Starting phenix.real_space_refine on Sun Jul 5 01:02:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jzy_22584/07_2026/7jzy_22584.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jzy_22584/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7jzy_22584/07_2026/7jzy_22584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jzy_22584/07_2026/7jzy_22584.map" model { file = "/net/cci-nas-00/data/ceres_data/7jzy_22584/07_2026/7jzy_22584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jzy_22584/07_2026/7jzy_22584.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7jzy_22584/07_2026/7jzy_22584.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jzy_22584/07_2026/7jzy_22584.cif" } 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-6108/lib/python3.11/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: 12 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: 6.17, per 1000 atoms: 0.25 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: 1.65 Conformation dependent library (CDL) restraints added in 1.3 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: 2.52 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: 4.32 Time building geometry restraints manager: 2.39 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: 14553 35.34 - 70.67: 394 70.67 - 106.01: 33 106.01 - 141.34: 1 141.34 - 176.68: 6 Dihedral angle restraints: 14987 sinusoidal: 6277 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 14984 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: 1.690 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: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 23.530 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 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: 0.8500 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 : 16.337 176.679 9357 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/Z covalent geometry : bond 0.00879 / 0.40 (25143) covalent geometry : angle 0.95991 / 0.54 (34415) hydrogen bonds : bond 0.18488 / 12.61 ( 991) hydrogen bonds : angle 7.69968 / 5.38 ( 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 : 0.803 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: 0.1838 time to fit residues: 116.0354 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 : 0.668 ------------------------------------------------------------------------------- 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... ** 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 C 165 GLN 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.137397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.099742 restraints weight = 40009.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.099931 restraints weight = 33064.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.100272 restraints weight = 29255.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.101324 restraints weight = 22891.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.101440 restraints weight = 20086.068| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- 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 = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (15 function evaluations) r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25143 Z= 0.134 Angle : 0.595 11.373 34415 Z= 0.313 Chirality : 0.041 0.298 3885 Planarity : 0.004 0.059 4315 Dihedral : 11.980 179.991 4033 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.88 % Allowed : 14.18 % Favored : 83.94 % 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: -2.36 (0.13), residues: 2995 helix: -0.52 (0.16), residues: 900 sheet: -0.79 (0.22), residues: 503 loop : -2.55 (0.13), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 46 TYR 0.019 0.001 TYR I 144 PHE 0.022 0.001 PHE C 173 TRP 0.022 0.001 TRP A 394 HIS 0.007 0.001 HIS D 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (25143) covalent geometry : angle 0.59496 / 0.31 (34415) hydrogen bonds : bond 0.03801 / 2.55 ( 991) hydrogen bonds : angle 5.08340 / 3.56 ( 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 371 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 327 time to evaluate : 0.883 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: 0.8052 (OUTLIER) cc_final: 0.7724 (p0) REVERT: B 124 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7638 (pm20) REVERT: C 2 ASP cc_start: 0.5861 (p0) cc_final: 0.5601 (p0) REVERT: C 186 TRP cc_start: 0.7827 (t-100) cc_final: 0.7592 (t-100) REVERT: D 146 ASN cc_start: 0.8101 (t0) cc_final: 0.7763 (t0) REVERT: D 195 PHE cc_start: 0.8012 (m-80) cc_final: 0.7769 (m-80) REVERT: D 206 LYS cc_start: 0.7883 (tptt) cc_final: 0.7586 (tptp) REVERT: D 211 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8591 (tt) REVERT: D 212 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.7963 (m-30) REVERT: D 275 HIS cc_start: 0.8575 (m170) cc_final: 0.8355 (m90) REVERT: D 294 ASP cc_start: 0.7296 (t70) cc_final: 0.7016 (t70) REVERT: E 74 ASN cc_start: 0.8262 (p0) cc_final: 0.7961 (p0) REVERT: E 146 ASN cc_start: 0.8888 (t0) cc_final: 0.8632 (t0) REVERT: F 90 ILE cc_start: 0.9145 (pt) cc_final: 0.8941 (mt) REVERT: F 203 ARG cc_start: 0.7577 (ptp-110) cc_final: 0.7307 (ttm110) REVERT: F 212 ASP cc_start: 0.8042 (m-30) cc_final: 0.7834 (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: 