 time to evaluate : 0.942 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: 0.8792 (mtpp) cc_final: 0.8565 (mtmt) REVERT: A 133 LYS cc_start: 0.7619 (tttp) cc_final: 0.6942 (tppt) REVERT: A 307 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7780 (mmt) REVERT: B 133 LYS cc_start: 0.7206 (tttt) cc_final: 0.6878 (tttp) REVERT: B 253 ARG cc_start: 0.8666 (mtp180) cc_final: 0.8241 (mtt90) REVERT: B 364 GLN cc_start: 0.7170 (tt0) cc_final: 0.6728 (tm-30) REVERT: C 248 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8729 (mm) REVERT: C 364 GLN cc_start: 0.7337 (tt0) cc_final: 0.6792 (tm-30) REVERT: D 248 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8784 (mm) REVERT: D 253 ARG cc_start: 0.8644 (mtm180) cc_final: 0.8320 (mtt90) REVERT: D 294 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8757 (tt0) REVERT: D 364 GLN cc_start: 0.7051 (tt0) cc_final: 0.6576 (tm-30) REVERT: E 133 LYS cc_start: 0.7246 (tttt) cc_final: 0.6948 (tppt) REVERT: E 261 LYS cc_start: 0.8961 (mttp) cc_final: 0.8641 (mmmt) REVERT: E 264 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8901 (tt) REVERT: E 389 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7376 (mt-10) REVERT: E 392 THR cc_start: 0.9079 (t) cc_final: 0.8840 (m) REVERT: F 115 LYS cc_start: 0.8850 (mtmt) cc_final: 0.8566 (mttt) REVERT: F 126 ARG cc_start: 0.8251 (mtp180) cc_final: 0.7850 (mtm180) REVERT: F 264 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8795 (tt) REVERT: G 122 LYS cc_start: 0.8728 (pttm) cc_final: 0.8458 (pttm) REVERT: G 248 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8764 (mm) REVERT: G 253 ARG cc_start: 0.8689 (mtm180) cc_final: 0.8331 (mtt90) REVERT: G 261 LYS cc_start: 0.9012 (mmtm) cc_final: 0.8775 (mmtt) REVERT: G 360 LYS cc_start: 0.7887 (mtpt) cc_final: 0.7337 (mptp) REVERT: G 364 GLN cc_start: 0.7402 (tt0) cc_final: 0.6742 (tm-30) REVERT: G 392 THR cc_start: 0.9156 (t) cc_final: 0.8875 (m) REVERT: H 133 LYS cc_start: 0.7645 (ttmm) cc_final: 0.7044 (tppt) REVERT: H 364 GLN cc_start: 0.7320 (tt0) cc_final: 0.6610 (tm-30) REVERT: H 388 ASN cc_start: 0.8179 (t0) cc_final: 0.7880 (m-40) REVERT: I 115 LYS cc_start: 0.8604 (mttt) cc_final: 0.8389 (mtmm) REVERT: I 248 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8468 (mm) REVERT: I 261 LYS cc_start: 0.9099 (mmtm) cc_final: 0.8789 (mmtp) REVERT: I 364 GLN cc_start: 0.7184 (tt0) cc_final: 0.6689 (tm-30) REVERT: J 133 LYS cc_start: 0.7238 (tttt) cc_final: 0.6739 (tppt) REVERT: J 253 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8295 (mtp85) REVERT: J 261 LYS cc_start: 0.9057 (mmmt) cc_final: 0.8754 (mmmt) REVERT: K 115 LYS cc_start: 0.8814 (mttt) cc_final: 0.8491 (mtmm) REVERT: K 133 LYS cc_start: 0.7805 (ttpp) cc_final: 0.7419 (ttmm) REVERT: K 261 LYS cc_start: 0.8875 (mmtt) cc_final: 0.8533 (mptm) REVERT: K 300 MET cc_start: 0.9249 (ttp) cc_final: 0.9016 (ttm) REVERT: L 133 LYS cc_start: 0.7562 (tttm) cc_final: 0.6989 (tppt) REVERT: L 248 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8687 (mm) REVERT: L 307 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7538 (mtt) REVERT: L 364 GLN cc_start: 0.7274 (tt0) cc_final: 0.6711 (tm-30) REVERT: M 253 ARG cc_start: 0.8591 (mtp180) cc_final: 0.8181 (mtt90) REVERT: M 264 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8794 (tt) REVERT: M 300 MET cc_start: 0.9281 (ttp) cc_final: 0.8783 (ttm) REVERT: M 388 ASN cc_start: 0.8333 (t0) cc_final: 0.8081 (m-40) REVERT: N 126 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7187 (mmp-170) REVERT: N 264 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8940 (tt) REVERT: N 300 MET cc_start: 0.9292 (ttp) cc_final: 0.8949 (ttm) REVERT: N 358 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.8002 (m-30) REVERT: N 388 ASN cc_start: 0.8301 (OUTLIER) cc_final: 0.7983 (t0) REVERT: O 133 LYS cc_start: 0.7399 (tttt) cc_final: 0.7050 (tppt) REVERT: O 261 LYS cc_start: 0.8911 (mttm) cc_final: 0.8587 (mmtt) REVERT: O 264 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8804 (tt) REVERT: O 292 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7878 (pp20) REVERT: O 300 MET cc_start: 0.9243 (ttp) cc_final: 0.8760 (ttp) REVERT: O 358 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.7951 (m-30) outliers start: 114 outliers final: 68 residues processed: 503 