Starting phenix.real_space_refine on Thu Mar 5 18:46:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jzy_22584/03_2026/7jzy_22584.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jzy_22584/03_2026/7jzy_22584.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jzy_22584/03_2026/7jzy_22584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jzy_22584/03_2026/7jzy_22584.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jzy_22584/03_2026/7jzy_22584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jzy_22584/03_2026/7jzy_22584.map" } resolution = 3.6 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= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians P 60 5.49 5 S 33 5.16 5 C 15198 2.51 5 N 4473 2.21 5 O 4775 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 155 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24539 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3088 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 24, 'TRANS': 402} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 356 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 297 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ASP:plan': 11, 'GLN:plan1': 9, 'GLU:plan': 9, 'ARG:plan': 11, 'HIS:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 234 Chain: "B" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2411 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 24, 'TRANS': 281} Chain breaks: 1 Chain: "C" Number of atoms: 1448 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 54 Conformer: "B" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 1480 Chain: "M" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1273 Classifications: {'DNA': 1, 'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 17, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 28, 'rna3p': 32} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2307 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 10, 'TRANS': 287} Chain breaks: 2 Chain: "E" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "F" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "G" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "H" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2554 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain breaks: 1 Chain: "I" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "J" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 545 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain: "K" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 545 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Time building chain proxies: 5.64, per 1000 atoms: 0.23 Number of scatterers: 24539 At special positions: 0 Unit cell: (130.2, 157.5, 150.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 P 60 15.00 O 4775 8.00 N 4473 7.00 C 15198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 1.1 seconds 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5630 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 55 sheets defined 32.3% alpha, 21.4% beta 6 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 2.87 Creating SS restraints... Processing helix chain 'A' and resid 9 through 31 Processing helix chain 'A' and resid 38 through 47 removed outlier: 4.423A pdb=" N THR A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 removed outlier: 3.715A pdb=" N ALA A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 114 through 122 removed outlier: 4.341A pdb=" N PHE A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 removed outlier: 3.834A pdb=" N GLU A 136 " --> pdb=" O ASN A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 160 removed outlier: 3.593A pdb=" N ALA A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 164 Processing helix chain 'A' and resid 196 through 212 Processing helix chain 'A' and resid 212 through 224 removed outlier: 4.011A pdb=" N ALA A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 258 removed outlier: 3.908A pdb=" N GLU A 257 " --> pdb=" O GLN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 294 through 306 removed outlier: 3.645A pdb=" N SER A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 344 removed outlier: 4.885A pdb=" N ALA A 317 " --> pdb=" O HIS A 313 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 removed outlier: 3.599A pdb=" N ALA A 349 " --> pdb=" O GLY A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 381 Processing helix chain 'A' and resid 386 through 396 removed outlier: 3.963A pdb=" N ARG A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 409 through 431 removed outlier: 3.799A pdb=" N ASP A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 48 removed outlier: 3.864A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 165 through 180 removed outlier: 3.542A pdb=" N ARG B 179 " --> pdb=" O ARG B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 204 removed outlier: 3.888A pdb=" N LEU B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 218 Processing helix chain 'B' and resid 291 through 295 removed outlier: 3.857A pdb=" N VAL B 295 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'C' and resid 16 through 36 removed outlier: 3.507A pdb=" N LEU C 20 " --> pdb=" O PRO C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 71 Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 108 through 121 removed outlier: 3.728A pdb=" N LEU C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 131 Processing helix chain 'D' and resid 51 through 55 removed outlier: 3.621A pdb=" N SER D 55 " --> pdb=" O ARG D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 148 Processing helix chain 'D' and resid 151 through 163 Processing helix chain 'D' and resid 209 through 223 Processing helix chain 'D' and resid 275 through 284 removed outlier: 3.512A pdb=" N ILE D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 332 removed outlier: 3.646A pdb=" N LEU D 326 " --> pdb=" O ASP D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 51 through 55 Processing helix chain 'E' and resid 82 through 91 Processing helix chain 'E' and resid 130 through 148 Processing helix chain 'E' and resid 151 through 163 Processing helix chain 'E' and resid 209 through 223 removed outlier: 3.510A pdb=" N ALA E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 284 Processing helix chain 'E' and resid 293 through 297 removed outlier: 3.523A pdb=" N LEU E 296 " --> pdb=" O GLU E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 332 removed outlier: 3.577A pdb=" N LEU E 326 " --> pdb=" O ASP E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 352 Processing helix chain 'F' and resid 51 through 55 Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.652A pdb=" N SER F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 148 removed outlier: 3.506A pdb=" N ARG F 134 " --> pdb=" O ASP F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 163 Processing helix chain 'F' and resid 210 through 224 Processing helix chain 'F' and resid 275 through 284 Processing helix chain 'F' and resid 322 through 332 removed outlier: 3.703A pdb=" N LEU F 326 " --> pdb=" O ASP F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 352 Processing helix chain 'G' and resid 82 through 91 Processing helix chain 'G' and resid 130 through 148 Processing helix chain 'G' and resid 151 through 163 Processing helix chain 'G' and resid 208 through 223 Processing helix chain 'G' and resid 275 through 284 Processing helix chain 'G' and resid 293 through 297 removed outlier: 3.644A pdb=" N LEU G 296 " --> pdb=" O GLU G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 332 removed outlier: 3.605A pdb=" N LEU G 326 " --> pdb=" O ASP G 322 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 352 Processing helix chain 'H' and resid 51 through 55 Processing helix chain 'H' and resid 82 through 92 removed outlier: 3.575A pdb=" N SER H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 148 Processing helix chain 'H' and resid 151 through 163 removed outlier: 3.506A