0.7883 (t0) REVERT: H 269 ARG cc_start: 0.8552 (ptp-170) cc_final: 0.8305 (ptp90) REVERT: H 304 TYR cc_start: 0.8309 (m-80) cc_final: 0.7998 (m-80) REVERT: I 249 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7580 (mm-30) REVERT: I 269 ARG cc_start: 0.7203 (mtm-85) cc_final: 0.6725 (mtm180) REVERT: I 310 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8193 (mt0) REVERT: J 29 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8438 (tt0) REVERT: K 58 LYS cc_start: 0.9109 (tttm) cc_final: 0.8540 (tttp) outliers start: 44 outliers final: 23 residues processed: 359 average time/residue: 0.1644 time to fit residues: 91.3524 Evaluate side-chains 302 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 274 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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: 7.9990 chunk 130 optimal weight: 9.9990 chunk 246 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 30 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 = 0.3587 r_free = 0.3587 target = 0.133249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.098126 restraints weight = 50025.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.097742 restraints weight = 37487.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.097806 restraints weight = 44292.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.099854 restraints weight = 25207.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.100778 restraints weight = 19436.995| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 25143 Z= 0.272 Angle : 0.665 13.337 34415 Z= 0.347 Chirality : 0.043 0.282 3885 Planarity : 0.005 0.057 4315 Dihedral : 11.932 179.225 4031 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.37 % Allowed : 16.02 % Favored : 80.61 % 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: -1.87 (0.14), residues: 2995 helix: 0.22 (0.16), residues: 910 sheet: -0.63 (0.22), residues: 508 loop : -2.44 (0.13), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 46 TYR 0.017 0.002 TYR I 144 PHE 0.018 0.002 PHE F 114 TRP 0.027 0.002 TRP D 330 HIS 0.010 0.001 HIS D 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.27 (25143) covalent geometry : angle 0.66502 / 0.35 (34415) hydrogen bonds : bond 0.04017 / 2.71 ( 991) hydrogen bonds : angle 4.92006 / 3.45 ( 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 366 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 287 time to evaluate : 0.880 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: 0.8293 (OUTLIER) cc_final: 0.7892 (p0) REVERT: A 235 TYR cc_start: 0.8825 (m-80) cc_final: 0.8371 (m-80) REVERT: A 396 ASN cc_start: 0.6540 (m110) cc_final: 0.6326 (m-40) REVERT: B 124 GLN cc_start: 0.7847 (mm-40) cc_final: 0.7573 (pm20) REVERT: C 19 GLN cc_start: 0.7775 (tt0) cc_final: 0.5859 (tt0) REVERT: C 153 GLN cc_start: 0.7819 (mp10) cc_final: 0.7596 (mp10) REVERT: D 146 ASN cc_start: 0.8103 (t0) cc_final: 0.7802 (t0) REVERT: D 195 PHE cc_start: 0.8091 (m-80) cc_final: 0.7776 (m-80) REVERT: D 206 LYS cc_start: 0.7821 (tptt) cc_final: 0.7614 (tptp) REVERT: D 212 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.7955 (m-30) REVERT: D 294 ASP cc_start: 0.7525 (t70) cc_final: 0.7194 (t70) REVERT: E 74 ASN cc_start: 0.8234 (p0) cc_final: 0.7889 (p0) REVERT: E 146 ASN cc_start: 0.8910 (t0) cc_final: 0.8692 (t0) REVERT: F 203 ARG cc_start: 0.7706 (ptp-110) cc_final: 0.7354 (ttm110) REVERT: F 212 ASP cc_start: 0.8033 (m-30) cc_final: 0.7823 (m-30) REVERT: G 155 ARG cc_start: 0.8041 (ttp80) cc_final: 0.7784 (ttp80) REVERT: H 146 ASN cc_start: 0.8308 (t0) cc_final: 0.7979 (t0) REVERT: H 269 ARG cc_start: 0.8649 (ptp-170) cc_final: 0.8383 (ptp90) REVERT: H 339 VAL cc_start: 0.8245 (t) cc_final: 0.7935 (p) REVERT: I 249 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7629 (mm-30) REVERT: I 277 GLN cc_start: 0.9165 (pm20) cc_final: 0.8753 (pt0) REVERT: I 312 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8271 (ptmm) REVERT: J 29 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8600 (tt0) outliers start: 79 outliers final: 47 residues processed: 351 average time/residue: 0.1574 time to fit residues: 85.5790 Evaluate side-chains 305 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 254 time to evaluate : 0.715 ------------------------------------------------------------------------------- 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 B residue 41 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 70 ILE 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 247 TRP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 90 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 189 VAL 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 H residue 308 THR 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 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: 1.9990 chunk 83 optimal weight: 30.0000 chunk 110 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 284 optimal weight: 0.0670 chunk 128 optimal weight: 0.0030 chunk 183 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 135 optimal weight: 8.9990 chunk 262 optimal weight: 4.9990 overall best weight: 0.9532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN ** 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 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS D 329 ASN E 51 GLN F 102 ASN F 260 GLN F 342 GLN I 94 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.137530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.101187 restraints weight = 49506.