average time/residue: 0.8168 time to fit residues: 464.0667 Evaluate side-chains 496 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 409 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 126 ARG 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 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 383 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 294 GLN 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 307 MET 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 F residue 383 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 G residue 325 SER Chi-restraints excluded: chain G residue 386 ASP Chi-restraints excluded: chain H residue 115 LYS 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 386 ASP 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 264 ILE Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 325 SER Chi-restraints excluded: chain M residue 383 SER Chi-restraints excluded: chain M residue 386 ASP 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 294 GLN 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 292 GLU Chi-restraints excluded: chain O residue 344 ASN 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: 1.9990 chunk 42 optimal weight: 8.9990 chunk 291 optimal weight: 7.9990 chunk 308 optimal weight: 9.9990 chunk 266 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 241 optimal weight: 9.9990 chunk 205 optimal weight: 10.0000 chunk 198 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 GLN C 336 GLN D 336 GLN ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 ASN G 336 GLN ** 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 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.144694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.115302 restraints weight = 28626.089| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.45 r_work: 0.3105 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 27420 Z= 0.140 Angle : 0.514 7.707 37395 Z= 0.262 Chirality : 0.046 0.164 4920 Planarity : 0.004 0.037 4530 Dihedral : 7.708 79.933 3752 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.32 % Allowed : 22.63 % Favored : 74.05 % 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: -0.46 (0.15), residues: 3285 helix: 0.27 (0.34), residues: 255 sheet: -0.29 (0.11), residues: 2130 loop : -0.08 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 126 TYR 0.019 0.002 TYR F 394 PHE 0.008 0.001 PHE A 194 HIS 0.002 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (27420) covalent geometry : angle 0.51380 / 0.26 (37395) hydrogen bonds : bond 0.02628 / 1.76 ( 1065) hydrogen bonds : angle 5.21804 / 3.61 ( 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 518 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 416 time to evaluate : 0.881 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: 0.8771 (mtpp) cc_final: 0.8536 (mtmt) REVERT: A 126 ARG cc_start: 0.8298 (mtp180) cc_final: 0.8011 (mtp85) REVERT: A 133 LYS cc_start: 0.7628 (tttp) cc_final: 0.6934 (tppt) REVERT: A 307 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7742 (mmt) REVERT: B 133 LYS cc_start: 0.7171 (tttt) cc_final: 0.6691 (tppt) REVERT: B 253 ARG cc_start: 0.8672 (mtp180) cc_final: 0.8232 (mtt90) REVERT: B 294 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8789 (tt0) REVERT: B 364 GLN cc_start: 0.7131 (tt0) cc_final: 0.6675 (tm-30) REVERT: C 248 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8733 (mm) REVERT: C 364 GLN cc_start: 0.7364 (tt0) cc_final: 0.6785 (tm-30) REVERT: D 182 LEU cc_start: 0.8616 (tt) cc_final: 0.8400 (tm) REVERT: D 248 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8786 (mm) REVERT: D 253 ARG cc_start: 0.8642 (mtm180) cc_final: 0.8374 (mtt90) REVERT: D 364 GLN cc_start: 0.7061 (tt0) cc_final: 0.6578 (tm-30) REVERT: E 133 LYS cc_start: 0.7250 (tttt) cc_final: 0.6953 (tppt) REVERT: E 261 LYS cc_start: 0.8961 (mttp) cc_final: 0.8639 (mmmt) REVERT: E 264 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8884 (tt) REVERT: E 389 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7338 (mt-10) REVERT: E 392 THR cc_start: 0.9070 (t) cc_final: 0.8831 (m) REVERT: F 115 LYS cc_start: 0.8844 (mtmt) cc_final: 0.8558 (mttt) REVERT: F 126 ARG cc_start: 0.8253 (mtp180) cc_final: 0.7845 (mtm180) REVERT: F 141 ASN cc_start: 0.8332 (m-40) cc_final: 