Starting phenix.real_space_refine on Sun Sep 13 16:52:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jzy_22584/09_2026/7jzy_22584.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jzy_22584/09_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_22584/09_2026/7jzy_22584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jzy_22584/09_2026/7jzy_22584.map" model { file = "/net/cci-nas-00/data/ceres_data/7jzy_22584/09_2026/7jzy_22584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jzy_22584/09_2026/7jzy_22584.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7jzy_22584/09_2026/7jzy_22584.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jzy_22584/09_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): 0.06s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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, 'RNAv2': 60} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 17, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 28, 'rna3p': 32} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2307 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 10, 'TRANS': 287} Chain breaks: 2 Chain: "E" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "F" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "G" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "H" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2554 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain breaks: 1 Chain: "I" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "J" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 545 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain: "K" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 545 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Time building chain proxies: 5.87, per 1000 atoms: 0.24 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: 1.92 Conformation dependent library (CDL) restraints added in 1.2 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: 2.80 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: 4.93 Time building geometry restraints manager: 2.64 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: 32717 2.11 - 4.23: 1468 4.23 - 6.34: 186 6.34 - 8.45: 33 8.45 - 10.57: 8 Bond angle restraints: 34412 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=" C GLY A 96 " pdb=" N SER A 97 " pdb=" CA SER A 97 " ideal model delta sigma weight residual 121.54 129.88 -8.34 1.91e+00 2.74e-01 1.91e+01 ... (remaining 34407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.70: 13753 23.70 - 47.40: 965 47.40 - 71.10: 226 71.10 - 94.80: 41 94.80 - 118.50: 1 Dihedral angle restraints: 14986 sinusoidal: 6276 harmonic: 8710 Sorted by residual: dihedral pdb=" C4' G M 40 " pdb=" C3' G M 40 " pdb=" C2' G M 40 " pdb=" C1' G M 40 " ideal model delta sinusoidal sigma weight residual 36.34 -38.82 75.16 1 3.10e+00 1.04e-01 7.43e+02 dihedral pdb=" C4' A M 3 " pdb=" C3' A M 3 " pdb=" C2' A M 3 " pdb=" C1' A M 3 " ideal model delta sinusoidal sigma weight residual 36.34 -38.64 74.99 1 3.10e+00 1.04e-01 7.40e+02 dihedral pdb=" C4' G M 19 " pdb=" C3' G M 19 " pdb=" C2' G M 19 " pdb=" C1' G M 19 " ideal model delta sinusoidal sigma weight residual 36.35 -38.01 74.36 1 3.10e+00 1.04e-01 7.30e+02 ... (remaining 14983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3277 0.077 - 0.154: 460 0.154 - 0.230: 87 0.230 - 0.307: 58 0.307 - 0.384: 3 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 2.46 2.07 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" C3' G M 40 " pdb=" C4' G M 40 " pdb=" O3' G M 40 " pdb=" C2' G M 40 " both_signs ideal model delta sigma weight residual False -2.50 -2.84 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" C2' A M 45 " pdb=" C3' A M 45 " pdb=" O2' A M 45 " pdb=" C1' A M 45 " both_signs ideal model delta sigma weight residual False -2.79 -2.47 -0.32 2.00e-01 2.50e+01 2.57e+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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.760 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.730 ------------------------------------------------------------------------------- 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 : 1.003 10.568 34412 Z= 0.550 Chirality : 0.066 0.384 3885 Planarity : 0.006 0.072 4315 Dihedral : 17.166 118.504 9356 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 0.00883 / 0.40 (25143) covalent geometry : angle 1.00262 / 0.55 (34412) 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 : 0.897 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: 0.2045 time to fit residues: 129.1371 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 : 0.856 ------------------------------------------------------------------------------- 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 165 GLN D 170 ASN F 56 GLN F 183 HIS G 51 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 342 GLN ** H 159 HIS ** 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 = 0.3663 r_free = 0.3663 target = 0.139150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.101156 restraints weight = 39962.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.102677 restraints weight = 33727.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.103056 restraints weight = 24398.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.103592 restraints weight = 19189.