Starting phenix.real_space_refine on Thu Feb 5 10:20:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e65_47550/02_2026/9e65_47550.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e65_47550/02_2026/9e65_47550.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e65_47550/02_2026/9e65_47550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e65_47550/02_2026/9e65_47550.map" model { file = "/net/cci-nas-00/data/ceres_data/9e65_47550/02_2026/9e65_47550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e65_47550/02_2026/9e65_47550.cif" } resolution = 2.8 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= 0.034 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 63 5.16 5 C 10815 2.51 5 N 2639 2.21 5 O 2793 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16310 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2186 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 8, 'TRANS': 286} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'PHE:plan': 5, 'HIS:plan': 1, 'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2186 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 8, 'TRANS': 286} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'PHE:plan': 5, 'HIS:plan': 1, 'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 73 Chain: "C" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2186 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 8, 'TRANS': 286} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'PHE:plan': 5, 'HIS:plan': 1, 'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 73 Chain: "D" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2186 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 8, 'TRANS': 286} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'PHE:plan': 5, 'HIS:plan': 1, 'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 73 Chain: "E" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2186 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 8, 'TRANS': 286} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'PHE:plan': 5, 'HIS:plan': 1, 'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 73 Chain: "F" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2186 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 8, 'TRANS': 286} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'PHE:plan': 5, 'HIS:plan': 1, 'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 73 Chain: "G" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2186 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 8, 'TRANS': 286} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'PHE:plan': 5, 'HIS:plan': 1, 'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 73 Chain: "A" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 157 Unusual residues: {'PTY': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 393 Unresolved non-hydrogen angles: 459 Unresolved non-hydrogen dihedrals: 338 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PTY:plan-1': 11, 'PTY:plan-2': 11} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 144 Unusual residues: {'PTY': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 356 Unresolved non-hydrogen angles: 416 Unresolved non-hydrogen dihedrals: 306 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PTY:plan-1': 10, 'PTY:plan-2': 10} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 131 Unusual residues: {'PTY': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 319 Unresolved non-hydrogen angles: 373 Unresolved non-hydrogen dihedrals: 274 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PTY:plan-1': 9, 'PTY:plan-2': 9} Unresolved non-hydrogen planarities: 54 Chain: "D" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 157 Unusual residues: {'PTY': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 393 Unresolved non-hydrogen angles: 459 Unresolved non-hydrogen dihedrals: 338 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PTY:plan-1': 11, 'PTY:plan-2': 11} Unresolved non-hydrogen planarities: 66 Chain: "E" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 144 Unusual residues: {'PTY': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 356 Unresolved non-hydrogen angles: 416 Unresolved non-hydrogen dihedrals: 306 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PTY:plan-1': 10, 'PTY:plan-2': 10} Unresolved non-hydrogen planarities: 60 Chain: "F" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 144 Unusual residues: {'PTY': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 356 Unresolved non-hydrogen angles: 416 Unresolved non-hydrogen dihedrals: 306 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PTY:plan-1': 10, 'PTY:plan-2': 10} Unresolved non-hydrogen planarities: 60 Chain: "G" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 131 Unusual residues: {'PTY': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 319 Unresolved non-hydrogen angles: 373 Unresolved non-hydrogen dihedrals: 274 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PTY:plan-1': 9, 'PTY:plan-2': 9} Unresolved non-hydrogen planarities: 54 Time building chain proxies: 4.19, per 1000 atoms: 0.26 Number of scatterers: 16310 At special positions: 0 Unit cell: (98.9, 99.76, 137.6, 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 63 16.00 O 2793 8.00 N 2639 7.00 C 10815 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: 1.40 Conformation dependent library (CDL) restraints added in 822.4 milliseconds 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3850 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 15 sheets defined 60.0% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 40 through 68 Processing helix chain 'A' and resid 74 through 107 Processing helix chain 'A' and resid 111 through 134 Processing helix chain 'A' and resid 141 through 160 Processing helix chain 'A' and resid 160 through 176 removed outlier: 3.591A pdb=" N LEU A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 223 Processing helix chain 'A' and resid 229 through 232 Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 247 through 265 removed outlier: 4.342A pdb=" N GLY A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N VAL A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'B' and resid 41 through 68 Processing helix chain 'B' and resid 74 through 107 Processing helix chain 'B' and resid 111 through 134 Processing helix chain 'B' and resid 141 through 160 Processing helix chain 'B' and resid 160 through 176 removed outlier: 3.593A pdb=" N LEU B 164 " --> pdb=" O GLY B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 223 Processing helix chain 'B' and resid 229 through 232 Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 247 through 265 removed outlier: 4.341A pdb=" N GLY B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N VAL B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'C' and resid 41 through 68 Processing helix chain 'C' and resid 74 through 107 Processing helix chain 'C' and resid 111 through 134 Processing helix chain 'C' and resid 141 through 160 Processing helix chain 'C' and resid 160 through 176 removed outlier: 3.593A pdb=" N LEU C 164 " --> pdb=" O GLY C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 223 Processing helix chain 'C' and resid 229 through 232 Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 265 removed outlier: 4.341A pdb=" N GLY C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL C 253 " --> pdb=" O ALA C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'D' and resid 41 through 68 Processing helix chain 'D' and resid 74 through 107 Processing helix chain 'D' and resid 111 through 134 Processing helix chain 'D' and resid 141 through 160 Processing helix chain 'D' and resid 160 through 176 removed outlier: 3.592A pdb=" N LEU D 164 " --> pdb=" O GLY D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 223 Processing helix chain 'D' and resid 229 through 232 Processing helix chain 'D' and resid 244 through 246 No H-bonds generated for 'chain 'D' and resid 244 through 246' Processing helix chain 'D' and resid 247 through 265 removed outlier: 4.342A pdb=" N GLY D 252 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N VAL D 253 " --> pdb=" O ALA D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'E' and resid 41 through 68 Processing helix chain 'E' and resid 74 through 107 Processing helix chain 'E' and resid 111 through 134 Processing helix chain 'E' and resid 141 through 160 Processing helix chain 'E' and resid 160 through 176 removed outlier: 3.592A pdb=" N LEU E 164 " --> pdb=" O GLY E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 