0.8131 (m110) REVERT: F 261 LYS cc_start: 0.8965 (mmtt) cc_final: 0.8364 (mmmt) REVERT: F 264 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8773 (tt) REVERT: F 400 THR cc_start: 0.8737 (m) cc_final: 0.8152 (p) REVERT: G 122 LYS cc_start: 0.8720 (pttm) cc_final: 0.8452 (pttm) REVERT: G 248 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8775 (mm) REVERT: G 253 ARG cc_start: 0.8700 (mtm180) cc_final: 0.8370 (mtt90) REVERT: G 261 LYS cc_start: 0.9037 (mmtm) cc_final: 0.8798 (mmtt) REVERT: G 360 LYS cc_start: 0.7875 (mtpt) cc_final: 0.7309 (mptp) REVERT: G 392 THR cc_start: 0.9150 (t) cc_final: 0.8860 (m) REVERT: H 133 LYS cc_start: 0.7583 (ttmm) cc_final: 0.7024 (tppt) REVERT: H 264 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8639 (tt) REVERT: H 364 GLN cc_start: 0.7300 (tt0) cc_final: 0.6533 (tm-30) REVERT: H 388 ASN cc_start: 0.8094 (t0) cc_final: 0.7808 (m-40) REVERT: I 115 LYS cc_start: 0.8663 (mttt) cc_final: 0.8392 (mtmm) REVERT: I 248 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8478 (mm) REVERT: I 261 LYS cc_start: 0.9102 (mmtm) cc_final: 0.8788 (mmtp) REVERT: J 133 LYS cc_start: 0.7221 (tttt) cc_final: 0.6763 (tppt) REVERT: J 253 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8318 (mtp85) REVERT: J 261 LYS cc_start: 0.9075 (mmmt) cc_final: 0.8760 (mmmt) REVERT: K 115 LYS cc_start: 0.8803 (mttt) cc_final: 0.8468 (mtmm) REVERT: K 133 LYS cc_start: 0.7794 (ttpp) cc_final: 0.7408 (ttmm) REVERT: K 300 MET cc_start: 0.9243 (ttp) cc_final: 0.9029 (ttm) REVERT: K 358 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.8008 (m-30) REVERT: L 133 LYS cc_start: 0.7551 (tttm) cc_final: 0.6999 (tppt) REVERT: L 307 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7557 (mtt) REVERT: L 364 GLN cc_start: 0.7325 (tt0) cc_final: 0.6733 (tm-30) REVERT: M 253 ARG cc_start: 0.8603 (mtp180) cc_final: 0.8179 (mtt90) REVERT: M 264 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8785 (tt) REVERT: M 300 MET cc_start: 0.9288 (ttp) cc_final: 0.8791 (ttm) REVERT: M 388 ASN cc_start: 0.8328 (t0) cc_final: 0.8093 (m-40) REVERT: N 126 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.7172 (mmp-170) REVERT: N 264 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8934 (tt) REVERT: N 300 MET cc_start: 0.9308 (ttp) cc_final: 0.8949 (ttm) REVERT: N 358 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.7996 (m-30) REVERT: N 388 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.8030 (t0) REVERT: O 133 LYS cc_start: 0.7406 (tttt) cc_final: 0.7043 (tppt) REVERT: O 261 LYS cc_start: 0.8900 (mttm) cc_final: 0.8569 (mmtt) REVERT: O 264 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8804 (tt) REVERT: O 292 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7881 (pp20) REVERT: O 300 MET cc_start: 0.9249 (ttp) cc_final: 0.8785 (ttp) outliers start: 102 outliers final: 67 residues processed: 490 average time/residue: 0.7709 time to fit residues: 427.0397 Evaluate side-chains 497 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 412 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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 126 ARG Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 154 SER 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 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 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 307 MET 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 F residue 383 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 G residue 325 SER Chi-restraints excluded: chain G residue 386 ASP Chi-restraints excluded: chain H residue 115 LYS 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 386 ASP 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 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 383 SER Chi-restraints excluded: chain M residue 386 ASP 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 294 GLN 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 344 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 238 optimal weight: 0.4980 chunk 142 optimal weight: 9.9990 chunk 325 optimal weight: 8.9990 chunk 289 optimal weight: 2.9990 chunk 205 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 158 optimal weight: 20.0000 chunk 226 optimal weight: 7.9990 chunk 237 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 