pdb=" N ARG H 155 " --> pdb=" O ALA H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 223 Processing helix chain 'H' and resid 275 through 284 Processing helix chain 'H' and resid 322 through 331 removed outlier: 3.538A pdb=" N LEU H 326 " --> pdb=" O ASP H 322 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 352 Processing helix chain 'I' and resid 51 through 55 removed outlier: 3.530A pdb=" N SER I 55 " --> pdb=" O ARG I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 90 Processing helix chain 'I' and resid 130 through 148 Processing helix chain 'I' and resid 152 through 163 Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 275 through 284 Processing helix chain 'I' and resid 322 through 332 removed outlier: 3.578A pdb=" N LEU I 326 " --> pdb=" O ASP I 322 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 352 Processing helix chain 'J' and resid 26 through 37 removed outlier: 3.584A pdb=" N ARG J 32 " --> pdb=" O SER J 28 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS J 36 " --> pdb=" O ARG J 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 37 removed outlier: 3.584A pdb=" N ARG K 32 " --> pdb=" O SER K 28 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS K 36 " --> pdb=" O ARG K 32 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 69 Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 192 removed outlier: 6.244A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 191 through 192 removed outlier: 6.244A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N PHE B 279 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ALA B 257 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU B 281 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TYR B 255 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TRP B 247 " --> pdb=" O TRP B 289 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 232 through 233 removed outlier: 3.518A pdb=" N PHE A 232 " --> pdb=" O PHE B 221 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 265 through 267 removed outlier: 6.005A pdb=" N LEU A 265 " --> pdb=" O TRP B 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 55 through 60 removed outlier: 4.088A pdb=" N VAL B 59 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU B 110 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU B 105 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N SER B 16 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL B 107 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG B 14 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER B 16 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.773A pdb=" N LEU B 105 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N SER B 16 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL B 107 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG B 14 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA B 157 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AB2, first strand: chain 'B' and resid 304 through 306 removed outlier: 3.547A pdb=" N SER B 317 " --> pdb=" O TYR B 304 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 41 through 43 Processing sheet with id=AB4, first strand: chain 'C' and resid 41 through 43 Processing sheet with id=AB5, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AB6, first strand: chain 'C' and resid 100 through 103 removed outlier: 4.192A pdb=" N PHE C 158 " --> pdb=" O VAL C 103 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 32 through 33 Processing sheet with id=AB8, first strand: chain 'D' and resid 38 through 39 removed outlier: 3.630A pdb=" N VAL D 118 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL D 228 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL D 179 " --> pdb=" O PHE D 195 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG D 191 " --> pdb=" O HIS D 183 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 38 through 39 Processing sheet with id=AC1, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AC2, first strand: chain 'D' and resid 248 through 249 removed outlier: 3.707A pdb=" N THR D 264 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 285 through 287 Processing sheet with id=AC4, first strand: chain 'D' and resid 306 through 307 Processing sheet with id=AC5, first strand: chain 'E' and resid 127 through 128 removed outlier: 3.742A pdb=" N ALA E 127 " --> pdb=" O ALA E 32 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 189 through 192 removed outlier: 6.789A pdb=" N HIS E 183 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ALA E 192 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE E 181 " --> pdb=" O ALA E 192 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 189 through 192 removed outlier: 6.789A pdb=" N HIS E 183 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ALA E 192 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE E 181 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU E 229 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL E 228 " --> pdb=" O VAL E 118 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 64 through 70 removed outlier: 3.500A pdb=" N GLY E 70 " --> pdb=" O ASN E 94 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN E 94 " --> pdb=" O GLY E 70 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 248 through 249 removed outlier: 4.113A pdb=" N THR E 264 " --> pdb=" O GLU E 249 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 306 through 307 removed outlier: 3.514A pdb=" N VAL E 307 " --> pdb=" O LYS E 312 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS E 312 " --> pdb=" O VAL E 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'F' and resid 127 through 128 removed outlier: 3.564A pdb=" N ALA F 127 " --> pdb=" O ALA F 32 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 38 through 39 removed outlier: 3.624A pdb=" N VAL F 118 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL F 228 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU F 229 " --> pdb=" O ILE F 184 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 189 through 192 removed outlier: 6.831A pdb=" N HIS F 183 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ALA F 192 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE F 181 " --> pdb=" O ALA F 192 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU F 229 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL F 228 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL F 118 " --> pdb=" O VAL F 228 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 63 through 70 removed outlier: 3.799A pdb=" N ASN F 94 " --> pdb=" O GLY F 70 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 285 through 287 Processing sheet with id=AD7, first strand: chain 'F' and resid 306 through 307 Processing sheet with id=AD8, first strand: chain 'G' and resid 127 through 128 Processing sheet with id=AD9, first strand: chain 'G' and resid 38 through 39 removed outlier: 3.627A pdb=" N VAL G 118 " --> pdb=" O VAL G 228 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 189 through 192 removed outlier: 6.819A pdb=" N HIS G 183 " --> pdb=" O ALA G 190 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ALA G 192 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE G 181 " --> pdb=" O ALA G 192 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL G 118 " --> pdb=" O VAL G 228 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 63 through 66 Processing sheet with id=AE3, first strand: chain 'G' and resid 69 through 70 removed outlier: 3.504A pdb=" N GLY G 70 " --> pdb=" O ASN G 94 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 285 through 287 Processing sheet with id=AE5, first strand: chain 'G' and resid 306 through 307 Processing sheet with id=AE6, first strand: chain 'H' and resid 127 through 128 Processing sheet with id=AE7, first strand: chain 'H' and resid 38 through 39 removed outlier: 4.323A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 189 through 192 removed outlier: 