223 Processing helix chain 'E' and resid 229 through 232 Processing helix chain 'E' and resid 244 through 246 No H-bonds generated for 'chain 'E' and resid 244 through 246' Processing helix chain 'E' and resid 247 through 265 removed outlier: 4.342A pdb=" N GLY E 252 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N VAL E 253 " --> pdb=" O ALA E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 320 Processing helix chain 'F' and resid 41 through 68 Processing helix chain 'F' and resid 74 through 107 Processing helix chain 'F' and resid 111 through 134 Processing helix chain 'F' and resid 141 through 160 Processing helix chain 'F' and resid 160 through 176 removed outlier: 3.593A pdb=" N LEU F 164 " --> pdb=" O GLY F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 223 Processing helix chain 'F' and resid 229 through 232 Processing helix chain 'F' and resid 244 through 246 No H-bonds generated for 'chain 'F' and resid 244 through 246' Processing helix chain 'F' and resid 247 through 265 removed outlier: 4.342A pdb=" N GLY F 252 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N VAL F 253 " --> pdb=" O ALA F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 320 Processing helix chain 'G' and resid 41 through 68 Processing helix chain 'G' and resid 74 through 107 Processing helix chain 'G' and resid 111 through 134 Processing helix chain 'G' and resid 141 through 160 Processing helix chain 'G' and resid 160 through 176 removed outlier: 3.593A pdb=" N LEU G 164 " --> pdb=" O GLY G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 223 Processing helix chain 'G' and resid 229 through 232 Processing helix chain 'G' and resid 244 through 246 No H-bonds generated for 'chain 'G' and resid 244 through 246' Processing helix chain 'G' and resid 247 through 265 removed outlier: 4.341A pdb=" N GLY G 252 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N VAL G 253 " --> pdb=" O ALA G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 320 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 185 removed outlier: 6.609A pdb=" N LYS A 205 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE A 199 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ILE A 203 " --> pdb=" O ILE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 removed outlier: 7.373A pdb=" N ILE B 203 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE B 199 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS B 205 " --> pdb=" O ALA B 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 235 through 243 removed outlier: 4.039A pdb=" N ARG A 235 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ASN A 287 " --> pdb=" O ASN A 279 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 333 removed outlier: 6.680A pdb=" N GLN A 329 " --> pdb=" O TYR G 332 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 226 through 227 removed outlier: 7.371A pdb=" N ILE C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE C 199 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LYS C 205 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 235 through 243 removed outlier: 4.039A pdb=" N ARG B 235 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN B 287 " --> pdb=" O ASN B 279 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 226 through 227 removed outlier: 7.371A pdb=" N ILE D 203 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE D 199 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS D 205 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 235 through 243 removed outlier: 4.039A pdb=" N ARG C 235 " --> pdb=" O THR C 294 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN C 287 " --> pdb=" O ASN C 279 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 226 through 227 removed outlier: 7.372A pdb=" N ILE E 203 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE E 199 " --> pdb=" O ILE E 203 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS E 205 " --> pdb=" O ALA E 197 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 235 through 243 removed outlier: 4.040A pdb=" N ARG D 235 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ASN D 287 " --> pdb=" O ASN D 279 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 226 through 227 removed outlier: 7.373A pdb=" N ILE F 203 " --> pdb=" O ILE F 199 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE F 199 " --> pdb=" O ILE F 203 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS F 205 " --> pdb=" O ALA F 197 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 235 through 243 removed outlier: 4.039A pdb=" N ARG E 235 " --> pdb=" O THR E 294 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN E 287 " --> pdb=" O ASN E 279 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 226 through 227 removed outlier: 7.372A pdb=" N ILE G 203 " --> pdb=" O ILE G 199 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ILE G 199 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS G 205 " --> pdb=" O ALA G 197 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 235 through 243 removed outlier: 4.039A pdb=" N ARG F 235 " --> pdb=" O THR F 294 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN F 287 " --> pdb=" O ASN F 279 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 235 through 243 removed outlier: 4.039A pdb=" N ARG G 235 " --> pdb=" O THR G 294 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ASN G 287 " --> pdb=" O ASN G 279 " (cutoff:3.500A) 1153 hydrogen bonds defined for protein. 3312 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: 2.93 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4981 1.34 - 1.46: 2190 1.46 - 1.57: 9230 1.57 - 1.69: 0 1.69 - 1.81: 119 Bond restraints: 16520 Sorted by residual: bond pdb=" C LEU F 132 " pdb=" N LEU F 133 " ideal model delta sigma weight residual 1.335 1.304 0.031 1.31e-02 5.83e+03 5.49e+00 bond pdb=" C LEU A 132 " pdb=" N LEU A 133 " ideal model delta sigma weight residual 1.335 1.305 0.030 1.31e-02 5.83e+03 5.26e+00 bond pdb=" C LEU G 132 " pdb=" N LEU G 133 " ideal model delta sigma weight residual 1.335 1.305 0.030 1.31e-02 5.83e+03 5.25e+00 bond pdb=" C LEU E 132 " pdb=" N LEU E 133 " ideal model delta sigma weight residual 1.335 1.305 0.030 1.31e-02 5.83e+03 5.14e+00 bond pdb=" C LEU B 132 " pdb=" N LEU B 133 " ideal model delta sigma weight residual 1.335 1.305 0.030 1.31e-02 5.83e+03 5.12e+00 ... (remaining 16515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 21656 2.35 - 4.70: 285 4.70 - 7.05: 81 7.05 - 9.41: 14 9.41 - 11.76: 7 Bond angle restraints: 22043 Sorted by residual: angle pdb=" N LEU B 133 " pdb=" CA LEU B 133 " pdb=" C LEU B 133 " ideal model delta sigma weight residual 111.28 116.26 -4.98 1.09e+00 8.42e-01 2.08e+01 angle pdb=" N LEU C 133 " pdb=" CA LEU C 133 " pdb=" C LEU C 133 " ideal model delta sigma weight residual 111.28 116.23 -4.95 1.09e+00 8.42e-01 2.06e+01 angle pdb=" N LEU A 133 " pdb=" CA LEU A 133 " pdb=" C LEU A 133 " ideal model delta sigma weight residual 111.28 116.23 -4.95 1.09e+00 8.42e-01 2.06e+01 angle pdb=" N LEU G 133 " pdb=" CA LEU G 133 " pdb=" C LEU G 133 " ideal model delta sigma weight residual 111.28 116.20 -4.92 1.09e+00 8.42e-01 2.04e+01 angle pdb=" N LEU E 133 " pdb=" CA LEU E 133 " pdb=" C LEU E 133 " ideal model delta sigma weight residual 111.28 116.20 -4.92 1.09e+00 8.42e-01 2.04e+01 ... (remaining 22038 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.73: 8471 14.73 - 29.45: 979 29.45 - 44.18: 378 44.18 - 58.90: 175 58.90 - 73.63: 7 Dihedral angle restraints: 10010 sinusoidal: 4046 harmonic: 5964 Sorted by residual: dihedral pdb=" CA ASP E 111 " pdb=" C ASP E 111 " pdb=" N ILE E 112 " pdb=" CA ILE E 112 " ideal model delta harmonic sigma weight residual -180.00 -160.20 -19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA ASP F 111 " pdb=" C ASP F 111 " pdb=" N ILE F 112 " pdb=" CA ILE F 112 " ideal model delta harmonic sigma weight residual -180.00 -160.23 -19.77 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA ASP B 111 " pdb=" C ASP B 111 " pdb=" N ILE B 112 " pdb=" CA ILE B 112 " ideal model delta harmonic sigma weight residual 180.00 -160.24 -19.76 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 10007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1643 0.041 - 0.082: 610 0.082 - 0.123: 175 0.123 - 0.164: 50 0.164 - 0.205: 14 Chirality restraints: 2492 Sorted by residual: chirality pdb=" CA LEU C 133 " pdb=" N LEU C 133 " pdb=" C LEU C 133 " pdb=" CB LEU C 133 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA LEU B 133 " pdb=" N LEU B 133 " pdb=" C