GLN C 336 GLN D 336 GLN ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 328 GLN G 336 GLN ** 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 = 0.3599 r_free = 0.3599 target = 0.143729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.114430 restraints weight = 28531.666| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.45 r_work: 0.3092 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 27420 Z= 0.161 Angle : 0.541 7.775 37395 Z= 0.275 Chirality : 0.046 0.157 4920 Planarity : 0.005 0.037 4530 Dihedral : 7.918 82.605 3752 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.35 % Allowed : 22.83 % Favored : 73.82 % 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: -0.46 (0.15), residues: 3285 helix: 0.33 (0.35), residues: 255 sheet: -0.29 (0.11), residues: 2130 loop : -0.07 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 126 TYR 0.021 0.002 TYR L 394 PHE 0.008 0.001 PHE I 194 HIS 0.002 0.001 HIS D 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (27420) covalent geometry : angle 0.54136 / 0.27 (37395) hydrogen bonds : bond 0.02777 / 1.86 ( 1065) hydrogen bonds : angle 5.29003 / 3.66 ( 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 523 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 420 time to evaluate : 0.989 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: 0.8779 (mtpp) cc_final: 0.8542 (mtmt) REVERT: A 133 LYS cc_start: 0.7651 (tttp) cc_final: 0.6910 (tppt) REVERT: A 253 ARG cc_start: 0.8541 (mtp180) cc_final: 0.8118 (mtt180) REVERT: A 307 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7751 (mmt) REVERT: B 133 LYS cc_start: 0.7233 (tttt) cc_final: 0.6762 (tppt) REVERT: B 253 ARG cc_start: 0.8678 (mtp180) cc_final: 0.8246 (mtt90) REVERT: B 294 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8778 (tt0) REVERT: B 364 GLN cc_start: 0.7160 (tt0) cc_final: 0.6733 (tm-30) REVERT: C 248 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8758 (mm) REVERT: C 253 ARG cc_start: 0.8602 (mtm180) cc_final: 0.8307 (mtt90) REVERT: C 364 GLN cc_start: 0.7375 (tt0) cc_final: 0.6786 (tm-30) REVERT: D 253 ARG cc_start: 0.8635 (mtm180) cc_final: 0.8377 (mtt90) REVERT: E 126 ARG cc_start: 0.8262 (mtp180) cc_final: 0.7907 (mtp85) REVERT: E 133 LYS cc_start: 0.7269 (tttt) cc_final: 0.6966 (tppt) REVERT: E 261 LYS cc_start: 0.8983 (mttp) cc_final: 0.8666 (mmmt) REVERT: E 264 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8909 (tt) REVERT: E 389 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7369 (mt-10) REVERT: E 392 THR cc_start: 0.9073 (t) cc_final: 0.8825 (m) REVERT: F 115 LYS cc_start: 0.8848 (mtmt) cc_final: 0.8572 (mttt) REVERT: F 261 LYS cc_start: 0.8968 (mmtt) cc_final: 0.8372 (mmmt) REVERT: F 264 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8813 (tt) REVERT: F 400 THR cc_start: 0.8742 (m) cc_final: 0.8177 (p) REVERT: G 122 LYS cc_start: 0.8725 (pttm) cc_final: 0.8475 (pttm) REVERT: G 248 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8784 (mm) REVERT: G 253 ARG cc_start: 0.8727 (mtm180) cc_final: 0.8377 (mtt90) REVERT: G 261 LYS cc_start: 0.9049 (mmtm) cc_final: 0.8807 (mmtt) REVERT: G 360 LYS cc_start: 0.7895 (mtpt) cc_final: 0.7332 (mptp) REVERT: G 364 GLN cc_start: 0.7439 (tt0) cc_final: 0.6769 (tm-30) REVERT: G 392 THR cc_start: 0.9164 (t) cc_final: 0.8883 (m) REVERT: H 133 LYS cc_start: 0.7458 (ttmm) cc_final: 0.6901 (tppt) REVERT: H 264 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8652 (tt) REVERT: H 364 GLN cc_start: 0.7298 (tt0) cc_final: 0.6526 (tm-30) REVERT: H 388 ASN cc_start: 0.8157 (t0) cc_final: 0.7849 (m-40) REVERT: I 115 LYS cc_start: 0.8774 (mttt) cc_final: 0.8480 (mtmm) REVERT: I 248 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8497 (mm) REVERT: I 261 LYS cc_start: 0.9093 (mmtm) cc_final: 0.8775 (mmtp) REVERT: J 133 LYS cc_start: 0.7283 (tttt) cc_final: 0.6759 (tppt) REVERT: J 253 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8301 (mtp85) REVERT: J 261 LYS cc_start: 0.9076 (mmmt) cc_final: 0.8762 (mmmt) REVERT: K 115 LYS cc_start: 0.8811 (mttt) cc_final: 0.8483 (mtmm) REVERT: K 133 LYS cc_start: 0.7796 (ttpp) cc_final: 0.7389 (ttmm) REVERT: K 346 ARG cc_start: 0.7828 (mtt180) cc_final: 0.7547 (ttm110) REVERT: L 126 ARG cc_start: 0.8081 (mtp180) cc_final: 0.7856 (mtm180) REVERT: L 133 LYS cc_start: 0.7588 (tttm) cc_final: 0.7011 (tppt) REVERT: L 307 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7586 (mtt) REVERT: L 364 GLN cc_start: 0.7347 (tt0) cc_final: 0.6762 (tm-30) REVERT: M 253 ARG cc_start: 0.8633 (mtp180) cc_final: 0.8199 (mtt90) REVERT: M 264 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8812 (tt) REVERT: M 300 MET cc_start: 0.9277 (ttp) cc_final: 0.8769 (ttm) REVERT: M 388 ASN cc_start: 0.8338 (t0) cc_final: 0.8101 (m-40) REVERT: N 126 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.7186 (mmp-170) REVERT: N 264 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8952 (tt) REVERT: N 300 MET cc_start: 0.9287 (ttp) cc_final: 0.9025 (ttm) REVERT: N 358 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.7986 (m-30) REVERT: N 388 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.8068 (t0) REVERT: O 133 LYS cc_start: 0.7440 (tttt) cc_final: 0.7070 (tppt) REVERT: O 261 LYS cc_start: 0.8924 (mttm) cc_final: 0.8600 (mmtt) REVERT: O 264 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8816 (tt) REVERT: O 292 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7914 (pp20) REVERT: O 300 MET cc_start: 0.9244 (ttp) cc_final: 0.8782 (ttp) REVERT: O 364 GLN cc_start: 0.7260 (tt0) cc_final: 0.6735 (tm-30) outliers start: 103 outliers final: 71 residues processed: 492 average time/residue: 0.8285 time to fit residues: 459.6831 Evaluate side-chains 501 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 414 time to evaluate : 1.298 ------------------------------------------------------------------------------- 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 148 SER Chi-restraints excluded: chain B residue 154 SER 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 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 383 SER Chi-restraints excluded: chain C residue 392 THR 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 307 MET 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 F residue 383 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 G residue 325 SER Chi-restraints excluded: chain G residue 386 ASP Chi-restraints excluded: chain H residue 115 LYS 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 325 SER Chi-restraints excluded: chain J residue 386 ASP 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 383 SER Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 133 LYS 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 383 SER Chi-restraints excluded: chain M residue 386 ASP 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 294 GLN 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 344 ASN 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: 10.0000 chunk 309 optimal weight: 3.9990 chunk 282 optimal weight: 9.9990 chunk 247 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 225 optimal weight: 0.5980 chunk 133 optimal weight: 6.9990 chunk 180 optimal weight: 8.9990 chunk 315 optimal weight: 0.6980 chunk 101 optimal weight: 10.0000 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 GLN ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 ASN G 336 GLN ** 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 = 0.3579 r_free = 0.3579 target = 0.141942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.112658 restraints weight = 28399.133| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.43 r_work: 0.3112 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 27420 Z= 0.227 Angle : 0.609 7.574 37395 Z= 0.309 Chirality : 0.048 0.168 4920 Planarity : 0.005 0.045 4530 Dihedral : 8.331 87.043 3752 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.32 % Allowed : 23.02 % Favored : 73.66 % 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: -0.53 (0.15), residues: 3285 helix: 0.30 (0.35), residues: 255 sheet: -0.35 (0.11), residues: 2130 loop : -0.08 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 126 TYR 0.022 0.003 TYR F 394 PHE 0.009 0.001 PHE A 194 HIS 0.003 0.001 HIS D 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.23 (27420) covalent geometry : angle 0.60917 / 0.31 (37395) hydrogen bonds : bond 0.03070 / 2.07 ( 1065) hydrogen bonds : angle 5.42975 / 3.75 ( 3015) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10294.69 seconds wall clock time: 187 minutes 38.39 seconds (11258.39 seconds total)