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.100343 restraints weight = 34081.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.101060 restraints weight = 32700.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.102110 restraints weight = 23206.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.102703 restraints weight = 20393.753| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25143 Z= 0.124 Angle : 0.558 12.755 34415 Z= 0.291 Chirality : 0.040 0.282 3885 Planarity : 0.003 0.053 4315 Dihedral : 11.702 177.950 4031 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.86 % Allowed : 17.21 % Favored : 79.92 % 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: 0.77 (0.17), residues: 912 sheet: -0.58 (0.22), residues: 510 loop : -2.25 (0.14), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 169 TYR 0.013 0.001 TYR D 324 PHE 0.011 0.001 PHE H 166 TRP 0.024 0.001 TRP A 394 HIS 0.008 0.001 HIS D 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (25143) covalent geometry : angle 0.55753 / 0.29 (34415) hydrogen bonds : bond 0.03233 / 2.16 ( 991) hydrogen bonds : angle 4.47881 / 3.15 ( 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 375 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 308 time to evaluate : 0.788 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: 0.8246 (OUTLIER) cc_final: 0.7983 (p0) REVERT: A 235 TYR cc_start: 0.8706 (m-80) cc_final: 0.8175 (m-80) REVERT: A 396 ASN cc_start: 0.6319 (m110) cc_final: 0.6055 (m-40) REVERT: A 414 TRP cc_start: 0.6533 (t60) cc_final: 0.6324 (t60) REVERT: C 2 ASP cc_start: 0.6477 (p0) cc_final: 0.6260 (p0) REVERT: D 146 ASN cc_start: 0.8153 (t0) cc_final: 0.7821 (t0) REVERT: D 195 PHE cc_start: 0.7987 (m-80) cc_final: 0.7720 (m-80) REVERT: D 206 LYS cc_start: 0.7883 (tptt) cc_final: 0.7673 (tptp) REVERT: D 294 ASP cc_start: 0.7564 (t70) cc_final: 0.7199 (t70) REVERT: E 74 ASN cc_start: 0.8122 (p0) cc_final: 0.7844 (p0) REVERT: E 146 ASN cc_start: 0.8924 (t0) cc_final: 0.8706 (t0) REVERT: F 203 ARG cc_start: 0.7689 (ptp-110) cc_final: 0.7289 (ttm110) REVERT: F 249 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7748 (mt-10) REVERT: G 155 ARG cc_start: 0.7984 (ttp80) cc_final: 0.7741 (ttp80) REVERT: H 269 ARG cc_start: 0.8556 (ptp-170) cc_final: 0.8334 (ptp90) REVERT: H 304 TYR cc_start: 0.8450 (m-80) cc_final: 0.8059 (m-80) REVERT: I 249 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7640 (mm-30) REVERT: I 269 ARG cc_start: 0.7257 (mtm180) cc_final: 0.6960 (mtm-85) REVERT: I 290 TYR cc_start: 0.8301 (p90) cc_final: 0.8040 (p90) REVERT: I 321 LEU cc_start: 0.8459 (mt) cc_final: 0.7985 (mp) outliers start: 67 outliers final: 44 residues processed: 357 average time/residue: 0.1670 time to fit residues: 92.0646 Evaluate side-chains 320 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 274 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 297 VAL Chi-restraints excluded: chain A residue 397 ARG 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 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 C residue 90 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 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 249 GLU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 304 TYR 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 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 50 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 131 optimal weight: 4.9990 chunk 219 optimal weight: 6.9990 chunk 117 optimal weight: 8.9990 chunk 223 optimal weight: 0.9980 chunk 232 optimal weight: 0.9990 chunk 229 optimal weight: 5.9990 chunk 2 optimal weight: 0.0870 chunk 269 optimal weight: 0.7980 chunk 228 optimal weight: 1.9990 chunk 280 optimal weight: 2.9990 chunk 243 optimal weight: 0.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN C 29 HIS C 82 HIS D 329 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 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 = 0.3653 r_free = 0.3653 target = 0.138424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.102032 restraints weight = 49807.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.101031 restraints weight = 35981.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.102020 restraints weight = 31899.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.102865 restraints weight = 23556.