LEU B 133 " pdb=" CB LEU B 133 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA LEU E 133 " pdb=" N LEU E 133 " pdb=" C LEU E 133 " pdb=" CB LEU E 133 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 2489 not shown) Planarity restraints: 2709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 132 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.89e+00 pdb=" C LEU D 132 " 0.052 2.00e-02 2.50e+03 pdb=" O LEU D 132 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU D 133 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 132 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.74e+00 pdb=" C LEU A 132 " 0.051 2.00e-02 2.50e+03 pdb=" O LEU A 132 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU A 133 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU G 132 " 0.015 2.00e-02 2.50e+03 2.95e-02 8.72e+00 pdb=" C LEU G 132 " -0.051 2.00e-02 2.50e+03 pdb=" O LEU G 132 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU G 133 " 0.017 2.00e-02 2.50e+03 ... (remaining 2706 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3715 2.79 - 3.32: 14694 3.32 - 3.85: 25755 3.85 - 4.37: 29767 4.37 - 4.90: 52075 Nonbonded interactions: 126006 Sorted by model distance: nonbonded pdb=" O LYS E 93 " pdb=" CG LEU E 96 " model vdw 2.265 3.470 nonbonded pdb=" O LYS B 93 " pdb=" CG LEU B 96 " model vdw 2.265 3.470 nonbonded pdb=" O LYS G 93 " pdb=" CG LEU G 96 " model vdw 2.265 3.470 nonbonded pdb=" O LYS A 93 " pdb=" CG LEU A 96 " model vdw 2.265 3.470 nonbonded pdb=" O LYS F 93 " pdb=" CG LEU F 96 " model vdw 2.266 3.470 ... (remaining 126001 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 40 through 334 or (resid 403 and (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 C20 or name C21 or name C22 or name C8 )) or resid 404 or resid 406)) selection = (chain 'B' and (resid 40 through 334 or (resid 403 and (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 C20 or name C21 or name C22 or name C8 )) or (resid 404 and (name C11 o \ r name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C \ 18 or name C8 )) or (resid 406 and (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 C20 or name \ C21 or name C22 or name C8 )))) selection = (chain 'C' and (resid 40 through 334 or (resid 403 and (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 C20 or name C21 or name C22 or name C8 )) or (resid 404 and (name C11 o \ r name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C \ 18 or name C8 )) or (resid 406 and (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 C20 or name \ C21 or name C22 or name C8 )))) selection = (chain 'D' and (resid 40 through 334 or (resid 403 and (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 C20 or name C21 or name C22 or name C8 )) or (resid 404 and (name C11 o \ r name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C \ 18 or name C8 )) or resid 406)) selection = (chain 'E' and (resid 40 through 334 or (resid 403 and (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 C20 or name C21 or name C22 or name C8 )) or (resid 404 and (name C11 o \ r name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C \ 18 or name C8 )) or (resid 406 and (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 C20 or name \ C21 or name C22 or name C8 )))) selection = (chain 'F' and (resid 40 through 334 or (resid 403 and (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 C20 or name C21 or name C22 or name C8 )) or (resid 404 and (name C11 o \ r name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C \ 18 or name C8 )) or (resid 406 and (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 C20 or name \ C21 or name C22 or name C8 )))) selection = (chain 'G' and (resid 40 through 334 or resid 403 or (resid 404 and (name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C1 \ 8 or name C8 )) or (resid 406 and (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 C20 or name \ C21 or name C22 or name C8 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.060 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.590 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16520 Z= 0.215 Angle : 0.776 11.758 22043 Z= 0.445 Chirality : 0.049 0.205 2492 Planarity : 0.005 0.030 2709 Dihedral : 16.131 73.631 6160 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.96 % Allowed : 23.31 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.19), residues: 2051 helix: 2.09 (0.15), residues: 1141 sheet: -0.69 (0.26), residues: 343 loop : -1.75 (0.23), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 120 TYR 0.010 0.001 TYR C 291 PHE 0.010 0.001 PHE A 167 TRP 0.006 0.001 TRP A 184 HIS 0.002 0.001 HIS F 320 Details of bonding type rmsd covalent geometry : bond 0.00422 (16520) covalent geometry : angle 0.77577 (22043) hydrogen bonds : bond 0.13425 ( 1153) hydrogen bonds : angle 5.60356 ( 3312) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 377 time to evaluate : 0.614 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.9397 (tm-30) cc_final: 0.9059 (tm-30) REVERT: B 102 GLU cc_start: 0.9418 (tm-30) cc_final: 0.9068 (tm-30) REVERT: B 123 LYS cc_start: 0.9508 (ptpp) cc_final: 0.9098 (ptpp) REVERT: B 133 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9134 (pp) REVERT: C 102 GLU cc_start: 0.9420 (tm-30) cc_final: 0.8598 (tm-30) REVERT: C 123 LYS cc_start: 0.9517 (ptpp) cc_final: 0.9118 (ptpp) REVERT: D 102 GLU cc_start: 0.9371 (tm-30) cc_final: 0.9047 (tm-30) REVERT: D 133 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9158 (pp) REVERT: E 102 GLU cc_start: 0.9412 (tm-30) cc_final: 0.9072 (tm-30) REVERT: F 99 ASN cc_start: 0.9633 (m-40) cc_final: 0.9343 (p0) REVERT: F 102 GLU cc_start: 0.9335 (tm-30) cc_final: 0.9123 (tm-30) REVERT: F 103 LYS cc_start: 0.9512 (mmmt) cc_final: 0.9293 (mmtm) REVERT: F 123 LYS cc_start: 0.9527 (ptpp) cc_final: 0.9112 (ptpp) REVERT: F 133 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9154 (pp) REVERT: G 102 GLU cc_start: 0.9372 (tm-30) cc_final: 0.9045 (tm-30) outliers start: 14 outliers final: 3 residues processed: 377 average time/residue: 0.6224 time to fit residues: 257.7900 Evaluate side-chains 340 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 334 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 140 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.0010 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 0.8980 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 10.0000 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 GLN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.094147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.057598 restraints weight = 38340.692| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 2.75 r_work: 0.2528 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16520 Z= 0.126 Angle : 0.689 11.288 22043 Z= 0.347 Chirality : 0.047 0.178 2492 Planarity : 0.004 0.111 2709 Dihedral : 10.438 58.871 3025 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.65 % Allowed : 23.17 % Favored : 72.18 % 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: 1.41 (0.18), residues: 2051 helix: 2.51 (0.15), residues: 1134 sheet: -0.06 (0.31), residues: 259 loop : -1.59 (0.21), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 271 TYR 0.013 0.001 TYR D 291 PHE 0.013 0.001 PHE B 148 TRP 0.006 0.000 TRP D 299 HIS 0.003 0.001 HIS G 137 Details of bonding type rmsd covalent geometry : bond 0.00258 (16520) covalent geometry : angle 0.68869 (22043) hydrogen bonds : bond 0.04423 ( 1153) hydrogen bonds : angle 3.97949 ( 3312) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 354 time to evaluate : 0.681 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 102 GLU cc_start: 0.9514 (tm-30) cc_final: 0.9107 (tm-30) REVERT: A 105 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8664 (mp-120) REVERT: A 246 GLU cc_start: 0.8746 (pm20) cc_final: 0.8539 (pm20) REVERT: A 250 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8727 (mmtm) REVERT: B 102 GLU cc_start: 0.9529 (tm-30) cc_final: 0.9127 (tm-30) REVERT: B 172 MET cc_start: 0.8911 (tmm) cc_final: 0.8703 (tmm) REVERT: B 246 GLU cc_start: 0.8698 (pm20) cc_final: 0.8408 (pm20) REVERT: B 250 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8648 (mmtm) REVERT: B 256 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8343 (pp20) REVERT: B 333 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8580 (mpp) REVERT: C 116 ARG cc_start: 0.8839 (mmp80) cc_final: 0.8589 (mmp80) REVERT: C 193 GLU cc_start: 0.9061 (tt0) cc_final: 0.8822 (tt0) REVERT: C 246 GLU cc_start: 0.8853 (pm20) cc_final: 