6.810A pdb=" N HIS H 183 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ALA H 192 " --> pdb=" O ILE H 181 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE H 181 " --> pdb=" O ALA H 192 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 64 through 70 removed outlier: 3.614A pdb=" N GLY H 70 " --> pdb=" O ASN H 94 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN H 94 " --> pdb=" O GLY H 70 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 285 through 287 Processing sheet with id=AF2, first strand: chain 'H' and resid 306 through 307 removed outlier: 3.783A pdb=" N LYS H 312 " --> pdb=" O VAL H 307 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 127 through 128 removed outlier: 3.611A pdb=" N ALA I 127 " --> pdb=" O ALA I 32 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA I 32 " --> pdb=" O ALA I 127 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 38 through 39 removed outlier: 4.741A pdb=" N LEU I 229 " --> pdb=" O ILE I 184 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 189 through 192 removed outlier: 6.677A pdb=" N HIS I 183 " --> pdb=" O ALA I 190 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ALA I 192 " --> pdb=" O ILE I 181 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE I 181 " --> pdb=" O ALA I 192 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LEU I 229 " --> pdb=" O ILE I 184 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 64 through 70 removed outlier: 3.616A pdb=" N GLY I 70 " --> pdb=" O ASN I 94 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA I 101 " --> pdb=" O VAL I 244 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 285 through 287 Processing sheet with id=AF8, first strand: chain 'I' and resid 306 through 307 removed outlier: 3.656A pdb=" N LYS I 312 " --> pdb=" O VAL I 307 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 20 through 24 removed outlier: 3.649A pdb=" N ALA J 56 " --> pdb=" O ILE J 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 20 through 24 removed outlier: 3.648A pdb=" N ALA K 56 " --> pdb=" O ILE K 47 " (cutoff:3.500A) 1057 hydrogen bonds defined for protein. 2883 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 4.54 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4773 1.32 - 1.45: 6345 1.45 - 1.57: 13855 1.57 - 1.69: 120 1.69 - 1.81: 50 Bond restraints: 25143 Sorted by residual: bond pdb=" C LEU B 181 " pdb=" N PRO B 182 " ideal model delta sigma weight residual 1.337 1.385 -0.048 9.80e-03 1.04e+04 2.45e+01 bond pdb=" N ASP G 253 " pdb=" CA ASP G 253 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.05e+00 bond pdb=" CD LYS I 257 " pdb=" CE LYS I 257 " ideal model delta sigma weight residual 1.520 1.439 0.081 3.00e-02 1.11e+03 7.32e+00 bond pdb=" N TYR A 125 " pdb=" CA TYR A 125 " ideal model delta sigma weight residual 1.458 1.491 -0.032 1.23e-02 6.61e+03 6.83e+00 bond pdb=" N LEU C 71 " pdb=" CA LEU C 71 " ideal model delta sigma weight residual 1.456 1.491 -0.034 1.31e-02 5.83e+03 6.77e+00 ... (remaining 25138 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 32926 2.11 - 4.23: 1314 4.23 - 6.34: 134 6.34 - 8.45: 33 8.45 - 10.57: 8 Bond angle restraints: 34415 Sorted by residual: angle pdb=" C GLN A 124 " pdb=" N TYR A 125 " pdb=" CA TYR A 125 " ideal model delta sigma weight residual 120.82 129.53 -8.71 1.50e+00 4.44e-01 3.37e+01 angle pdb=" C LYS H 77 " pdb=" N THR H 78 " pdb=" CA THR H 78 " ideal model delta sigma weight residual 121.54 132.11 -10.57 1.91e+00 2.74e-01 3.06e+01 angle pdb=" C LEU A 32 " pdb=" N GLN A 33 " pdb=" CA GLN A 33 " ideal model delta sigma weight residual 123.10 127.51 -4.41 9.60e-01 1.09e+00 2.11e+01 angle pdb=" C LYS F 77 " pdb=" N THR F 78 " pdb=" CA THR F 78 " ideal model delta sigma weight residual 121.54 129.90 -8.36 1.91e+00 2.74e-01 1.92e+01 angle pdb=" C4' C M 37 " pdb=" C3' C M 37 " pdb=" O3' C M 37 " ideal model delta sigma weight residual 109.40 115.95 -6.55 1.50e+00 4.44e-01 1.91e+01 ... (remaining 34410 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 14655 35.34 - 70.67: 492 70.67 - 106.01: 49 106.01 - 141.34: 1 141.34 - 176.68: 6 Dihedral angle restraints: 15203 sinusoidal: 6493 harmonic: 8710 Sorted by residual: dihedral pdb=" O4' U M 33 " pdb=" C1' U M 33 " pdb=" N1 U M 33 " pdb=" C2 U M 33 " ideal model delta sinusoidal sigma weight residual 200.00 44.21 155.79 1 1.50e+01 4.44e-03 8.16e+01 dihedral pdb=" O4' U M 21 " pdb=" C1' U M 21 " pdb=" N1 U M 21 " pdb=" C2 U M 21 " ideal model delta sinusoidal sigma weight residual 200.00 45.69 154.31 1 1.50e+01 4.44e-03 8.11e+01 dihedral pdb=" O4' C M 38 " pdb=" C1' C M 38 " pdb=" N1 C M 38 " pdb=" C2 C M 38 " ideal model delta sinusoidal sigma weight residual -128.00 48.68 -176.68 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 15200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3421 0.079 - 0.158: 431 0.158 - 0.236: 30 0.236 - 0.315: 2 0.315 - 0.394: 1 Chirality restraints: 3885 Sorted by residual: chirality pdb=" C1' U M 33 " pdb=" O4' U M 33 " pdb=" C2' U M 33 " pdb=" N1 U M 33 " both_signs ideal model delta sigma weight residual False 2.47 2.07 0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" CB THR B 318 " pdb=" CA THR B 318 " pdb=" OG1 THR B 318 " pdb=" CG2 THR B 318 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C3' A M 36 " pdb=" C4' A M 36 " pdb=" O3' A M 36 " pdb=" C2' A M 36 " both_signs ideal model delta sigma weight residual False -2.48 -2.76 0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 3882 not shown) Planarity restraints: 4315 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 186 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C GLN D 186 " -0.055 2.00e-02 2.50e+03 pdb=" O GLN D 186 " 0.020 2.00e-02 2.50e+03 pdb=" N GLY D 187 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 300 " -0.016 2.00e-02 2.50e+03 3.13e-02 9.82e+00 pdb=" C ASP B 300 " 0.054 2.00e-02 2.50e+03 pdb=" O ASP B 300 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU B 301 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 71 " 0.048 5.00e-02 4.00e+02 7.20e-02 8.30e+00 pdb=" N PRO A 72 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " 0.041 5.00e-02 4.00e+02 ... (remaining 4312 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5173 2.77 - 3.30: 21534 3.30 - 3.83: 41266 3.83 - 4.37: 48830 4.37 - 4.90: 82946 Nonbonded interactions: 199749 Sorted by model distance: nonbonded pdb=" OH TYR E 324 " pdb=" O SER F 73 " model vdw 2.236 3.040 nonbonded pdb=" OH TYR G 324 " pdb=" O SER H 73 " model vdw 2.250 3.040 nonbonded pdb=" OG SER B 24 " pdb=" O PHE B 31 " model vdw 2.252 3.040 nonbonded pdb=" O2' C M 31 " pdb=" O ARG F 69 " model vdw 2.264 3.040 nonbonded pdb=" OH TYR D 324 " pdb=" O SER E 73 " model vdw 2.265 3.040 ... (remaining 199744 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: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = (chain 'E' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'F' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'G' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'H' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'I' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) } ncs_group { reference = chain 'J' selection = chain 'K' } 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=0.37 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 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: 0.380 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 24.260 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 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 : 0.009 0.081 25143 Z= 0.400 Angle : 0.960 10.568 34415 Z= 0.544 Chirality : 0.053 0.394 3885 Planarity : 0.006 0.072 4315 Dihedral : 17.371 176.679 9573 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.85 % Allowed : 10.25 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % 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: -3.78 (0.12), residues: 2995 helix: -2.61 (0.12), residues: 