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.104381 restraints weight = 20782.517| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (11 function evaluations) r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2359 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= 0.116 Angle : 0.556 12.566 34415 Z= 0.287 Chirality : 0.040 0.272 3885 Planarity : 0.003 0.060 4315 Dihedral : 11.544 177.331 4028 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.12 % Allowed : 18.58 % Favored : 78.30 % 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: -1.13 (0.15), residues: 2995 helix: 1.19 (0.17), residues: 901 sheet: -0.39 (0.23), residues: 498 loop : -2.14 (0.14), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 46 TYR 0.023 0.001 TYR I 144 PHE 0.011 0.001 PHE A 425 TRP 0.022 0.001 TRP A 394 HIS 0.005 0.001 HIS D 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (25143) covalent geometry : angle 0.55573 / 0.29 (34415) hydrogen bonds : bond 0.03106 / 2.08 ( 991) hydrogen bonds : angle 4.32443 / 3.04 ( 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 369 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 296 time to evaluate : 0.693 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: 0.8313 (OUTLIER) cc_final: 0.7905 (p0) REVERT: A 391 PHE cc_start: 0.6983 (t80) cc_final: 0.6771 (t80) REVERT: A 396 ASN cc_start: 0.6213 (m110) cc_final: 0.5958 (m-40) REVERT: A 414 TRP cc_start: 0.6364 (t60) cc_final: 0.6059 (t60) REVERT: B 281 GLU cc_start: 0.7958 (pp20) cc_final: 0.7383 (pp20) REVERT: B 282 ASN cc_start: 0.9011 (OUTLIER) cc_final: 0.7934 (m110) REVERT: D 146 ASN cc_start: 0.8096 (t0) cc_final: 0.7765 (t0) REVERT: D 195 PHE cc_start: 0.7849 (m-80) cc_final: 0.7571 (m-80) REVERT: D 206 LYS cc_start: 0.7913 (tptt) cc_final: 0.7712 (tptp) REVERT: D 294 ASP cc_start: 0.7508 (t70) cc_final: 0.7146 (t70) REVERT: E 74 ASN cc_start: 0.8146 (p0) cc_final: 0.7844 (p0) REVERT: E 146 ASN cc_start: 0.8911 (t0) cc_final: 0.8688 (t0) REVERT: F 203 ARG cc_start: 0.7660 (ptp-110) cc_final: 0.7296 (ttm110) REVERT: F 249 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7836 (mt-10) REVERT: F 250 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7888 (pp) REVERT: H 146 ASN cc_start: 0.8257 (t0) cc_final: 0.7918 (t0) REVERT: H 269 ARG cc_start: 0.8547 (ptp-170) cc_final: 0.8312 (ptp90) REVERT: H 285 THR cc_start: 0.8844 (m) cc_final: 0.8518 (p) REVERT: H 304 TYR cc_start: 0.8379 (m-80) cc_final: 0.8029 (m-80) REVERT: I 249 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7630 (mm-30) REVERT: I 290 TYR cc_start: 0.8290 (p90) cc_final: 0.8055 (p90) REVERT: I 321 LEU cc_start: 0.8444 (mt) cc_final: 0.7951 (mp) REVERT: K 47 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8155 (mm) outliers start: 73 outliers final: 51 residues processed: 350 average time/residue: 0.1499 time to fit residues: 82.2445 Evaluate side-chains 334 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 278 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 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 111 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 148 CYS 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 90 VAL 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 302 GLU 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 105 SER 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 30 VAL Chi-restraints excluded: chain G residue 86 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 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 K residue 35 SER 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: 0.0970 chunk 53 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 272 optimal weight: 1.9990 chunk 268 optimal weight: 0.9990 chunk 148 optimal weight: 0.5980 chunk 145 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 288 optimal weight: 0.7980 chunk 296 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN C 29 HIS D 329 ASN E 342 GLN F 260 GLN G 183 HIS ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 94 ASN ** I 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 227 HIS I 342 GLN J 51 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.139218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.102970 restraints weight = 47358.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.101692 restraints weight = 33174.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.102784 restraints weight = 31122.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.103391 restraints weight = 23539.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.105391 restraints weight = 20697.692| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2531 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= 0.108 Angle : 0.544 12.371 34415 Z= 0.280 Chirality : 0.039 0.269 3885 Planarity : 0.003 0.060 4315 Dihedral : 11.445 176.915 4028 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.08 % Allowed : 19.01 % Favored : 77.92 % 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: -0.93 (0.15), residues: 2995 helix: 1.46 (0.17), residues: 901 sheet: -0.30 (0.23), residues: 506 loop : -2.07 (0.14), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 315 TYR 0.019 0.001 TYR I 144 PHE 0.010 0.001 PHE C 173 TRP 0.027 0.001 TRP A 394 HIS 0.005 0.001 HIS D 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (25143) covalent geometry : angle 0.54397 / 0.28 (34415) hydrogen bonds : bond 0.02994 / 2.00 ( 991) hydrogen bonds : angle 4.20154 / 2.95 ( 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 381 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 309 time to evaluate : 0.913 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: 0.8331 (OUTLIER) cc_final: 0.7924 (p0) REVERT: A 332 GLU cc_start: 0.8094 (tp30) cc_final: 0.7853 (tt0) REVERT: A 391 PHE cc_start: 0.6994 (t80) cc_final: 0.6767 (t80) REVERT: A 414 TRP cc_start: 0.6353 (t60) cc_final: 