0.8614 (pm20) REVERT: C 256 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8322 (pp20) REVERT: D 100 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8715 (pp30) REVERT: D 102 GLU cc_start: 0.9470 (tm-30) cc_final: 0.9079 (tm-30) REVERT: D 116 ARG cc_start: 0.8968 (ttt180) cc_final: 0.8476 (tpt170) REVERT: D 133 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9291 (tm) REVERT: D 246 GLU cc_start: 0.8848 (pm20) cc_final: 0.8589 (pm20) REVERT: D 280 GLN cc_start: 0.9178 (OUTLIER) cc_final: 0.8774 (tt0) REVERT: E 102 GLU cc_start: 0.9565 (tm-30) cc_final: 0.9161 (tm-30) REVERT: E 116 ARG cc_start: 0.8840 (ttt180) cc_final: 0.8245 (tpt170) REVERT: E 246 GLU cc_start: 0.8690 (pm20) cc_final: 0.8483 (pm20) REVERT: E 250 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8769 (mmtm) REVERT: E 256 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8324 (pp20) REVERT: F 99 ASN cc_start: 0.9723 (m-40) cc_final: 0.9512 (m110) REVERT: F 102 GLU cc_start: 0.9505 (tm-30) cc_final: 0.9114 (tm-30) REVERT: F 116 ARG cc_start: 0.8944 (ttt180) cc_final: 0.8516 (tpt170) REVERT: F 136 GLU cc_start: 0.8511 (pp20) cc_final: 0.8008 (pm20) REVERT: F 172 MET cc_start: 0.8893 (tmm) cc_final: 0.8685 (tmm) REVERT: F 246 GLU cc_start: 0.8652 (pm20) cc_final: 0.8403 (pm20) REVERT: F 256 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8361 (pp20) REVERT: F 333 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8516 (mpp) REVERT: G 102 GLU cc_start: 0.9525 (tm-30) cc_final: 0.9116 (tm-30) REVERT: G 105 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8690 (mp-120) REVERT: G 116 ARG cc_start: 0.8934 (ttt180) cc_final: 0.8468 (tpt170) REVERT: G 246 GLU cc_start: 0.8849 (pm20) cc_final: 0.8560 (pm20) REVERT: G 250 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8711 (mmtm) REVERT: G 301 GLU cc_start: 0.9199 (mp0) cc_final: 0.8994 (mp0) outliers start: 68 outliers final: 4 residues processed: 377 average time/residue: 0.6859 time to fit residues: 282.5793 Evaluate side-chains 333 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 318 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLN Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 333 MET Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain G residue 250 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 164 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 30 optimal weight: 30.0000 chunk 105 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 184 optimal weight: 6.9990 chunk 131 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 GLN ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.092455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.055371 restraints weight = 39101.502| |-----------------------------------------------------------------------------| r_work (start): 0.2637 rms_B_bonded: 2.79 r_work: 0.2471 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16520 Z= 0.169 Angle : 0.698 13.937 22043 Z= 0.350 Chirality : 0.049 0.267 2492 Planarity : 0.004 0.102 2709 Dihedral : 9.653 59.111 3021 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.17 % Allowed : 24.40 % Favored : 71.43 % 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: 1.46 (0.18), residues: 2051 helix: 2.60 (0.14), residues: 1127 sheet: 0.03 (0.32), residues: 259 loop : -1.63 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 271 TYR 0.020 0.002 TYR C 174 PHE 0.030 0.002 PHE C 101 TRP 0.007 0.001 TRP E 184 HIS 0.003 0.001 HIS D 320 Details of bonding type rmsd covalent geometry : bond 0.00389 (16520) covalent geometry : angle 0.69792 (22043) hydrogen bonds : bond 0.04447 ( 1153) hydrogen bonds : angle 3.89008 ( 3312) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 337 time to evaluate : 0.559 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: A 100 GLN cc_start: 0.9217 (pp30) cc_final: 0.8950 (pp30) REVERT: A 102 GLU cc_start: 0.9575 (tm-30) cc_final: 0.9228 (tm-30) REVERT: A 231 ARG cc_start: 0.9593 (OUTLIER) cc_final: 0.9289 (mtm-85) REVERT: A 246 GLU cc_start: 0.8882 (pm20) cc_final: 0.8634 (pm20) REVERT: B 102 GLU cc_start: 0.9583 (tm-30) cc_final: 0.9238 (tm-30) REVERT: B 103 LYS cc_start: 0.9704 (mmmt) cc_final: 0.9470 (mmtm) REVERT: B 118 MET cc_start: 0.9216 (tpp) cc_final: 0.9011 (tpp) REVERT: B 158 MET cc_start: 0.9240 (mmm) cc_final: 0.8950 (mtp) REVERT: B 246 GLU cc_start: 0.8865 (pm20) cc_final: 0.8551 (pm20) REVERT: B 256 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8416 (pp20) REVERT: C 148 PHE cc_start: 0.9163 (t80) cc_final: 0.8917 (t80) REVERT: C 193 GLU cc_start: 0.9218 (tt0) cc_final: 0.8968 (tt0) REVERT: C 246 GLU cc_start: 0.8922 (pm20) cc_final: 0.8674 (pm20) REVERT: C 256 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8450 (pp20) REVERT: D 102 GLU cc_start: 0.9537 (tm-30) cc_final: 0.9179 (tm-30) REVERT: D 116 ARG cc_start: 0.8922 (ttt180) cc_final: 0.8441 (tpt170) REVERT: D 118 MET cc_start: 0.9234 (mmm) cc_final: 0.8911 (tpp) REVERT: D 133 LEU cc_start: 0.9713 (OUTLIER) cc_final: 0.9304 (tm) REVERT: D 148 PHE cc_start: 0.9222 (t80) cc_final: 0.8788 (t80) REVERT: D 246 GLU cc_start: 0.8951 (pm20) cc_final: 0.8685 (pm20) REVERT: E 102 GLU cc_start: 0.9591 (tm-30) cc_final: 0.9260 (tm-30) REVERT: E 116 ARG cc_start: 0.8845 (ttt180) cc_final: 0.8288 (tpt170) REVERT: E 246 GLU cc_start: 0.8841 (pm20) cc_final: 0.8574 (pm20) REVERT: E 250 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8791 (mmtm) REVERT: E 256 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8430 (pp20) REVERT: F 99 ASN cc_start: 0.9719 (m-40) cc_final: 0.9502 (m110) REVERT: F 102 GLU cc_start: 0.9550 (tm-30) cc_final: 0.9170 (tm-30) REVERT: F 136 GLU cc_start: 0.8791 (pp20) cc_final: 0.8406 (pm20) REVERT: F 172 MET cc_start: 0.8980 (tmm) cc_final: 0.8717 (tmm) REVERT: F 246 GLU cc_start: 0.8822 (pm20) cc_final: 0.8531 (pm20) REVERT: F 250 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8547 (mmtm) REVERT: F 256 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8474 (pp20) REVERT: F 333 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8648 (mpp) REVERT: G 100 GLN cc_start: 0.9215 (pp30) cc_final: 0.8908 (pp30) REVERT: G 102 GLU cc_start: 0.9583 (tm-30) cc_final: 0.9260 (tm-30) REVERT: G 116 ARG cc_start: 0.8929 (ttt180) cc_final: 0.8421 (tpt170) REVERT: G 136 GLU cc_start: 0.8844 (pp20) cc_final: 0.8636 (pm20) REVERT: G 231 ARG cc_start: 0.9630 (OUTLIER) cc_final: 0.9256 (mtt180) REVERT: G 246 GLU cc_start: 0.8945 (pm20) cc_final: 0.8680 (pm20) REVERT: G 250 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8710 (mmtm) outliers start: 61 outliers final: 10 residues processed: 365 average time/residue: 0.7202 time to fit residues: 286.0410 Evaluate side-chains 326 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 309 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain D residue 104 GLN Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain F residue 104 GLN Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 333 MET Chi-restraints excluded: chain G residue 231 ARG Chi-restraints excluded: chain G residue 250 LYS Chi-restraints excluded: chain G residue 289 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 134 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 177 optimal weight: 50.0000 chunk 148 optimal weight: 50.0000 chunk 61 optimal weight: 50.0000 chunk 141 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.092873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.055939 restraints weight = 38264.385| |-----------------------------------------------------------------------------| r_work (start): 0.2662 rms_B_bonded: 2.79 r_work: 0.2493 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 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 : 0.004 0.050 16520 Z= 0.155 Angle : 0.700 13.825 22043 Z= 0.347 Chirality : 0.047 0.214 2492 Planarity : 0.003 0.030 2709 Dihedral : 9.001 56.595 3015 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.94 % Allowed : 24.88 % Favored : 72.18 % 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: 1.55 (0.18), residues: 2051 helix: 2.71 (0.14), residues: 1127 sheet: 0.09 (0.33), residues: 259 loop : -1.69 (0.20), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 271 TYR 0.015 0.001 TYR A 291 PHE 0.029 0.001 PHE F 101 TRP 0.006 0.001 TRP E 184 HIS 0.003 0.001 HIS E 137 Details of bonding type rmsd covalent geometry : bond 0.00357 (16520) covalent geometry : angle 0.70028 (22043) hydrogen bonds : bond 0.04197 ( 1153) hydrogen bonds : angle 3.75040 ( 3312) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 338 time to evaluate : 0.623 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: A 102 GLU cc_start: 0.9596 (tm-30) cc_final: 0.9184 (tm-30) REVERT: A 140 MET cc_start: 0.7028 (OUTLIER) cc_final: 0.5704 (mmp) REVERT: A 148 PHE cc_start: 0.9241 (t80) cc_final: 0.9002 (t80) REVERT: A 246 GLU cc_start: 0.8914 (pm20) cc_final: 0.8666 (pm20) REVERT: A 289 MET cc_start: 0.9452 (OUTLIER) cc_final: 0.9084 (ppp) REVERT: B 97 LEU cc_start: 0.9800 (mm) cc_final: 0.9584 (mm) REVERT: B 102 GLU cc_start: 0.9583 (tm-30) cc_final: 0.9213 (tm-30) REVERT: B 103 LYS cc_start: 0.9752 (mmmt) cc_final: 0.9495 (mmtm) REVERT: B 116 ARG cc_start: 0.8897 (ttt180) cc_final: 0.8507 (tpt170) REVERT: B 118 MET cc_start: 0.9190 (tpp) cc_final: 0.8866 (tpp) REVERT: B 140 MET cc_start: 0.7338 (OUTLIER) cc_final: 0.5907 (mmp) REVERT: B 148 PHE cc_start: 0.9216 (t80) cc_final: 0.8935 (t80) REVERT: B 246 GLU cc_start: 0.8901 (pm20) cc_final: 0.8585 (pm20) REVERT: B 250 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8584 (mmtp) REVERT: B 256 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8446 (pp20) REVERT: C 136 GLU cc_start: 0.8593 (pp20) cc_final: 0.8283 (pm20) REVERT: C 193 GLU cc_start: 0.9219 (tt0) cc_final: 0.8976 (tt0) REVERT: C 246 GLU cc_start: 0.8996 (pm20) cc_final: 0.8727 (pm20) REVERT: C 250 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8866 (mmtm) REVERT: C 256 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8416 (pp20) REVERT: D 140 MET cc_start: 0.7648 (mmt) cc_final: 0.6611 (mmm) REVERT: D 142 LEU cc_start: 0.8734 (mm) cc_final: 0.8464 (mm) REVERT: D 148 PHE cc_start: 0.9214 (t80) cc_final: 0.8824 (t80) REVERT: D 246 GLU cc_start: 0.8990 (pm20) cc_final: 0.8757 (pm20) REVERT: D 250 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8904 (mmtm) REVERT: E 100 GLN cc_start: 0.8785 (pp30) cc_final: 0.8459 (pp30) REVERT: E 140 MET cc_start: 0.7213 (OUTLIER) cc_final: 0.6528 (mmp) REVERT: E 193 GLU cc_start: 0.9139 (tt0) cc_final: 0.8890 (tt0) REVERT: E 246 GLU cc_start: 0.8883 (pm20) cc_final: 0.8647 (pm20) REVERT: E 250 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8773 (mmtm) REVERT: E 256 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8407 (pp20) REVERT: F 99 ASN cc_start: 0.9724 (m-40) cc_final: 0.9519 (m110) REVERT: F 102 GLU cc_start: 0.9478 (tm-30) cc_final: 0.9272 (tm-30) REVERT: F 107 LYS cc_start: 0.9702 (pptt) cc_final: 0.9478 (pptt) REVERT: F 136 GLU cc_start: 0.8766 (pp20) cc_final: 0.8479 (pm20) REVERT: F 172 MET cc_start: 0.9024 (tmm) cc_final: 0.8737 (tmm) REVERT: F 246 GLU cc_start: 0.8911 (pm20) cc_final: 0.8600 (pm20) REVERT: F 250 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8519 (mmtm) REVERT: F 256 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8481 (pp20) REVERT: F 289 MET cc_start: 0.9408 (ptm) cc_final: 0.9056 (ppp) REVERT: G 102 GLU cc_start: 0.9492 (tm-30) cc_final: 0.9272 (tm-30) REVERT: G 116 ARG cc_start: 0.8885 (ttt180) cc_final: 0.8517 (tpt170) REVERT: G 231 ARG cc_start: 0.9616 (OUTLIER) cc_final: 0.9218 (mtt180) REVERT: G 246 GLU cc_start: 0.8950 (pm20) cc_final: 0.8709 (pm20) REVERT: G 250 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8659 (mmtm) REVERT: G 289 MET cc_start: 0.9452 (OUTLIER) cc_final: 0.9230 (ppp) outliers start: 43 outliers final: 8 residues processed: 359 average time/residue: 0.7193 time to fit residues: 281.5905 Evaluate side-chains 327 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 307 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 231 ARG Chi-restraints excluded: chain G residue 250 LYS Chi-restraints excluded: chain G residue 289 MET Chi-restraints excluded: chain G residue 319 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 152 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 119 optimal weight: 50.0000 chunk 156 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 199 optimal weight: 5.9990 chunk 14 optimal weight: 0.0020 chunk 25 optimal weight: 0.3980 chunk 195 optimal weight: 1.9990 overall best weight: 1.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN C 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.092624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.055368 restraints weight = 38563.284| |-----------------------------------------------------------------------------| r_work (start): 0.2638 rms_B_bonded: 2.82 r_work: 0.2464 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16520 Z= 0.155 Angle : 0.722 14.268 22043 Z= 0.359 Chirality : 0.048 0.447 2492 Planarity : 0.003 0.037 2709 Dihedral : 8.628 54.918 3010 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.87 % Allowed : 25.36 % Favored : 71.77 % 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: 1.59 (0.18), residues: 2051 helix: 2.78 (0.14), residues: 1127 sheet: 0.13 (0.34), residues: 259 loop : -1.77 (0.19), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 271 TYR 0.021 0.001 TYR G 174 PHE 0.033 0.001 PHE D 101 TRP 0.006 0.001 TRP E 184 HIS 0.002 0.001 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00358 (16520) covalent geometry : angle 0.72204 (22043) hydrogen bonds : bond 0.04108 ( 1153) hydrogen bonds : angle 3.73210 ( 3312) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 324 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLN cc_start: 0.9255 (pp30) cc_final: 0.8969 (pp30) REVERT: A 102 GLU cc_start: 0.9616 (tm-30) cc_final: 0.9342 (tm-30) REVERT: A 116 ARG cc_start: 0.8942 (ttt180) cc_final: 0.8396 (tpt170) REVERT: A 246 GLU cc_start: 0.8943 (pm20) cc_final: 0.8668 (pm20) REVERT: A 289 MET cc_start: 0.9447 (OUTLIER) cc_final: 0.9087 (ppp) REVERT: B 102 GLU cc_start: 0.9597 (tm-30) cc_final: 0.9258 (tm-30) REVERT: B 107 LYS cc_start: 0.9719 (pptt) cc_final: 0.9510 (pptt) REVERT: B 116 ARG cc_start: 0.8880 (ttt180) cc_final: 0.8476 (tpt170) REVERT: B 133 LEU cc_start: 0.9464 (tm) cc_final: 0.9256 (pp) REVERT: B 158 MET cc_start: 0.9202 (mtp) cc_final: 0.8684 (mtp) REVERT: B 246 GLU cc_start: 0.8945 (pm20) cc_final: 0.8689 (pm20) REVERT: B 250 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8577 (mmtp) REVERT: B 256 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8470 (pp20) REVERT: B 280 GLN cc_start: 0.9139 (tm-30) cc_final: 0.8889 (tm-30) REVERT: C 103 LYS cc_start: 0.9753 (mmmt) cc_final: 0.9513 (mmtm) REVERT: C 193 GLU cc_start: 0.9227 (tt0) cc_final: 0.9012 (tt0) REVERT: C 246 GLU cc_start: 0.9005 (pm20) cc_final: 0.8767 (pm20) REVERT: C 256 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8458 (pp20) REVERT: D 118 MET cc_start: 0.9265 (mmm) cc_final: 0.8898 (tpp) REVERT: D 148 PHE cc_start: 0.9211 (t80) cc_final: 0.8816 (t80) REVERT: D 246 GLU cc_start: 0.9008 (pm20) cc_final: 0.8793 (pm20) REVERT: E 100 GLN cc_start: 0.8787 (pp30) cc_final: 0.8339 (pp30) REVERT: E 193 GLU cc_start: 0.9138 (tt0) cc_final: 0.8887 (tt0) REVERT: E 250 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8768 (mmtm) REVERT: E 256 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8433 (pp20) REVERT: F 99 ASN cc_start: 0.9715 (m-40) cc_final: 0.9507 (m110) REVERT: F 102 GLU cc_start: 0.9516 (tm-30) cc_final: 0.9301 (tm-30) REVERT: F 107 LYS cc_start: 0.9723 (pptt) cc_final: 0.9521 (pptt) REVERT: F 116 ARG cc_start: 0.8884 (ttt180) cc_final: 0.8340 (tpt170) REVERT: F 133 LEU cc_start: 0.9562 (OUTLIER) cc_final: 0.9267 (tm) REVERT: F 136 GLU cc_start: 0.8813 (pp20) cc_final: 0.8526 (pm20) REVERT: F 140 MET cc_start: 0.7599 (mmt) cc_final: 0.6360 (mmp) REVERT: F 172 MET cc_start: 0.9054 (tmm) cc_final: 0.8747 (tmm) REVERT: F 246 GLU cc_start: 0.8939 (pm20) cc_final: 0.8620 (pm20) REVERT: F 250 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8500 (mmtm) REVERT: F 256 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8528 (pp20) REVERT: F 280 GLN cc_start: 0.9084 (tm-30) cc_final: 0.8819 (tm-30) REVERT: F 289 MET cc_start: 0.9410 (ptm) cc_final: 0.9047 (ppp) REVERT: G 100 GLN cc_start: 0.9134 (pp30) cc_final: 0.8925 (pp30) REVERT: G 102 GLU cc_start: 0.9537 (tm-30) cc_final: 0.9313 (tm-30) REVERT: G 116 ARG cc_start: 0.8864 (ttt180) cc_final: 0.8502 (tpt170) REVERT: G 133 LEU cc_start: 0.9369 (tm) cc_final: 0.9158 (pp) REVERT: G 140 MET cc_start: 0.5638 (ptm) cc_final: 0.4917 (ptm) REVERT: G 246 GLU cc_start: 0.8971 (pm20) cc_final: 0.8739 (pm20) REVERT: G 289 MET cc_start: 0.9464 (OUTLIER) cc_final: 0.9242 (ppp) outliers start: 42 outliers final: 18 residues processed: 350 average time/residue: 0.6742 time to fit residues: 257.7107 Evaluate side-chains 332 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 308 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 250 LYS Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 289 MET Chi-restraints excluded: chain G residue 319 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 186 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 80 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 111 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 121 optimal weight: 8.