902 sheet: -1.18 (0.22), residues: 482 loop : -2.95 (0.12), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG K 46 TYR 0.018 0.003 TYR E 290 PHE 0.026 0.002 PHE A 287 TRP 0.025 0.002 TRP A 414 HIS 0.011 0.002 HIS D 343 Details of bonding type rmsd covalent geometry : bond 0.00879 (25143) covalent geometry : angle 0.95991 (34415) hydrogen bonds : bond 0.18488 ( 991) hydrogen bonds : angle 7.69968 ( 2911) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 418 time to evaluate : 0.827 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 216 LYS cc_start: 0.8820 (tppt) cc_final: 0.7886 (ptmm) REVERT: B 124 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7620 (pm20) REVERT: D 146 ASN cc_start: 0.8180 (t0) cc_final: 0.7814 (t0) REVERT: D 159 HIS cc_start: 0.7826 (m90) cc_final: 0.7611 (m-70) REVERT: D 195 PHE cc_start: 0.8131 (m-80) cc_final: 0.7863 (m-80) REVERT: D 206 LYS cc_start: 0.7649 (tptt) cc_final: 0.7307 (tptp) REVERT: D 278 LYS cc_start: 0.8863 (tttp) cc_final: 0.8598 (tttt) REVERT: D 294 ASP cc_start: 0.7455 (t70) cc_final: 0.7210 (t70) REVERT: E 74 ASN cc_start: 0.8420 (p0) cc_final: 0.7916 (p0) REVERT: E 146 ASN cc_start: 0.8863 (t0) cc_final: 0.8590 (t0) REVERT: F 90 ILE cc_start: 0.9164 (pt) cc_final: 0.8849 (mt) REVERT: F 94 ASN cc_start: 0.8581 (p0) cc_final: 0.8338 (p0) REVERT: F 203 ARG cc_start: 0.7593 (ptp-110) cc_final: 0.7257 (ttm110) REVERT: F 212 ASP cc_start: 0.8084 (m-30) cc_final: 0.7844 (m-30) REVERT: G 290 TYR cc_start: 0.8867 (p90) cc_final: 0.8654 (p90) REVERT: H 146 ASN cc_start: 0.8273 (t0) cc_final: 0.7905 (t0) REVERT: H 251 ILE cc_start: 0.8545 (pt) cc_final: 0.8329 (pt) REVERT: H 269 ARG cc_start: 0.8549 (ptp-170) cc_final: 0.8273 (ptp90) REVERT: I 249 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7625 (mm-30) REVERT: I 312 LYS cc_start: 0.8754 (tttm) cc_final: 0.8393 (ttpp) REVERT: J 29 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8454 (tt0) REVERT: K 58 LYS cc_start: 0.9313 (tttm) cc_final: 0.8782 (tttp) outliers start: 20 outliers final: 5 residues processed: 430 average time/residue: 0.1959 time to fit residues: 123.2518 Evaluate side-chains 267 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 261 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain J residue 29 GLN Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 50 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 4.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN A 396 ASN B 69 GLN B 195 GLN B 306 HIS C 29 HIS D 170 ASN F 56 GLN F 183 HIS G 51 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 242 GLN ** H 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 51 GLN I 94 ASN I 96 GLN I 183 HIS I 310 GLN J 51 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.137768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.099174 restraints weight = 39942.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.100225 restraints weight = 32591.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.100442 restraints weight = 24209.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.101788 restraints weight = 19887.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.101779 restraints weight = 17271.359| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25143 Z= 0.135 Angle : 0.595 11.227 34415 Z= 0.313 Chirality : 0.041 0.301 3885 Planarity : 0.004 0.059 4315 Dihedral : 15.218 179.469 4249 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.88 % Allowed : 14.27 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.13), residues: 2995 helix: -0.53 (0.16), residues: 900 sheet: -0.79 (0.22), residues: 503 loop : -2.56 (0.13), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 73 TYR 0.019 0.001 TYR I 144 PHE 0.021 0.001 PHE C 173 TRP 0.022 0.001 TRP A 394 HIS 0.006 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00287 (25143) covalent geometry : angle 0.59474 (34415) hydrogen bonds : bond 0.03852 ( 991) hydrogen bonds : angle 5.08991 ( 2911) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 326 time to evaluate : 0.771 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 116 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7712 (p0) REVERT: B 124 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7635 (pm20) REVERT: C 2 ASP cc_start: 0.5809 (p0) cc_final: 0.5561 (p0) REVERT: C 186 TRP cc_start: 0.7805 (t-100) cc_final: 0.7575 (t-100) REVERT: D 146 ASN cc_start: 0.8085 (t0) cc_final: 0.7748 (t0) REVERT: D 195 PHE cc_start: 0.8014 (m-80) cc_final: 0.7774 (m-80) REVERT: D 206 LYS cc_start: 0.7879 (tptt) cc_final: 0.7616 (tptp) REVERT: D 211 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8579 (tt) REVERT: D 212 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.7937 (m-30) REVERT: D 294 ASP cc_start: 0.7279 (t70) cc_final: 0.6998 (t70) REVERT: E 74 ASN cc_start: 0.8256 (p0) cc_final: 0.7952 (p0) REVERT: E 146 ASN cc_start: 0.8887 (t0) cc_final: 0.8631 (t0) REVERT: F 90 ILE cc_start: 0.9147 (pt) cc_final: 0.8941 (mt) REVERT: F 203 ARG cc_start: 0.7575 (ptp-110) cc_final: 0.7308 (ttm110) REVERT: F 212 ASP cc_start: 0.8036 (m-30) cc_final: 0.7830 (m-30) REVERT: G 155 ARG cc_start: 0.7983 (ttp80) cc_final: 0.7759 (ttp80) REVERT: H 146 ASN cc_start: 0.8242 (t0) cc_final: 0.7892 (t0) REVERT: H 269 ARG cc_start: 0.8527 (ptp-170) cc_final: 0.8287 (ptp90) REVERT: H 304 TYR cc_start: 0.8313 (m-80) cc_final: 0.8006 (m-80) REVERT: I 249 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7583 (mm-30) REVERT: I 310 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8199 (mt0) REVERT: J 29 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8575 (tt0) REVERT: K 58 LYS cc_start: 0.9110 (tttm) cc_final: 0.8541 (tttp) outliers start: 44 outliers final: 23 residues processed: 358 average time/residue: 0.1723 time to fit residues: 95.4058 Evaluate side-chains 300 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 272 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 310 GLN Chi-restraints excluded: chain J residue 29 GLN Chi-restraints excluded: chain K residue 50 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 89 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 chunk 246 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 73 optimal weight: 0.0020 overall best weight: 2.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 HIS C 29 HIS C 165 GLN D 248 GLN D 281 ASN D 329 ASN F 260 GLN F 281 ASN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN G 310 GLN G 342 GLN ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 94 ASN I 148 GLN I 159 HIS I 310 GLN ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.134915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.099069 restraints weight = 49910.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.098350 restraints weight = 32367.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.098387 restraints weight = 39721.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.100672 restraints weight = 23460.