0.6146 (t60) REVERT: B 281 GLU cc_start: 0.8092 (pp20) cc_final: 0.7447 (pp20) REVERT: B 282 ASN cc_start: 0.9038 (OUTLIER) cc_final: 0.8007 (m110) REVERT: C 56 GLU cc_start: 0.6148 (tp30) cc_final: 0.5878 (tp30) REVERT: D 146 ASN cc_start: 0.8136 (t0) cc_final: 0.7805 (t0) REVERT: D 195 PHE cc_start: 0.7830 (m-80) cc_final: 0.7577 (m-80) REVERT: D 294 ASP cc_start: 0.7581 (t70) cc_final: 0.7199 (t70) REVERT: E 74 ASN cc_start: 0.8144 (p0) cc_final: 0.7876 (p0) REVERT: E 146 ASN cc_start: 0.8879 (t0) cc_final: 0.8655 (t0) REVERT: F 203 ARG cc_start: 0.7652 (ptp-110) cc_final: 0.7260 (ttm110) REVERT: F 249 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7866 (mt-10) REVERT: F 250 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7801 (pp) REVERT: H 146 ASN cc_start: 0.8210 (t0) cc_final: 0.7867 (t0) REVERT: H 269 ARG cc_start: 0.8543 (ptp-170) cc_final: 0.8296 (ptp90) REVERT: H 285 THR cc_start: 0.8742 (m) cc_final: 0.8477 (p) REVERT: H 304 TYR cc_start: 0.8304 (m-80) cc_final: 0.7996 (m-80) REVERT: H 321 LEU cc_start: 0.8437 (tp) cc_final: 0.8182 (tp) REVERT: I 249 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7611 (mm-30) REVERT: I 269 ARG cc_start: 0.7333 (mtm-85) cc_final: 0.6777 (mtm-85) REVERT: I 290 TYR cc_start: 0.8256 (p90) cc_final: 0.8014 (p90) REVERT: I 321 LEU cc_start: 0.8483 (mt) cc_final: 0.7976 (mp) REVERT: I 333 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7900 (mtt90) REVERT: K 57 TYR cc_start: 0.7971 (p90) cc_final: 0.7708 (p90) outliers start: 72 outliers final: 53 residues processed: 363 average time/residue: 0.1554 time to fit residues: 87.7249 Evaluate side-chains 336 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 278 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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 297 VAL Chi-restraints excluded: chain B residue 54 ILE 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 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 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 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 212 ASP Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 302 GLU 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 105 SER 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 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 348 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 297 optimal weight: 4.9990 chunk 170 optimal weight: 0.9990 chunk 210 optimal weight: 0.9990 chunk 231 optimal weight: 0.6980 chunk 244 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS D 329 ASN F 159 HIS ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 94 ASN ** 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 = 0.3646 r_free = 0.3646 target = 0.138027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.101568 restraints weight = 39763.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.101688 restraints weight = 33940.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.102395 restraints weight = 31630.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.102886 restraints weight = 22987.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.103353 restraints weight = 20746.614| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25143 Z= 0.140 Angle : 0.555 12.140 34415 Z= 0.286 Chirality : 0.040 0.267 3885 Planarity : 0.003 0.058 4315 Dihedral : 11.413 176.772 4027 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.16 % Allowed : 19.52 % Favored : 77.32 % 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: -0.86 (0.15), residues: 2995 helix: 1.56 (0.17), residues: 902 sheet: -0.26 (0.23), residues: 506 loop : -2.06 (0.14), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 156 TYR 0.018 0.001 TYR A 235 PHE 0.011 0.001 PHE G 114 TRP 0.030 0.001 TRP A 394 HIS 0.008 0.001 HIS I 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (25143) covalent geometry : angle 0.55472 / 0.29 (34415) hydrogen bonds : bond 0.03048 / 2.04 ( 991) hydrogen bonds : angle 4.21720 / 2.97 ( 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 357 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 283 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 TYR cc_start: 0.8555 (m-80) cc_final: 0.8268 (m-80) REVERT: A 414 TRP cc_start: 0.6278 (t60) cc_final: 0.6009 (t60) REVERT: B 281 GLU cc_start: 0.8135 (pp20) cc_final: 0.7475 (pp20) REVERT: B 282 ASN cc_start: 0.9045 (OUTLIER) cc_final: 0.8022 (m110) REVERT: D 44 MET cc_start: 0.8201 (ptp) cc_final: 0.7893 (ptp) REVERT: D 146 ASN cc_start: 0.8093 (t0) cc_final: 0.7766 (t0) REVERT: D 159 HIS cc_start: 0.7947 (m-70) cc_final: 0.7715 (m170) REVERT: D 195 PHE cc_start: 0.7856 (m-80) cc_final: 0.7600 (m-80) REVERT: D 212 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7676 (m-30) REVERT: D 294 ASP cc_start: 0.7503 (t70) cc_final: 0.7142 (t70) REVERT: E 74 ASN cc_start: 0.8122 (p0) cc_final: 0.7831 (p0) REVERT: E 146 ASN cc_start: 0.8888 (t0) cc_final: 0.8668 (t0) REVERT: F 203 ARG cc_start: 0.7651 (ptp-110) cc_final: 0.7220 (ttm110) REVERT: F 249 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7856 (mt-10) REVERT: F 250 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7883 (pp) REVERT: H 146 ASN cc_start: 0.8260 (t0) cc_final: 0.7917 (t0) REVERT: H 269 ARG cc_start: 0.8519 (ptp-170) cc_final: 0.8283 (ptp90) REVERT: H 285 THR cc_start: 0.8694 (m) cc_final: 0.8441 (p) REVERT: I 249 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7567 (mm-30) REVERT: I 290 TYR cc_start: 0.8261 (p90) cc_final: 0.8037 (p90) REVERT: I 321 LEU cc_start: 0.8436 (mt) cc_final: 0.7980 (mp) REVERT: I 333 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7874 (mtt90) REVERT: K 57 TYR cc_start: 0.8128 (p90) cc_final: 0.7740 (p90) outliers start: 74 outliers final: 60 residues processed: 341 average time/residue: 0.1478 time to fit residues: 79.7027 Evaluate side-chains 337 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 272 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 198 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 54 ILE 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 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 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 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 302 GLU 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 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 205 optimal weight: 2.9990 chunk 240 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 242 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 198 optimal weight: 0.9990 chunk 239 optimal weight: 4.9990 chunk 225 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 251 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN C 29 HIS D 329 ASN E 96 GLN ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 ASN I 310 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.134260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.097911 restraints weight = 40673.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.096826 restraints weight = 34010.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.097565 restraints weight = 32959.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.098175 restraints weight = 24393.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.098532 restraints weight = 21950.971| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 25143 Z= 0.227 Angle : 0.625 12.965 34415 Z= 0.322 Chirality : 0.042 0.254 3885 Planarity : 0.004 0.061 4315 Dihedral : 11.571 177.498 4027 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.99 % Allowed : 19.39 % 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: -0.95 (0.15), residues: 2995 helix: 1.40 (0.17), residues: 906 sheet: -0.21 (0.23), residues: 490 loop : -2.10 (0.14), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 32 TYR 0.021 0.002 TYR D 324 PHE 0.017 0.002 PHE F 114 TRP 0.033 0.002 TRP A 394 HIS 0.007 0.001 HIS I 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.23 (25143) covalent geometry : angle 0.62467 / 0.32 (34415) hydrogen bonds : bond 0.03453 / 2.31 ( 991) hydrogen bonds : angle 4.42836 / 3.13 ( 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 342 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 272 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 TYR cc_start: 0.8694 (m-80) cc_final: 0.8451 (m-80) REVERT: A 287 PHE cc_start: 0.6061 (OUTLIER) cc_final: 0.5561 (t80) REVERT: A 414 TRP cc_start: 0.6420 (t60) cc_final: 0.6158 (t60) REVERT: B 156 ASN cc_start: 0.7195 (m110) cc_final: 0.6887 (m-40) REVERT: D 146 ASN cc_start: 0.7970 (t0) cc_final: 0.7654 (t0) REVERT: D 195 PHE cc_start: 0.7839 (m-80) cc_final: 0.7579 (m-80) REVERT: D 212 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7723 (m-30) REVERT: D 294 ASP cc_start: 0.7414 (t70) cc_final: 0.7133 (t0) REVERT: E 74 ASN cc_start: 0.8006 (p0) cc_final: 0.7740 (p0) REVERT: E 146 ASN cc_start: 0.8931 (t0) cc_final: 0.8720 (t0) REVERT: F 203 ARG cc_start: 0.7708 (ptp-110) cc_final: 0.7192 (ttm110) REVERT: F 249 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7905 (mt-10) REVERT: G 73 SER cc_start: 0.8713 (t) cc_final: 0.8323 (t) REVERT: G 155 ARG cc_start: 0.7999 (ttp80) cc_final: 0.7736 (ttp80) REVERT: H 128 CYS cc_start: 0.8421 (p) cc_final: 0.8196 (t) REVERT: H 146 ASN cc_start: 0.8280 (t0) cc_final: 0.7959 (t0) REVERT: H 269 ARG cc_start: 0.8555 (ptp-170) cc_final: 0.8333 (ptp90) REVERT: H 321 LEU cc_start: 0.8530 (tp) cc_final: 0.8321 (tp) REVERT: H 339 VAL cc_start: 0.8250 (t) cc_final: 0.7961 (p) REVERT: I 249 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7697 (mm-30) REVERT: I 290 TYR cc_start: 0.8330 (p90) cc_final: 0.8023 (p90) REVERT: I 321 LEU cc_start: 0.8436 (mt) cc_final: 0.7966 (mp) REVERT: I 333 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7963 (mtt90) outliers start: 70 outliers final: 54 residues processed: 330 average time/residue: 0.1768 time to fit residues: 91.5276 Evaluate side-chains 318 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 260 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 209 THR Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 VAL 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 244 VAL Chi-restraints excluded: chain D residue 277 GLN 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 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 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 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 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: 2.9990 chunk 248 optimal weight: 4.9990 chunk 264 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 270 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 202 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 285 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 299 optimal weight: 9.