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.093866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.056602 restraints weight = 38172.081| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 2.77 r_work: 0.2493 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16520 Z= 0.133 Angle : 0.743 15.146 22043 Z= 0.365 Chirality : 0.048 0.429 2492 Planarity : 0.003 0.040 2709 Dihedral : 8.310 57.316 3010 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.53 % Allowed : 27.27 % Favored : 70.20 % 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: 1.70 (0.18), residues: 2051 helix: 2.91 (0.14), residues: 1120 sheet: 0.20 (0.34), residues: 259 loop : -1.77 (0.19), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 271 TYR 0.013 0.001 TYR F 291 PHE 0.030 0.001 PHE F 101 TRP 0.004 0.001 TRP F 184 HIS 0.002 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00300 (16520) covalent geometry : angle 0.74343 (22043) hydrogen bonds : bond 0.03792 ( 1153) hydrogen bonds : angle 3.62020 ( 3312) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 321 time to evaluate : 0.620 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: A 102 GLU cc_start: 0.9552 (tm-30) cc_final: 0.9339 (tm-30) REVERT: A 246 GLU cc_start: 0.8936 (pm20) cc_final: 0.8652 (pm20) REVERT: A 250 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8619 (mmtp) REVERT: A 289 MET cc_start: 0.9422 (OUTLIER) cc_final: 0.9053 (ppp) REVERT: B 102 GLU cc_start: 0.9617 (tm-30) cc_final: 0.9218 (tm-30) REVERT: B 116 ARG cc_start: 0.8891 (ttt180) cc_final: 0.8478 (tpt170) REVERT: B 133 LEU cc_start: 0.9454 (tm) cc_final: 0.9229 (pp) REVERT: B 140 MET cc_start: 0.6983 (mmp) cc_final: 0.5684 (mmp) REVERT: B 246 GLU cc_start: 0.8945 (pm20) cc_final: 0.8676 (pm20) REVERT: B 250 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8449 (mmtp) REVERT: B 256 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8469 (pp20) REVERT: B 301 GLU cc_start: 0.9327 (mt-10) cc_final: 0.9103 (mp0) REVERT: C 100 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8600 (pp30) REVERT: C 136 GLU cc_start: 0.8623 (pp20) cc_final: 0.8379 (pm20) REVERT: C 193 GLU cc_start: 0.9176 (tt0) cc_final: 0.8960 (tt0) REVERT: C 246 GLU cc_start: 0.9018 (pm20) cc_final: 0.8764 (pm20) REVERT: C 250 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8846 (mmtm) REVERT: C 256 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8422 (pp20) REVERT: D 103 LYS cc_start: 0.9646 (mmmt) cc_final: 0.9418 (mmtm) REVERT: D 118 MET cc_start: 0.9322 (mmm) cc_final: 0.9038 (tpp) REVERT: D 140 MET cc_start: 0.6957 (OUTLIER) cc_final: 0.5681 (mmp) REVERT: D 246 GLU cc_start: 0.9007 (pm20) cc_final: 0.8776 (pm20) REVERT: D 301 GLU cc_start: 0.9059 (mp0) cc_final: 0.8697 (pm20) REVERT: E 102 GLU cc_start: 0.9551 (tm-30) cc_final: 0.9176 (tp30) REVERT: E 140 MET cc_start: 0.6282 (OUTLIER) cc_final: 0.5237 (mmp) REVERT: E 172 MET cc_start: 0.8973 (tmm) cc_final: 0.8741 (tmm) REVERT: E 193 GLU cc_start: 0.9097 (tt0) cc_final: 0.8857 (tt0) REVERT: E 256 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8429 (pp20) REVERT: E 280 GLN cc_start: 0.9009 (tm-30) cc_final: 0.8719 (tm-30) REVERT: F 99 ASN cc_start: 0.9716 (m-40) cc_final: 0.9497 (m110) REVERT: F 102 GLU cc_start: 0.9517 (tm-30) cc_final: 0.9306 (tm-30) REVERT: F 107 LYS cc_start: 0.9759 (pptt) cc_final: 0.9539 (pptt) REVERT: F 116 ARG cc_start: 0.8911 (ttt180) cc_final: 0.8387 (tpt170) REVERT: F 172 MET cc_start: 0.9014 (tmm) cc_final: 0.8709 (tmm) REVERT: F 246 GLU cc_start: 0.8935 (pm20) cc_final: 0.8662 (pm20) REVERT: F 250 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8455 (mmtm) REVERT: F 256 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8500 (pp20) REVERT: F 289 MET cc_start: 0.9383 (ptm) cc_final: 0.9091 (ppp) REVERT: G 100 GLN cc_start: 0.9132 (pp30) cc_final: 0.8845 (pp30) REVERT: G 102 GLU cc_start: 0.9552 (tm-30) cc_final: 0.9349 (tm-30) REVERT: G 116 ARG cc_start: 0.8852 (ttt180) cc_final: 0.8402 (tpt170) REVERT: G 133 LEU cc_start: 0.9374 (tm) cc_final: 0.9114 (pp) REVERT: G 246 GLU cc_start: 0.8957 (pm20) cc_final: 0.8725 (pm20) REVERT: G 301 GLU cc_start: 0.9041 (mp0) cc_final: 0.8680 (pm20) outliers start: 37 outliers final: 13 residues processed: 345 average time/residue: 0.6488 time to fit residues: 244.3782 Evaluate side-chains 336 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 315 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 319 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 21 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 4 optimal weight: 40.0000 chunk 99 optimal weight: 0.8980 chunk 165 optimal weight: 3.9990 chunk 58 optimal weight: 50.0000 chunk 14 optimal weight: 0.4980 chunk 197 optimal weight: 3.9990 chunk 146 optimal weight: 30.0000 chunk 7 optimal weight: 5.9990 chunk 0 optimal weight: 60.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 105 GLN D 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.092794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.055310 restraints weight = 38365.117| |-----------------------------------------------------------------------------| r_work (start): 0.2648 rms_B_bonded: 2.80 r_work: 0.2474 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16520 Z= 0.159 Angle : 0.788 16.050 22043 Z= 0.386 Chirality : 0.049 0.262 2492 Planarity : 0.004 0.048 2709 Dihedral : 8.245 59.550 3010 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.91 % Allowed : 28.64 % Favored : 69.45 % 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: 1.76 (0.18), residues: 2051 helix: 2.99 (0.14), residues: 1120 sheet: 0.21 (0.34), residues: 259 loop : -1.78 (0.19), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 271 TYR 0.015 0.001 TYR A 291 PHE 0.033 0.001 PHE B 101 TRP 0.006 0.001 TRP E 184 HIS 0.002 0.001 HIS D 320 Details of bonding type rmsd covalent geometry : bond 0.00364 (16520) covalent geometry : angle 0.78829 (22043) hydrogen bonds : bond 0.04055 ( 1153) hydrogen bonds : angle 3.59844 ( 3312) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 323 time to evaluate : 0.603 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: A 95 PHE cc_start: 0.9524 (m-10) cc_final: 0.9268 (m-80) REVERT: A 102 GLU cc_start: 0.9571 (tm-30) cc_final: 0.9336 (tm-30) REVERT: A 116 ARG cc_start: 0.8925 (ttt180) cc_final: 0.8538 (tpt170) REVERT: A 246 GLU cc_start: 0.8986 (pm20) cc_final: 0.8730 (pm20) REVERT: A 250 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8630 (mmtp) REVERT: A 289 MET cc_start: 0.9434 (OUTLIER) cc_final: 0.9048 (ppp) REVERT: B 102 GLU cc_start: 0.9615 (tm-30) cc_final: 0.9208 (tp30) REVERT: B 116 ARG cc_start: 0.8872 (ttt180) cc_final: 0.8667 (tpt170) REVERT: B 118 MET cc_start: 0.9253 (tpp) cc_final: 0.8925 (mmm) REVERT: B 123 LYS cc_start: 0.9227 (ptpp) cc_final: 0.8772 (pttm) REVERT: B 133 LEU cc_start: 0.9449 (tm) cc_final: 0.9228 (pp) REVERT: B 246 GLU cc_start: 0.8972 (pm20) cc_final: 0.8747 (pm20) REVERT: B 250 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8496 (mmtp) REVERT: B 256 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8496 (pp20) REVERT: B 280 GLN cc_start: 0.9080 (tm-30) cc_final: 0.8775 (tm-30) REVERT: C 100 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8599 (pp30) REVERT: C 103 LYS cc_start: 0.9730 (mmmt) cc_final: 0.9521 (mmpt) REVERT: C 133 LEU cc_start: 0.9390 (tm) cc_final: 0.9184 (pp) REVERT: C 136 GLU cc_start: 0.8607 (pp20) cc_final: 0.8350 (pm20) REVERT: C 193 GLU cc_start: 0.9225 (tt0) cc_final: 0.8999 (tt0) REVERT: C 246 GLU cc_start: 0.9022 (pm20) cc_final: 0.8781 (pm20) REVERT: C 250 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8874 (mmtm) REVERT: C 256 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8473 (pp20) REVERT: D 133 LEU cc_start: 0.9428 (tm) cc_final: 0.9205 (pp) REVERT: D 246 GLU cc_start: 0.9017 (pm20) cc_final: 0.8783 (pm20) REVERT: E 107 LYS cc_start: 0.9670 (pptt) cc_final: 0.9462 (pptt) REVERT: E 172 MET cc_start: 0.8997 (tmm) cc_final: 0.8781 (tmm) REVERT: E 193 GLU cc_start: 0.9154 (tt0) cc_final: 0.8888 (tt0) REVERT: E 256 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8444 (pp20) REVERT: F 99 ASN cc_start: 0.9724 (m-40) cc_final: 0.9493 (m110) REVERT: F 102 