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.101048 restraints weight = 17656.869| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 25143 Z= 0.228 Angle : 0.629 13.149 34415 Z= 0.328 Chirality : 0.042 0.289 3885 Planarity : 0.004 0.055 4315 Dihedral : 15.087 179.166 4247 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.16 % Allowed : 15.98 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % 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: -1.81 (0.14), residues: 2995 helix: 0.27 (0.16), residues: 913 sheet: -0.64 (0.22), residues: 510 loop : -2.39 (0.13), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 46 TYR 0.019 0.002 TYR I 144 PHE 0.016 0.002 PHE F 114 TRP 0.025 0.001 TRP D 330 HIS 0.008 0.001 HIS D 343 Details of bonding type rmsd covalent geometry : bond 0.00522 (25143) covalent geometry : angle 0.62901 (34415) hydrogen bonds : bond 0.03815 ( 991) hydrogen bonds : angle 4.82325 ( 2911) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 289 time to evaluate : 0.791 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 116 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.8054 (p0) REVERT: B 82 ASN cc_start: 0.9363 (m-40) cc_final: 0.9004 (m-40) REVERT: B 124 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7600 (pm20) REVERT: D 146 ASN cc_start: 0.8132 (t0) cc_final: 0.7821 (t0) REVERT: D 195 PHE cc_start: 0.8043 (m-80) cc_final: 0.7762 (m-80) REVERT: D 206 LYS cc_start: 0.7887 (tptt) cc_final: 0.7593 (tptp) REVERT: D 211 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8472 (tt) REVERT: D 212 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.8011 (m-30) REVERT: D 294 ASP cc_start: 0.7535 (t70) cc_final: 0.7206 (t70) REVERT: E 74 ASN cc_start: 0.8270 (p0) cc_final: 0.7951 (p0) REVERT: E 146 ASN cc_start: 0.8937 (t0) cc_final: 0.8722 (t0) REVERT: F 203 ARG cc_start: 0.7728 (ptp-110) cc_final: 0.7333 (ttm110) REVERT: F 212 ASP cc_start: 0.8058 (m-30) cc_final: 0.7832 (m-30) REVERT: G 155 ARG cc_start: 0.8014 (ttp80) cc_final: 0.7778 (ttp80) REVERT: H 146 ASN cc_start: 0.8338 (t0) cc_final: 0.7937 (t0) REVERT: H 269 ARG cc_start: 0.8669 (ptp-170) cc_final: 0.8396 (ptp90) REVERT: H 304 TYR cc_start: 0.8490 (m-80) cc_final: 0.8121 (m-80) REVERT: I 249 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7545 (mm-30) REVERT: I 277 GLN cc_start: 0.9155 (pm20) cc_final: 0.8751 (pt0) REVERT: I 312 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8278 (ptmm) REVERT: I 321 LEU cc_start: 0.8357 (mt) cc_final: 0.7831 (mp) REVERT: J 29 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8620 (tt0) outliers start: 74 outliers final: 46 residues processed: 350 average time/residue: 0.1838 time to fit residues: 98.6948 Evaluate side-chains 308 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 257 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 304 TYR Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain J residue 29 GLN Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 50 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 160 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 284 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 135 optimal weight: 0.0170 chunk 262 optimal weight: 3.9990 overall best weight: 1.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN A 396 ASN ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 HIS C 29 HIS D 329 ASN F 102 ASN F 260 GLN F 342 GLN G 260 GLN I 94 ASN I 227 HIS I 342 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.135820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.100866 restraints weight = 49709.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.100067 restraints weight = 36973.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.100636 restraints weight = 39593.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.102016 restraints weight = 24118.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.103951 restraints weight = 20336.832| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25143 Z= 0.156 Angle : 0.572 12.690 34415 Z= 0.298 Chirality : 0.040 0.280 3885 Planarity : 0.004 0.055 4315 Dihedral : 15.014 178.154 4247 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.33 % Allowed : 16.57 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % 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: -1.45 (0.14), residues: 2995 helix: 0.76 (0.17), residues: 912 sheet: -0.57 (0.22), residues: 510 loop : -2.26 (0.14), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 46 TYR 0.013 0.001 TYR D 324 PHE 0.013 0.001 PHE G 114 TRP 0.024 0.001 TRP A 394 HIS 0.005 0.001 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00348 (25143) covalent geometry : angle 0.57169 (34415) hydrogen bonds : bond 0.03306 ( 991) hydrogen bonds : angle 4.51839 ( 2911) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 294 time to evaluate : 0.628 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 116 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.7993 (p0) REVERT: A 287 PHE cc_start: 0.6383 (OUTLIER) cc_final: 0.5820 (t80) REVERT: B 82 ASN cc_start: 0.9340 (m-40) cc_final: 0.8956 (m-40) REVERT: B 124 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7606 (pm20) REVERT: C 153 GLN cc_start: 0.7353 (mp10) cc_final: 0.7132 (mp10) REVERT: D 146 ASN cc_start: 0.8020 (t0) cc_final: 0.7697 (t0) REVERT: D 195 PHE cc_start: 0.8019 (m-80) cc_final: 0.7754 (m-80) REVERT: D 206 LYS cc_start: 0.7874 (tptt) cc_final: 0.7602 (tptp) REVERT: D 211 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8479 (tt) REVERT: D 212 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.7983 (m-30) REVERT: D 294 ASP cc_start: 0.7585 (t70) cc_final: 0.7210 (t70) REVERT: E 74 ASN cc_start: 0.8150 (p0) cc_final: 0.7842 (p0) REVERT: E 146 ASN cc_start: 0.8922 (t0) cc_final: 0.8706 (t0) REVERT: F 203 ARG cc_start: 0.7665 (ptp-110) cc_final: 0.7277 (ttm110) REVERT: F 249 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7944 (mt-10) REVERT: G 155 ARG cc_start: 0.7930 (ttp80) cc_final: 0.7673 (ttp80) REVERT: H 146 ASN cc_start: 0.8228 (t0) cc_final: 0.7838 (t0) REVERT: H 211 LEU cc_start: 0.8519 (mt) cc_final: 0.8281 (tt) REVERT: H 269 ARG cc_start: 0.8592 (ptp-170) cc_final: 0.8359 (ptp90) REVERT: H 304 TYR cc_start: 0.8462 (m-80) cc_final: 0.8079 (m-80) REVERT: I 249 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7539 (mm-30) REVERT: I 290 TYR cc_start: 0.8364 (p90) cc_final: 0.8070 (p90) REVERT: I 321 LEU cc_start: 0.8400 (mt) cc_final: 0.7919 (mp) outliers start: 78 outliers final: 49 residues processed: 356 average time/residue: 0.1725 time to fit residues: 94.9987 Evaluate side-chains 326 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 272 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 262 SER Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain H residue 331 VAL Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 304 TYR Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 50 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 131 optimal weight: 5.9990 chunk 219 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 223 optimal weight: 3.9990 chunk 232 optimal weight: 0.9990 chunk 229 optimal weight: 5.9990 chunk 2 optimal weight: 0.4980 chunk 269 optimal weight: 0.9980 chunk 228 optimal weight: 2.9990 chunk 280 optimal weight: 6.9990 chunk 243 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS C 82 HIS D 329 ASN ** F 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 94 ASN I 227 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.137108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.100749 restraints weight = 49900.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.099576 restraints weight = 33417.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.100411 restraints weight = 32210.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.101433 restraints weight = 23495.