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS D 329 ASN ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.137006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.099443 restraints weight = 40261.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.100013 restraints weight = 31461.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.100582 restraints weight = 25693.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.100971 restraints weight = 20108.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.101259 restraints weight = 18611.954| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- 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: 4 | |-----------------------------------------------------------------------------| |-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: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25143 Z= 0.195 Angle : 0.602 13.050 34415 Z= 0.309 Chirality : 0.041 0.253 3885 Planarity : 0.004 0.062 4315 Dihedral : 11.561 177.742 4027 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.03 % Allowed : 19.52 % 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: -0.92 (0.15), residues: 2995 helix: 1.43 (0.17), residues: 906 sheet: -0.13 (0.23), residues: 500 loop : -2.11 (0.14), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 32 TYR 0.022 0.002 TYR A 179 PHE 0.014 0.001 PHE G 114 TRP 0.038 0.001 TRP A 394 HIS 0.007 0.001 HIS I 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 (25143) covalent geometry : angle 0.60173 / 0.31 (34415) hydrogen bonds : bond 0.03284 / 2.20 ( 991) hydrogen bonds : angle 4.38915 / 3.10 ( 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 344 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 273 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 TYR cc_start: 0.8706 (m-80) cc_final: 0.8489 (m-80) REVERT: A 287 PHE cc_start: 0.6043 (OUTLIER) cc_final: 0.5566 (t80) REVERT: A 414 TRP cc_start: 0.6356 (t60) cc_final: 0.6111 (t60) REVERT: B 156 ASN cc_start: 0.7200 (m110) cc_final: 0.6779 (m-40) REVERT: B 281 GLU cc_start: 0.8104 (pp20) cc_final: 0.7501 (pp20) REVERT: D 146 ASN cc_start: 0.8052 (t0) cc_final: 0.7745 (t0) REVERT: D 159 HIS cc_start: 0.7910 (m-70) cc_final: 0.7672 (m170) REVERT: D 195 PHE cc_start: 0.7822 (m-80) cc_final: 0.7556 (m-80) REVERT: D 212 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7654 (m-30) REVERT: D 294 ASP cc_start: 0.7390 (t70) cc_final: 0.7126 (t0) REVERT: E 348 ASN cc_start: 0.9040 (t0) cc_final: 0.8474 (t0) REVERT: F 203 ARG cc_start: 0.7644 (ptp-110) cc_final: 0.7113 (ttm110) REVERT: F 249 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7770 (mt-10) REVERT: G 73 SER cc_start: 0.8718 (t) cc_final: 0.8334 (t) REVERT: G 155 ARG cc_start: 0.7983 (ttp80) cc_final: 0.7729 (ttp80) REVERT: H 146 ASN cc_start: 0.8307 (t0) cc_final: 0.7956 (t0) REVERT: H 269 ARG cc_start: 0.8552 (ptp-170) cc_final: 0.8344 (ptp90) REVERT: H 321 LEU cc_start: 0.8524 (tp) cc_final: 0.8308 (tp) REVERT: H 339 VAL cc_start: 0.8222 (t) cc_final: 0.7932 (p) REVERT: I 249 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7694 (mm-30) REVERT: I 290 TYR cc_start: 0.8367 (p90) cc_final: 0.8054 (p90) REVERT: I 321 LEU cc_start: 0.8433 (mt) cc_final: 0.7970 (mp) REVERT: I 333 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8004 (mtt90) outliers start: 71 outliers final: 58 residues processed: 328 average time/residue: 0.1737 time to fit residues: 89.6380 Evaluate side-chains 328 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 266 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 209 THR Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 VAL 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 230 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 96 GLN 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 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 67 SER Chi-restraints excluded: chain G residue 86 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 Chi-restraints excluded: chain K residue 35 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 301 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 254 optimal weight: 0.6980 chunk 215 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 229 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN C 29 HIS D 329 ASN ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 277 GLN ** I 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.139065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.102063 restraints weight = 42328.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.101475 restraints weight = 33476.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.102398 restraints weight = 30045.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.103408 restraints weight = 22321.