GLU cc_start: 0.9523 (tm-30) cc_final: 0.9302 (tm-30) REVERT: F 107 LYS cc_start: 0.9765 (pptt) cc_final: 0.9559 (pptt) REVERT: F 116 ARG cc_start: 0.8876 (ttt180) cc_final: 0.8466 (tpt170) REVERT: F 133 LEU cc_start: 0.9540 (tm) cc_final: 0.9146 (pp) REVERT: F 140 MET cc_start: 0.7049 (mmm) cc_final: 0.6069 (mmp) REVERT: F 172 MET cc_start: 0.9039 (tmm) cc_final: 0.8753 (tmm) REVERT: F 246 GLU cc_start: 0.8936 (pm20) cc_final: 0.8619 (pm20) REVERT: F 250 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8483 (mmtm) REVERT: F 256 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8548 (pp20) REVERT: F 289 MET cc_start: 0.9398 (ptm) cc_final: 0.9044 (ppp) REVERT: G 102 GLU cc_start: 0.9570 (tm-30) cc_final: 0.9337 (tm-30) REVERT: G 116 ARG cc_start: 0.8863 (ttt180) cc_final: 0.8404 (tpt170) REVERT: G 133 LEU cc_start: 0.9401 (tm) cc_final: 0.9147 (pp) REVERT: G 246 GLU cc_start: 0.8980 (pm20) cc_final: 0.8751 (pm20) REVERT: G 301 GLU cc_start: 0.9086 (mp0) cc_final: 0.8696 (pm20) outliers start: 28 outliers final: 15 residues processed: 342 average time/residue: 0.7013 time to fit residues: 261.4553 Evaluate side-chains 331 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 310 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain G residue 126 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 64 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 116 optimal weight: 60.0000 chunk 98 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 105 GLN ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.094043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.056635 restraints weight = 38417.440| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 2.79 r_work: 0.2500 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16520 Z= 0.140 Angle : 0.813 16.957 22043 Z= 0.395 Chirality : 0.049 0.250 2492 Planarity : 0.004 0.052 2709 Dihedral : 8.043 59.917 3010 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.57 % Allowed : 30.01 % Favored : 68.42 % 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: 1.76 (0.18), residues: 2051 helix: 2.97 (0.14), residues: 1120 sheet: 0.22 (0.34), residues: 259 loop : -1.75 (0.19), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 271 TYR 0.023 0.001 TYR B 174 PHE 0.033 0.001 PHE F 101 TRP 0.004 0.001 TRP E 184 HIS 0.002 0.001 HIS G 137 Details of bonding type rmsd covalent geometry : bond 0.00315 (16520) covalent geometry : angle 0.81299 (22043) hydrogen bonds : bond 0.03848 ( 1153) hydrogen bonds : angle 3.54223 ( 3312) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 319 time to evaluate : 0.636 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: A 95 PHE cc_start: 0.9528 (m-10) cc_final: 0.9276 (m-80) REVERT: A 116 ARG cc_start: 0.8949 (ttt180) cc_final: 0.8547 (tpt170) REVERT: A 133 LEU cc_start: 0.9442 (tm) cc_final: 0.9161 (pp) REVERT: A 246 GLU cc_start: 0.8964 (pm20) cc_final: 0.8708 (pm20) REVERT: A 250 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8631 (mmtp) REVERT: A 289 MET cc_start: 0.9421 (OUTLIER) cc_final: 0.9062 (ppp) REVERT: B 102 GLU cc_start: 0.9607 (tm-30) cc_final: 0.8656 (tp30) REVERT: B 112 ILE cc_start: 0.9565 (pp) cc_final: 0.9049 (pp) REVERT: B 133 LEU cc_start: 0.9449 (tm) cc_final: 0.9198 (pp) REVERT: B 246 GLU cc_start: 0.8956 (pm20) cc_final: 0.8738 (pm20) REVERT: B 250 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8450 (mmtp) REVERT: B 256 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8490 (pp20) REVERT: C 95 PHE cc_start: 0.9500 (m-10) cc_final: 0.9258 (m-80) REVERT: C 100 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8612 (pp30) REVERT: C 103 LYS cc_start: 0.9760 (mmmt) cc_final: 0.9501 (mmpt) REVERT: C 133 LEU cc_start: 0.9395 (tm) cc_final: 0.9178 (pp) REVERT: C 193 GLU cc_start: 0.9178 (tt0) cc_final: 0.8968 (tt0) REVERT: C 246 GLU cc_start: 0.9020 (pm20) cc_final: 0.8773 (pm20) REVERT: C 250 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8870 (mmtm) REVERT: C 256 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8442 (pp20) REVERT: D 123 LYS cc_start: 0.9219 (ptpp) cc_final: 0.8822 (pttm) REVERT: D 133 LEU cc_start: 0.9415 (tm) cc_final: 0.9204 (pp) REVERT: D 246 GLU cc_start: 0.9004 (pm20) cc_final: 0.8766 (pm20) REVERT: D 301 GLU cc_start: 0.9057 (mp0) cc_final: 0.8719 (pm20) REVERT: E 95 PHE cc_start: 0.9503 (m-10) cc_final: 0.9217 (m-80) REVERT: E 102 GLU cc_start: 0.9585 (tm-30) cc_final: 0.9243 (tp30) REVERT: E 107 LYS cc_start: 0.9695 (pptt) cc_final: 0.9474 (pptt) REVERT: E 133 LEU cc_start: 0.9447 (tm) cc_final: 0.9198 (pp) REVERT: E 154 LEU cc_start: 0.9300 (tm) cc_final: 0.9099 (tm) REVERT: E 158 MET cc_start: 0.8846 (mtp) cc_final: 0.8263 (mtm) REVERT: E 172 MET cc_start: 0.9052 (tmm) cc_final: 0.8811 (tmm) REVERT: E 193 GLU cc_start: 0.9095 (tt0) cc_final: 0.8846 (tt0) REVERT: E 256 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8404 (pp20) REVERT: F 99 ASN cc_start: 0.9711 (m-40) cc_final: 0.9442 (m110) REVERT: F 102 GLU cc_start: 0.9553 (tm-30) cc_final: 0.9105 (tm-30) REVERT: F 116 ARG cc_start: 0.8890 (ttt180) cc_final: 0.8648 (tpt170) REVERT: F 172 MET cc_start: 0.9059 (tmm) cc_final: 0.8747 (tmm) REVERT: F 246 GLU cc_start: 0.8934 (pm20) cc_final: 0.8663 (pm20) REVERT: F 250 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8482 (mmtm) REVERT: F 256 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8519 (pp20) REVERT: F 289 MET cc_start: 0.9381 (ptm) cc_final: 0.9102 (ppp) REVERT: G 102 GLU cc_start: 0.9571 (tm-30) cc_final: 0.9339 (tm-30) REVERT: G 116 ARG cc_start: 0.8876 (ttt180) cc_final: 0.8401 (tpt170) REVERT: G 133 LEU cc_start: 0.9410 (tm) cc_final: 0.9166 (pp) REVERT: G 191 ASN cc_start: 0.9324 (t0) cc_final: 0.9078 (t0) REVERT: G 246 GLU cc_start: 0.8981 (pm20) cc_final: 0.8751 (pm20) REVERT: G 280 GLN cc_start: 0.8819 (tm-30) cc_final: 0.8609 (tp-100) REVERT: G 301 GLU cc_start: 0.9082 (mp0) cc_final: 0.8732 (pm20) REVERT: G 315 ASP cc_start: 0.9508 (t0) cc_final: 0.9291 (t0) outliers start: 23 outliers final: 18 residues processed: 336 average time/residue: 0.6858 time to fit residues: 251.4296 Evaluate side-chains 334 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 310 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 164 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 109 optimal weight: 0.6980 chunk 31 optimal weight: 60.0000 chunk 103 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 145 optimal weight: 60.0000 chunk 48 optimal weight: 4.9990 chunk 189 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 116 optimal weight: 50.0000 chunk 188 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.091348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.054086 restraints weight = 38428.434| |-----------------------------------------------------------------------------| r_work (start): 0.2622 rms_B_bonded: 2.73 r_work: 0.2440 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 16520 Z= 0.233 Angle : 0.884 17.823 22043 Z= 0.438 Chirality : 0.051 0.234 2492 Planarity : 0.005 0.118 2709 Dihedral : 8.179 56.052 3010 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.37 % Allowed : 30.90 % Favored : 67.74 % 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: 1.65 (0.18), residues: 2051 helix: 2.84 (0.14), residues: 1127 sheet: 0.23 (0.35), residues: 259 loop : -1.78 (0.19), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 271 TYR 0.018 0.001 TYR F 291 PHE 0.034 0.002 PHE A 101 TRP 0.010 0.001 TRP F 184 HIS 0.005 0.002 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00547 (16520) covalent geometry : angle 0.88427 (22043) hydrogen bonds : bond 0.04781 ( 1153) hydrogen bonds : angle 3.81828 ( 3312) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 318 time to evaluate : 0.491 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: A 95 PHE cc_start: 0.9539 (m-10) cc_final: 0.9282 (m-80) REVERT: A 116 ARG cc_start: 0.8915 (ttt180) cc_final: 0.8481 (tpt170) REVERT: A 133 LEU cc_start: 0.9492 (tm) cc_final: 0.9189 (pp) REVERT: A 246 GLU cc_start: 0.9021 (pm20) cc_final: 0.8796 (pm20) REVERT: A 280 GLN cc_start: 0.8972 (tm-30) cc_final: 0.8709 (tp-100) REVERT: B 133 LEU cc_start: 0.9474 (tm) cc_final: 0.9208 (pp) REVERT: B 246 GLU cc_start: 0.9019 (pm20) cc_final: 0.8758 (pm20) REVERT: B 250 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8558 (mmtp) REVERT: B 256 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8489 (pp20) REVERT: C 95 PHE cc_start: 0.9512 (m-10) cc_final: 0.9260 (m-80) REVERT: C 103 LYS cc_start: 0.9788 (mmmt) cc_final: 0.9535 (mmpt) REVERT: C 116 ARG