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.102034 restraints weight = 20726.902| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25143 Z= 0.140 Angle : 0.561 12.432 34415 Z= 0.290 Chirality : 0.040 0.274 3885 Planarity : 0.004 0.060 4315 Dihedral : 14.931 177.563 4244 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.29 % Allowed : 18.24 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.15), residues: 2995 helix: 1.13 (0.17), residues: 905 sheet: -0.39 (0.23), residues: 498 loop : -2.15 (0.14), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 169 TYR 0.024 0.001 TYR I 144 PHE 0.012 0.001 PHE A 391 TRP 0.023 0.001 TRP A 394 HIS 0.005 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00313 (25143) covalent geometry : angle 0.56085 (34415) hydrogen bonds : bond 0.03180 ( 991) hydrogen bonds : angle 4.37672 ( 2911) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 293 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.7927 (p0) REVERT: A 235 TYR cc_start: 0.8651 (m-80) cc_final: 0.8325 (m-80) REVERT: B 82 ASN cc_start: 0.9357 (m-40) cc_final: 0.9098 (m-40) REVERT: B 282 ASN cc_start: 0.8969 (OUTLIER) cc_final: 0.8684 (m110) REVERT: C 2 ASP cc_start: 0.6594 (p0) cc_final: 0.6372 (p0) REVERT: C 56 GLU cc_start: 0.6312 (tp30) cc_final: 0.6014 (tp30) REVERT: D 146 ASN cc_start: 0.8150 (t0) cc_final: 0.7818 (t0) REVERT: D 195 PHE cc_start: 0.7976 (m-80) cc_final: 0.7694 (m-80) REVERT: D 206 LYS cc_start: 0.7805 (tptt) cc_final: 0.7582 (tptp) REVERT: D 212 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.8010 (m-30) REVERT: D 294 ASP cc_start: 0.7525 (t70) cc_final: 0.7162 (t70) REVERT: E 74 ASN cc_start: 0.8145 (p0) cc_final: 0.7847 (p0) REVERT: E 146 ASN cc_start: 0.8906 (t0) cc_final: 0.8697 (t0) REVERT: F 203 ARG cc_start: 0.7612 (ptp-110) cc_final: 0.7159 (ttm110) REVERT: G 155 ARG cc_start: 0.7957 (ttp80) cc_final: 0.7612 (ttp80) REVERT: H 211 LEU cc_start: 0.8498 (mt) cc_final: 0.8273 (tt) REVERT: H 269 ARG cc_start: 0.8562 (ptp-170) cc_final: 0.8330 (ptp90) REVERT: H 285 THR cc_start: 0.8890 (m) cc_final: 0.8567 (p) REVERT: H 304 TYR cc_start: 0.8435 (m-80) cc_final: 0.8078 (m-80) REVERT: H 321 LEU cc_start: 0.8571 (tp) cc_final: 0.8370 (tp) REVERT: I 203 ARG cc_start: 0.7142 (mtp180) cc_final: 0.6886 (mtp85) REVERT: I 249 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7601 (mm-30) REVERT: I 290 TYR cc_start: 0.8299 (p90) cc_final: 0.8075 (p90) REVERT: I 321 LEU cc_start: 0.8458 (mt) cc_final: 0.7955 (mp) REVERT: K 47 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.8025 (mm) REVERT: K 58 LYS cc_start: 0.9121 (tttm) cc_final: 0.8552 (tttp) outliers start: 77 outliers final: 54 residues processed: 352 average time/residue: 0.1679 time to fit residues: 91.5138 Evaluate side-chains 328 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 270 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 414 TRP Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 260 GLN Chi-restraints excluded: chain G residue 262 SER Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 331 VAL Chi-restraints excluded: chain H residue 348 ASN Chi-restraints excluded: chain I residue 94 ASN Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 304 TYR Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 50 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 62 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 165 optimal weight: 1.9990 chunk 272 optimal weight: 1.9990 chunk 268 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 207 optimal weight: 0.8980 chunk 288 optimal weight: 10.0000 chunk 296 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN A 396 ASN ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS D 329 ASN F 159 HIS G 183 HIS H 148 GLN I 94 ASN I 227 HIS J 51 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.136232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.101333 restraints weight = 47634.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.099990 restraints weight = 34135.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.100616 restraints weight = 37467.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.102039 restraints weight = 24750.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.102498 restraints weight = 21055.363| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25143 Z= 0.155 Angle : 0.571 12.290 34415 Z= 0.294 Chirality : 0.040 0.272 3885 Planarity : 0.004 0.060 4315 Dihedral : 14.884 177.405 4244 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.42 % Allowed : 19.14 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % 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: -1.04 (0.15), residues: 2995 helix: 1.33 (0.17), residues: 899 sheet: -0.35 (0.23), residues: 498 loop : -2.12 (0.14), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 46 TYR 0.019 0.001 TYR C 97 PHE 0.012 0.001 PHE G 114 TRP 0.027 0.001 TRP A 394 HIS 0.010 0.001 HIS D 159 Details of bonding type rmsd covalent geometry : bond 0.00351 (25143) covalent geometry : angle 0.57072 (34415) hydrogen bonds : bond 0.03192 ( 991) hydrogen bonds : angle 4.35015 ( 2911) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 280 time to evaluate : 0.885 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 287 PHE cc_start: 0.6163 (OUTLIER) cc_final: 0.5665 (t80) REVERT: B 82 ASN cc_start: 0.9348 (m-40) cc_final: 0.9063 (m-40) REVERT: B 282 ASN cc_start: 0.9034 (OUTLIER) cc_final: 0.8712 (m110) REVERT: D 146 ASN cc_start: 0.8050 (t0) cc_final: 0.7720 (t0) REVERT: D 195 PHE cc_start: 0.7868 (m-80) cc_final: 0.7590 (m-80) REVERT: D 206 LYS cc_start: 0.7867 (tptt) cc_final: 0.7654 (tptp) REVERT: D 212 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7912 (m-30) REVERT: D 294 ASP cc_start: 0.7487 (t70) cc_final: 0.7111 (t70) REVERT: E 74 ASN cc_start: 0.8117 (p0) cc_final: 0.7830 (p0) REVERT: E 146 ASN cc_start: 0.8888 (t0) cc_final: 0.8673 (t0) REVERT: F 203 ARG cc_start: 0.7570 (ptp-110) cc_final: 0.7107 (ttm110) REVERT: F 249 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7839 (mt-10) REVERT: G 155 ARG cc_start: 0.7940 (ttp80) cc_final: 0.7593 (ttp80) REVERT: H 211 LEU cc_start: 0.8510 (mt) cc_final: 0.8304 (tt) REVERT: H 269 ARG cc_start: 0.8527 (ptp-170) cc_final: 0.8301 (ptp90) REVERT: H 285 THR cc_start: 0.8928 (m) cc_final: 0.8645 (p) REVERT: H 304 TYR cc_start: 0.8439 (m-80) cc_final: 0.8055 (m-80) REVERT: I 249 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7593 (mm-30) REVERT: I 290 TYR cc_start: 0.8295 (p90) cc_final: 0.8080 (p90) REVERT: I 321 LEU cc_start: 0.8459 (mt) cc_final: 0.7969 (mp) REVERT: I 333 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7912 (mtt90) outliers start: 80 outliers final: 62 residues processed: 343 average time/residue: 0.1691 time to fit residues: 90.4368 Evaluate side-chains 327 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 260 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 414 TRP Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 43 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 262 SER Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 331 VAL Chi-restraints excluded: chain H residue 348 ASN Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 304 TYR Chi-restraints excluded: chain I residue 333 ARG Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain K residue 35 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 297 optimal weight: 6.9990 chunk 170 optimal weight: 0.6980 chunk 210 optimal weight: 0.8980 chunk 231 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS D 329 ASN E 342 GLN F 260 GLN I 94 ASN ** I 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 51 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.137407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.099063 restraints weight = 39778.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.100296 restraints weight = 32999.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.100865 restraints weight = 23653.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.101634 restraints weight = 19259.