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.103542 restraints weight = 19811.196| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- 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: 4 | |-----------------------------------------------------------------------------| |-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: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25143 Z= 0.138 Angle : 0.567 12.620 34415 Z= 0.291 Chirality : 0.040 0.255 3885 Planarity : 0.003 0.060 4315 Dihedral : 11.457 177.270 4027 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.65 % Allowed : 19.86 % Favored : 77.49 % 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: -0.81 (0.15), residues: 2995 helix: 1.60 (0.17), residues: 908 sheet: -0.23 (0.23), residues: 514 loop : -2.05 (0.14), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 32 TYR 0.015 0.001 TYR A 235 PHE 0.013 0.001 PHE G 114 TRP 0.033 0.001 TRP A 394 HIS 0.007 0.001 HIS I 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (25143) covalent geometry : angle 0.56655 / 0.29 (34415) hydrogen bonds : bond 0.03017 / 2.01 ( 991) hydrogen bonds : angle 4.20128 / 2.98 ( 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 349 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 287 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 156 ASN cc_start: 0.7172 (m110) cc_final: 0.6640 (m-40) REVERT: B 281 GLU cc_start: 0.8100 (pp20) cc_final: 0.7475 (pp20) REVERT: D 146 ASN cc_start: 0.8032 (t0) cc_final: 0.7708 (t0) REVERT: D 159 HIS cc_start: 0.7853 (m-70) cc_final: 0.7598 (m170) REVERT: D 195 PHE cc_start: 0.7860 (m-80) cc_final: 0.7624 (m-80) REVERT: D 206 LYS cc_start: 0.7759 (tptp) cc_final: 0.7531 (pttt) REVERT: D 212 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7619 (m-30) REVERT: D 275 HIS cc_start: 0.8527 (m170) cc_final: 0.8149 (m90) REVERT: E 348 ASN cc_start: 0.9012 (t0) cc_final: 0.8491 (t0) REVERT: F 203 ARG cc_start: 0.7642 (ptp-110) cc_final: 0.7195 (ttm110) REVERT: F 249 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7783 (mt-10) REVERT: G 73 SER cc_start: 0.8619 (t) cc_final: 0.8192 (t) REVERT: H 146 ASN cc_start: 0.8205 (t0) cc_final: 0.7828 (t0) REVERT: H 339 VAL cc_start: 0.8166 (t) cc_final: 0.7858 (p) REVERT: I 249 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7706 (mm-30) REVERT: I 290 TYR cc_start: 0.8293 (p90) cc_final: 0.8014 (p90) REVERT: I 321 LEU cc_start: 0.8474 (mt) cc_final: 0.8018 (mp) REVERT: I 333 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7958 (mtt90) REVERT: K 46 ARG cc_start: 0.6843 (ttp80) cc_final: 0.6617 (ttp80) outliers start: 62 outliers final: 53 residues processed: 334 average time/residue: 0.1763 time to fit residues: 92.3663 Evaluate side-chains 330 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 274 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU 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 397 ARG Chi-restraints excluded: chain B residue 41 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 98 VAL Chi-restraints excluded: chain B residue 111 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 263 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 VAL 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 230 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 96 GLN 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 143 THR 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 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 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 Chi-restraints excluded: chain K residue 35 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 105 optimal weight: 6.9990 chunk 219 optimal weight: 0.9990 chunk 223 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 271 optimal weight: 0.0570 chunk 266 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 278 optimal weight: 6.9990 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS D 329 ASN ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3653 r_free = 0.3653 target = 0.138356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.101703 restraints weight = 42476.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.101676 restraints weight = 31757.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.102447 restraints weight = 29093.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.102874 restraints weight = 22444.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.103441 restraints weight = 19767.750| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25143 Z= 0.159 Angle : 0.585 12.300 34415 Z= 0.299 Chirality : 0.040 0.253 3885 Planarity : 0.004 0.060 4315 Dihedral : 11.473 177.158 4027 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.28 % Favored : 93.69 % Rotamer: Outliers : 2.73 % Allowed : 20.29 % Favored : 76.98 % 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: 1.60 (0.17), residues: 909 sheet: -0.17 (0.23), residues: 508 loop : -2.06 (0.14), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 32 TYR 0.012 0.001 TYR C 97 PHE 0.040 0.001 PHE A 425 TRP 0.039 0.001 TRP A 394 HIS 0.007 0.001 HIS I 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (25143) covalent geometry : angle 0.58452 / 0.30 (34415) hydrogen bonds : bond 0.03106 / 2.08 ( 991) hydrogen bonds : angle 4.26980 / 3.03 ( 2911) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3899.31 seconds wall clock time: 68 minutes 16.85 seconds (4096.85 seconds total)