cc_start: 0.9106 (mmp80) cc_final: 0.8685 (mmp80) REVERT: C 193 GLU cc_start: 0.9270 (tt0) cc_final: 0.9020 (tt0) REVERT: C 246 GLU cc_start: 0.9018 (pm20) cc_final: 0.8778 (pm20) REVERT: C 250 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8935 (mmtm) REVERT: D 95 PHE cc_start: 0.9502 (m-10) cc_final: 0.9253 (m-80) REVERT: D 103 LYS cc_start: 0.9637 (mmmt) cc_final: 0.9401 (mmtm) REVERT: D 116 ARG cc_start: 0.8914 (ttt180) cc_final: 0.8569 (tpt170) REVERT: D 246 GLU cc_start: 0.9030 (pm20) cc_final: 0.8757 (pm20) REVERT: D 301 GLU cc_start: 0.9097 (mp0) cc_final: 0.8747 (pm20) REVERT: E 95 PHE cc_start: 0.9473 (m-10) cc_final: 0.9207 (m-80) REVERT: E 102 GLU cc_start: 0.9588 (tm-30) cc_final: 0.9255 (tp30) REVERT: E 107 LYS cc_start: 0.9693 (pptt) cc_final: 0.9475 (pptt) REVERT: E 172 MET cc_start: 0.9029 (tmm) cc_final: 0.8808 (tmm) REVERT: F 95 PHE cc_start: 0.9488 (m-10) cc_final: 0.9158 (m-80) REVERT: F 99 ASN cc_start: 0.9707 (m-40) cc_final: 0.9453 (m110) REVERT: F 102 GLU cc_start: 0.9609 (tm-30) cc_final: 0.9396 (tm-30) REVERT: F 103 LYS cc_start: 0.9689 (mmmt) cc_final: 0.9411 (mmtm) REVERT: F 116 ARG cc_start: 0.8885 (ttt180) cc_final: 0.8629 (tpt170) REVERT: F 172 MET cc_start: 0.9114 (tmm) cc_final: 0.8832 (tmm) REVERT: F 246 GLU cc_start: 0.8980 (pm20) cc_final: 0.8758 (pm20) REVERT: F 250 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8571 (mmtm) REVERT: F 315 ASP cc_start: 0.9418 (t0) cc_final: 0.9205 (t0) REVERT: G 95 PHE cc_start: 0.9549 (m-10) cc_final: 0.9288 (m-80) REVERT: G 102 GLU cc_start: 0.9618 (tm-30) cc_final: 0.9375 (tm-30) REVERT: G 116 ARG cc_start: 0.8858 (ttt180) cc_final: 0.8359 (tpt170) REVERT: G 133 LEU cc_start: 0.9452 (tm) cc_final: 0.9217 (pp) REVERT: G 246 GLU cc_start: 0.9009 (pm20) cc_final: 0.8768 (pm20) outliers start: 20 outliers final: 20 residues processed: 333 average time/residue: 0.6629 time to fit residues: 241.2064 Evaluate side-chains 331 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 308 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 319 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 46 optimal weight: 0.7980 chunk 118 optimal weight: 60.0000 chunk 106 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 29 optimal weight: 60.0000 chunk 93 optimal weight: 10.0000 chunk 4 optimal weight: 40.0000 chunk 111 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 GLN C 105 GLN ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.093142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.055810 restraints weight = 38284.144| |-----------------------------------------------------------------------------| r_work (start): 0.2662 rms_B_bonded: 2.76 r_work: 0.2490 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 16520 Z= 0.156 Angle : 0.898 18.953 22043 Z= 0.434 Chirality : 0.052 0.362 2492 Planarity : 0.005 0.135 2709 Dihedral : 7.837 53.060 3010 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.09 % Allowed : 31.58 % Favored : 67.33 % 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: 1.63 (0.18), residues: 2051 helix: 2.80 (0.15), residues: 1127 sheet: 0.20 (0.34), residues: 259 loop : -1.75 (0.19), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 271 TYR 0.021 0.001 TYR G 174 PHE 0.039 0.001 PHE C 138 TRP 0.005 0.001 TRP B 299 HIS 0.003 0.001 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00361 (16520) covalent geometry : angle 0.89751 (22043) hydrogen bonds : bond 0.04041 ( 1153) hydrogen bonds : angle 3.70041 ( 3312) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 317 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 PHE cc_start: 0.9559 (m-10) cc_final: 0.9276 (m-80) REVERT: A 116 ARG cc_start: 0.8959 (ttt180) cc_final: 0.8606 (tpt170) REVERT: A 133 LEU cc_start: 0.9478 (tm) cc_final: 0.9197 (pp) REVERT: A 246 GLU cc_start: 0.8967 (pm20) cc_final: 0.8715 (pm20) REVERT: A 280 GLN cc_start: 0.8874 (tm-30) cc_final: 0.8612 (tp-100) REVERT: A 289 MET cc_start: 0.9412 (OUTLIER) cc_final: 0.9074 (ppp) REVERT: B 116 ARG cc_start: 0.9001 (mmp80) cc_final: 0.8529 (mmp80) REVERT: B 133 LEU cc_start: 0.9463 (tm) cc_final: 0.9187 (pp) REVERT: B 193 GLU cc_start: 0.9188 (tt0) cc_final: 0.8925 (tt0) REVERT: B 246 GLU cc_start: 0.8964 (pm20) cc_final: 0.8709 (pm20) REVERT: B 250 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8463 (mmtp) REVERT: B 256 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8519 (pp20) REVERT: C 95 PHE cc_start: 0.9518 (m-10) cc_final: 0.9243 (m-80) REVERT: C 103 LYS cc_start: 0.9780 (mmmt) cc_final: 0.9575 (mmpt) REVERT: C 116 ARG cc_start: 0.9114 (mmp80) cc_final: 0.8691 (mmp80) REVERT: C 193 GLU cc_start: 0.9230 (tt0) cc_final: 0.9006 (tt0) REVERT: C 246 GLU cc_start: 0.8984 (pm20) cc_final: 0.8749 (pm20) REVERT: C 250 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8869 (mmtm) REVERT: C 256 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8496 (pp20) REVERT: D 95 PHE cc_start: 0.9491 (m-10) cc_final: 0.9230 (m-80) REVERT: D 103 LYS cc_start: 0.9630 (mmmt) cc_final: 0.9403 (mmtm) REVERT: D 108 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.9119 (mmtm) REVERT: D 246 GLU cc_start: 0.9018 (pm20) cc_final: 0.8782 (pm20) REVERT: D 301 GLU cc_start: 0.9057 (mp0) cc_final: 0.8728 (pm20) REVERT: E 95 PHE cc_start: 0.9489 (m-10) cc_final: 0.9212 (m-80) REVERT: E 102 GLU cc_start: 0.9583 (tm-30) cc_final: 0.9289 (tp30) REVERT: E 107 LYS cc_start: 0.9694 (pptt) cc_final: 0.9482 (pptt) REVERT: E 154 LEU cc_start: 0.9294 (tm) cc_final: 0.9088 (tm) REVERT: E 158 MET cc_start: 0.8869 (mtp) cc_final: 0.8328 (mtm) REVERT: E 172 MET cc_start: 0.9038 (tmm) cc_final: 0.8832 (tmm) REVERT: E 193 GLU cc_start: 0.9127 (tt0) cc_final: 0.8899 (tt0) REVERT: E 256 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8431 (pp20) REVERT: F 99 ASN cc_start: 0.9684 (m-40) cc_final: 0.9418 (m110) REVERT: F 102 GLU cc_start: 0.9593 (tm-30) cc_final: 0.9355 (tm-30) REVERT: F 103 LYS cc_start: 0.9699 (mmmt) cc_final: 0.9419 (mmtm) REVERT: F 116 ARG cc_start: 0.8909 (ttt180) cc_final: 0.8660 (tpt170) REVERT: F 172 MET cc_start: 0.9043 (tmm) cc_final: 0.8735 (tmm) REVERT: F 246 GLU cc_start: 0.8922 (pm20) cc_final: 0.8673 (pm20) REVERT: F 250 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8517 (mmtm) REVERT: F 256 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8482 (pp20) REVERT: F 289 MET cc_start: 0.9363 (ptm) cc_final: 0.9077 (ppp) REVERT: F 315 ASP cc_start: 0.9409 (t0) cc_final: 0.9206 (t0) REVERT: G 95 PHE cc_start: 0.9558 (m-10) cc_final: 0.9298 (m-80) REVERT: G 102 GLU cc_start: 0.9616 (tm-30) cc_final: 0.9383 (tm-30) REVERT: G 116 ARG cc_start: 0.8880 (ttt180) cc_final: 0.8358 (tpt170) REVERT: G 133 LEU cc_start: 0.9455 (tm) cc_final: 0.9221 (pp) REVERT: G 191 ASN cc_start: 0.9345 (t0) cc_final: 0.9105 (t0) REVERT: G 246 GLU cc_start: 0.8984 (pm20) cc_final: 0.8724 (pm20) REVERT: G 315 ASP cc_start: 0.9509 (t0) cc_final: 0.9293 (t0) outliers start: 16 outliers final: 19 residues processed: 332 average time/residue: 0.6623 time to fit residues: 240.3525 Evaluate side-chains 329 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 305 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 44 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 145 optimal weight: 60.0000 chunk 115 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 62 optimal weight: 30.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 GLN C 105 GLN ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.093404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.056057 restraints weight = 38117.946| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 2.78 r_work: 0.2499 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 16520 Z= 0.152 Angle : 0.915 18.754 22043 Z= 0.442 Chirality : 0.054 0.402 2492 Planarity : 0.004 0.077 2709 Dihedral : 7.664 50.598 3010 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.09 % Allowed : 31.72 % Favored : 67.19 % 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: 1.67 (0.18), residues: 2051 helix: 2.85 (0.15), residues: 1120 sheet: 0.19 (0.35), residues: 259 loop : -1.69 (0.19), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 271 TYR 0.013 0.001 TYR A 291 PHE 0.033 0.001 PHE E 101 TRP 0.004 0.001 TRP E 184 HIS 0.005 0.001 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00354 (16520) covalent geometry : angle 0.91463 (22043) hydrogen bonds : bond 0.03998 ( 1153) hydrogen bonds : angle 3.69497 ( 3312) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6525.95 seconds wall clock time: 111 minutes 44.77 seconds (6704.77 seconds total)