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.101664 restraints weight = 17128.164| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25143 Z= 0.127 Angle : 0.555 12.287 34415 Z= 0.286 Chirality : 0.040 0.269 3885 Planarity : 0.003 0.061 4315 Dihedral : 14.831 176.925 4243 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.29 % Allowed : 19.31 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.15), residues: 2995 helix: 1.52 (0.17), residues: 900 sheet: -0.23 (0.23), residues: 502 loop : -2.08 (0.14), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 32 TYR 0.017 0.001 TYR C 97 PHE 0.010 0.001 PHE G 114 TRP 0.030 0.001 TRP A 394 HIS 0.007 0.001 HIS I 227 Details of bonding type rmsd covalent geometry : bond 0.00287 (25143) covalent geometry : angle 0.55476 (34415) hydrogen bonds : bond 0.03029 ( 991) hydrogen bonds : angle 4.22299 ( 2911) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 294 time to evaluate : 1.053 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 287 PHE cc_start: 0.6062 (OUTLIER) cc_final: 0.5546 (t80) REVERT: A 397 ARG cc_start: 0.6631 (tmm-80) cc_final: 0.6374 (ttp-170) REVERT: B 82 ASN cc_start: 0.9339 (m-40) cc_final: 0.9070 (m-40) REVERT: B 281 GLU cc_start: 0.8105 (pp20) cc_final: 0.7453 (pp20) REVERT: B 282 ASN cc_start: 0.9034 (OUTLIER) cc_final: 0.8019 (m110) REVERT: D 146 ASN cc_start: 0.8044 (t0) cc_final: 0.7694 (t0) REVERT: D 195 PHE cc_start: 0.7915 (m-80) cc_final: 0.7653 (m-80) REVERT: D 294 ASP cc_start: 0.7469 (t70) cc_final: 0.7168 (t70) REVERT: E 146 ASN cc_start: 0.8886 (t0) cc_final: 0.8685 (t0) REVERT: F 203 ARG cc_start: 0.7644 (ptp-110) cc_final: 0.7245 (ttm110) REVERT: F 249 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7853 (mt-10) REVERT: G 73 SER cc_start: 0.8503 (t) cc_final: 0.8171 (t) REVERT: H 269 ARG cc_start: 0.8502 (ptp-170) cc_final: 0.8288 (ptp90) REVERT: H 285 THR cc_start: 0.8736 (m) cc_final: 0.8509 (p) REVERT: H 339 VAL cc_start: 0.8155 (t) cc_final: 0.7828 (p) REVERT: I 249 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7668 (mm-30) REVERT: I 290 TYR cc_start: 0.8294 (p90) cc_final: 0.8035 (p90) REVERT: I 321 LEU cc_start: 0.8408 (mt) cc_final: 0.7976 (mp) REVERT: I 333 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7856 (mtt90) REVERT: K 47 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8127 (mm) outliers start: 77 outliers final: 61 residues processed: 350 average time/residue: 0.1641 time to fit residues: 91.0558 Evaluate side-chains 337 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 271 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 43 LEU Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 262 SER Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 348 ASN Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 331 VAL Chi-restraints excluded: chain H residue 348 ASN Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 94 ASN Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 304 TYR Chi-restraints excluded: chain I residue 333 ARG Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 47 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 205 optimal weight: 0.0970 chunk 240 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 242 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 198 optimal weight: 0.9980 chunk 239 optimal weight: 2.9990 chunk 225 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 251 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS D 329 ASN I 94 ASN ** I 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 51 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.137379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.101196 restraints weight = 40426.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.100088 restraints weight = 33811.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.100885 restraints weight = 32056.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.101504 restraints weight = 23753.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.101889 restraints weight = 21453.564| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25143 Z= 0.122 Angle : 0.551 11.942 34415 Z= 0.283 Chirality : 0.039 0.267 3885 Planarity : 0.003 0.060 4315 Dihedral : 14.806 176.643 4243 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.08 % Allowed : 19.48 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % 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: -0.80 (0.15), residues: 2995 helix: 1.64 (0.17), residues: 900 sheet: -0.19 (0.23), residues: 502 loop : -2.05 (0.14), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 32 TYR 0.017 0.001 TYR D 324 PHE 0.009 0.001 PHE G 114 TRP 0.033 0.001 TRP A 394 HIS 0.008 0.001 HIS I 227 Details of bonding type rmsd covalent geometry : bond 0.00278 (25143) covalent geometry : angle 0.55093 (34415) hydrogen bonds : bond 0.02991 ( 991) hydrogen bonds : angle 4.15940 ( 2911) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 289 time to evaluate : 0.955 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 287 PHE cc_start: 0.6087 (OUTLIER) cc_final: 0.5565 (t80) REVERT: B 82 ASN cc_start: 0.9313 (m-40) cc_final: 0.9080 (m-40) REVERT: B 156 ASN cc_start: 0.7143 (m110) cc_final: 0.6831 (m-40) REVERT: B 281 GLU cc_start: 0.8087 (pp20) cc_final: 0.7451 (pp20) REVERT: B 282 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8015 (m110) REVERT: D 146 ASN cc_start: 0.8082 (t0) cc_final: 0.7764 (t0) REVERT: D 159 HIS cc_start: 0.7837 (m-70) cc_final: 0.7573 (m-70) REVERT: D 195 PHE cc_start: 0.7861 (m-80) cc_final: 0.7605 (m-80) REVERT: D 212 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7746 (m-30) REVERT: D 294 ASP cc_start: 0.7390 (t70) cc_final: 0.7098 (t0) REVERT: E 348 ASN cc_start: 0.8980 (t0) cc_final: 0.8570 (t0) REVERT: F 203 ARG cc_start: 0.7639 (ptp-110) cc_final: 0.7234 (ttm110) REVERT: F 249 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7823 (mt-10) REVERT: G 73 SER cc_start: 0.8539 (t) cc_final: 0.8172 (t) REVERT: H 269 ARG cc_start: 0.8495 (ptp-170) cc_final: 0.8284 (ptp90) REVERT: H 321 LEU cc_start: 0.8446 (tp) cc_final: 0.8230 (tp) REVERT: H 339 VAL cc_start: 0.8180 (t) cc_final: 0.7852 (p) REVERT: I 249 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7665 (mm-30) REVERT: I 290 TYR cc_start: 0.8245 (p90) cc_final: 0.7987 (p90) REVERT: I 321 LEU cc_start: 0.8395 (mt) cc_final: 0.7958 (mp) REVERT: I 333 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7864 (mtt90) REVERT: K 57 TYR cc_start: 0.8155 (p90) cc_final: 0.7793 (p90) outliers start: 72 outliers final: 61 residues processed: 343 average time/residue: 0.1620 time to fit residues: 88.3360 Evaluate side-chains 344 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 278 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 43 LEU Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 260 GLN Chi-restraints excluded: chain G residue 262 SER Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 348 ASN Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 331 VAL Chi-restraints excluded: chain H residue 348 ASN Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 304 TYR Chi-restraints excluded: chain I residue 333 ARG Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain K residue 2 LYS Chi-restraints excluded: chain K residue 35 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 260 optimal weight: 0.0770 chunk 248 optimal weight: 1.9990 chunk 264 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 270 optimal weight: 0.9980 chunk 197 optimal weight: 0.8980 chunk 202 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 285 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 299 optimal weight: 6.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS D 329 ASN ** I 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.139014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.102757 restraints weight = 40495.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.102402 restraints weight = 33312.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.102785 restraints weight = 33643.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.103504 restraints weight = 24891.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.103928 restraints weight = 21602.679| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25143 Z= 0.110 Angle : 0.546 13.699 34415 Z= 0.280 Chirality : 0.039 0.265 3885 Planarity : 0.003 0.059 4315 Dihedral : 14.768 176.924 4243 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.65 % Allowed : 19.74 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.15), residues: 2995 helix: 1.73 (0.17), residues: 901 sheet: -0.10 (0.23), residues: 496 loop : -2.01 (0.14), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 32 TYR 0.014 0.001 TYR C 97 PHE 0.008 0.001 PHE G 114 TRP 0.035 0.001 TRP A 394 HIS 0.007 0.001 HIS I 227 Details of bonding type rmsd covalent geometry : bond 0.00248 (25143) covalent geometry : angle 0.54637 (34415) hydrogen bonds : bond 0.02908 ( 991) hydrogen bonds : angle 4.09571 ( 2911) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 295 time to evaluate : 0.825 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 287 PHE cc_start: 0.5984 (OUTLIER) cc_final: 0.5523 (t80) REVERT: A 397 ARG cc_start: 0.6670 (tmm-80) cc_final: 0.6048 (mtm110) REVERT: B 156 ASN cc_start: 0.7137 (m110) cc_final: 0.6823 (m-40) REVERT: B 281 GLU cc_start: 0.8113 (pp20) cc_final: 0.7435 (pp20) REVERT: B 282 ASN cc_start: 0.9031 (OUTLIER) cc_final: 0.8038 (m110) REVERT: D 146 ASN cc_start: 0.8077 (t0) cc_final: 0.7777 (t0) REVERT: D 206 LYS cc_start: 0.7747 (tptp) cc_final: 0.7439 (pttt) REVERT: D 212 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7657 (m-30) REVERT: D 294 ASP cc_start: 0.7335 (t70) cc_final: 0.7060 (t0) REVERT: E 348 ASN cc_start: 0.8956 (t0) cc_final: 0.8570 (t0) REVERT: F 203 ARG cc_start: 0.7622 (ptp-110) cc_final: 0.7191 (ttm110) REVERT: F 249 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7835 (mt-10) REVERT: F 250 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7805 (pp) REVERT: G 73 SER cc_start: 0.8487 (t) cc_final: 0.8117 (t) REVERT: H 25 LEU cc_start: 0.8520 (tp) cc_final: 0.8085 (tp) REVERT: H 128 CYS cc_start: 0.8478 (p) cc_final: 0.8141 (t) REVERT: H 321 LEU cc_start: 0.8456 (tp) cc_final: 0.8242 (tp) REVERT: H 339 VAL cc_start: 0.8158 (t) cc_final: 0.7820 (p) REVERT: I 249 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7648 (mm-30) REVERT: I 269 ARG cc_start: 0.7398 (mtm180) cc_final: 0.6817 (mtm-85) REVERT: I 290 TYR cc_start: 0.8183 (p90) cc_final: 0.7963 (p90) REVERT: I 321 LEU cc_start: 0.8337 (mt) cc_final: 0.7953 (mp) REVERT: I 333 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7826 (mtt90) REVERT: K 57 TYR cc_start: 0.8137 (p90) cc_final: 0.7769 (p90) outliers start: 62 outliers final: 54 residues processed: 340 average time/residue: 0.1634 time to fit residues: 88.2354 Evaluate side-chains 342 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 282 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 414 TRP Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 43 LEU Chi-restraints excluded: chain G residue 260 GLN Chi-restraints excluded: chain G residue 262 SER Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 348 ASN Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 348 ASN Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 304 TYR Chi-restraints excluded: chain I residue 333 ARG Chi-restraints excluded: chain K residue 2 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 301 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 254 optimal weight: 0.5980 chunk 215 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 229 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS C 30 GLN D 329 ASN E 96 GLN ** I 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.138231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.101497 restraints weight = 42428.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.100770 restraints weight = 31708.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.101897 restraints weight = 30716.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.102258 restraints weight = 22875.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.103966 restraints weight = 19823.794| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 25143 Z= 0.174 Angle : 0.588 12.878 34415 Z= 0.301 Chirality : 0.041 0.261 3885 Planarity : 0.004 0.061 4315 Dihedral : 14.759 176.884 4243 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.45 % Favored : 93.52 % Rotamer: Outliers : 2.95 % Allowed : 19.78 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % 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: -0.77 (0.15), residues: 2995 helix: 1.64 (0.17), residues: 908 sheet: -0.19 (0.23), residues: 508 loop : -2.03 (0.14), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 32 TYR 0.015 0.002 TYR A 179 PHE 0.029 0.001 PHE A 425 TRP 0.031 0.001 TRP A 394 HIS 0.008 0.001 HIS I 227 Details of bonding type rmsd covalent geometry : bond 0.00401 (25143) covalent geometry : angle 0.58787 (34415) hydrogen bonds : bond 0.03140 ( 991) hydrogen bonds : angle 4.24533 ( 2911) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 281 time to evaluate : 0.828 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 287 PHE cc_start: 0.5971 (OUTLIER) cc_final: 0.5593 (t80) REVERT: A 397 ARG cc_start: 0.6858 (tmm-80) cc_final: 0.6239 (mtm110) REVERT: B 156 ASN cc_start: 0.7162 (m110) cc_final: 0.6662 (m-40) REVERT: B 281 GLU cc_start: 0.8109 (pp20) cc_final: 0.7430 (pp20) REVERT: D 146 ASN cc_start: 0.8033 (t0) cc_final: 0.7704 (t0) REVERT: D 206 LYS cc_start: 0.7719 (tptp) cc_final: 0.7380 (pttt) REVERT: D 212 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7583 (m-30) REVERT: E 348 ASN cc_start: 0.9066 (t0) cc_final: 0.8485 (t0) REVERT: F 203 ARG cc_start: 0.7631 (ptp-110) cc_final: 0.7203 (ttm110) REVERT: F 249 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7906 (mt-10) REVERT: G 73 SER cc_start: 0.8693 (t) cc_final: 0.8291 (t) REVERT: G 155 ARG cc_start: 0.7916 (ttp80) cc_final: 0.7658 (ttp80) REVERT: H 128 CYS cc_start: 0.8500 (p) cc_final: 0.8231 (t) REVERT: H 339 VAL cc_start: 0.8222 (t) cc_final: 0.7898 (p) REVERT: I 249 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7694 (mm-30) REVERT: I 290 TYR cc_start: 0.8276 (p90) cc_final: 0.8002 (p90) REVERT: I 321 LEU cc_start: 0.8446 (mt) cc_final: 0.7991 (mp) REVERT: I 333 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7957 (mtt90) outliers start: 69 outliers final: 51 residues processed: 333 average time/residue: 0.1651 time to fit residues: 87.0537 Evaluate side-chains 331 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 276 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 43 LEU Chi-restraints excluded: chain G residue 262 SER Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 348 ASN Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 304 TYR Chi-restraints excluded: chain I residue 333 ARG Chi-restraints excluded: chain K residue 2 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 105 optimal weight: 5.9990 chunk 219 optimal weight: 0.9990 chunk 223 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 271 optimal weight: 1.9990 chunk 266 optimal weight: 0.7980 chunk 185 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 278 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS D 329 ASN F 260 GLN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.139276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.102727 restraints weight = 42448.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.101985 restraints weight = 31814.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.103334 restraints weight = 29870.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.103638 restraints weight = 22008.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.105174 restraints weight = 19444.969| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25143 Z= 0.140 Angle : 0.569 13.551 34415 Z= 0.291 Chirality : 0.040 0.260 3885 Planarity : 0.003 0.059 4315 Dihedral : 14.759 176.895 4243 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.65 % Allowed : 20.08 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % 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: -0.72 (0.15), residues: 2995 helix: 1.69 (0.17), residues: 908 sheet: -0.15 (0.23), residues: 508 loop : -2.00 (0.14), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 32 TYR 0.014 0.001 TYR A 179 PHE 0.038 0.001 PHE A 425 TRP 0.035 0.001 TRP A 394 HIS 0.007 0.001 HIS I 227 Details of bonding type rmsd covalent geometry : bond 0.00321 (25143) covalent geometry : angle 0.56949 (34415) hydrogen bonds : bond 0.03003 ( 991) hydrogen bonds : angle 4.18115 ( 2911) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4014.89 seconds wall clock time: 70 minutes 2.94 seconds (4202.94 seconds total)