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.103742 restraints weight = 17195.720| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (13 function evaluations) r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25143 Z= 0.179 Angle : 0.936 22.732 34412 Z= 0.407 Chirality : 0.082 1.337 3885 Planarity : 0.004 0.058 4315 Dihedral : 11.548 139.829 4032 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.88 % Allowed : 14.14 % Favored : 83.98 % 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: -2.34 (0.13), residues: 2995 helix: -0.49 (0.16), residues: 900 sheet: -0.74 (0.22), residues: 499 loop : -2.54 (0.13), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 73 TYR 0.020 0.001 TYR I 144 PHE 0.021 0.001 PHE C 173 TRP 0.022 0.001 TRP D 330 HIS 0.006 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.18 (25143) covalent geometry : angle 0.93585 / 0.41 (34412) hydrogen bonds : bond 0.03741 / 2.52 ( 991) hydrogen bonds : angle 5.04005 / 3.53 ( 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 375 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 331 time to evaluate : 0.856 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: 0.8010 (OUTLIER) cc_final: 0.7688 (p0) REVERT: B 124 GLN cc_start: 0.7849 (mm-40) cc_final: 0.7645 (pm20) REVERT: C 186 TRP cc_start: 0.7828 (t-100) cc_final: 0.7592 (t-100) REVERT: D 146 ASN cc_start: 0.8041 (t0) cc_final: 0.7709 (t0) REVERT: D 195 PHE cc_start: 0.8003 (m-80) cc_final: 0.7770 (m-80) REVERT: D 206 LYS cc_start: 0.7887 (tptt) cc_final: 0.7636 (tptp) REVERT: D 211 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8546 (tt) REVERT: D 212 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.7919 (m-30) REVERT: D 278 LYS cc_start: 0.8578 (tttp) cc_final: 0.8198 (tttt) REVERT: D 294 ASP cc_start: 0.7246 (t70) cc_final: 0.6974 (t70) REVERT: E 74 ASN cc_start: 0.8233 (p0) cc_final: 0.7925 (p0) REVERT: E 146 ASN cc_start: 0.8884 (t0) cc_final: 0.8628 (t0) REVERT: F 90 ILE cc_start: 0.9132 (pt) cc_final: 0.8884 (mt) REVERT: F 203 ARG cc_start: 0.7565 (ptp-110) cc_final: 0.7306 (ttm110) REVERT: F 212 ASP cc_start: 0.8015 (m-30) cc_final: 0.7812 (m-30) REVERT: G 155 ARG cc_start: 0.7949 (ttp80) cc_final: 0.7737 (ttp80) REVERT: H 146 ASN cc_start: 0.8200 (t0) cc_final: 0.7842 (t0) REVERT: H 269 ARG cc_start: 0.8531 (ptp-170) cc_final: 0.8300 (ptp90) REVERT: H 304 TYR cc_start: 0.8259 (m-80) cc_final: 0.7957 (m-80) REVERT: I 249 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7621 (mm-30) REVERT: I 269 ARG cc_start: 0.7228 (mtm-85) cc_final: 0.6739 (mtm180) REVERT: J 29 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8542 (tt0) REVERT: K 58 LYS cc_start: 0.9131 (tttm) cc_final: 0.8586 (tttp) outliers start: 44 outliers final: 22 residues processed: 361 average time/residue: 0.1792 time to fit residues: 100.0807 Evaluate side-chains 297 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 271 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 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 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: 10.0000 chunk 246 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 131 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 73 optimal weight: 0.9980 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 HIS D 248 GLN D 329 ASN F 260 GLN F 281 ASN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 310 GLN ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 94 ASN I 148 GLN I 159 HIS ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.136123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.100250 restraints weight = 49830.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.099306 restraints weight = 31428.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.099414 restraints weight = 39684.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.101734 restraints weight = 23934.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.102090 restraints weight = 17990.884| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (7 function evaluations) r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 25143 Z= 0.241 Angle : 0.797 15.273 34412 Z= 0.373 Chirality : 0.063 0.879 3885 Planarity : 0.004 0.060 4315 Dihedral : 11.821 155.340 4030 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.08 % Allowed : 16.10 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.14), residues: 2995 helix: 0.28 (0.16), residues: 913 sheet: -0.62 (0.22), residues: 510 loop : -2.41 (0.13), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 397 TYR 0.026 0.002 TYR G 324 PHE 0.017 0.002 PHE F 114 TRP 0.026 0.001 TRP D 330 HIS 0.008 0.001 HIS D 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.24 (25143) covalent geometry : angle 0.79744 / 0.37 (34412) hydrogen bonds : bond 0.03807 / 2.56 ( 991) hydrogen bonds : angle 4.83559 / 3.39 ( 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 359 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 287 time to evaluate : 0.923 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: 0.8289 (OUTLIER) cc_final: 0.8063 (p0) REVERT: A 332 GLU cc_start: 0.8106 (tp30) cc_final: 0.7902 (tt0) REVERT: B 124 GLN cc_start: 0.7886 (mm-40) cc_final: 0.7594 (pm20) REVERT: D 146 ASN cc_start: 0.8125 (t0) cc_final: 0.7801 (t0) REVERT: D 195 PHE cc_start: 0.8045 (m-80) cc_final: 0.7776 (m-80) REVERT: D 206 LYS cc_start: 0.7934 (tptt) cc_final: 0.7651 (tptp) REVERT: D 211 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8470 (tt) REVERT: D 212 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8004 (m-30) REVERT: D 294 ASP cc_start: 0.7539 (t70) cc_final: 0.7212 (t70) REVERT: E 74 ASN cc_start: 0.8256 (p0) cc_final: 0.7937 (p0) REVERT: E 146 ASN cc_start: 0.8930 (t0) cc_final: 0.8716 (t0) REVERT: F 203 ARG cc_start: 0.7728 (ptp-110) cc_final: 0.7338 (ttm110) REVERT: F 212 ASP cc_start: 0.8032 (m-30) cc_final: 0.7809 (m-30) REVERT: G 155 ARG cc_start: 0.8005 (ttp80) cc_final: 0.7773 (ttp80) REVERT: H 146 ASN cc_start: 0.8333 (t0) cc_final: 0.7935 (t0) REVERT: H 269 ARG cc_start: 0.8656 (ptp-170) cc_final: 0.8384 (ptp90) REVERT: H 304 TYR cc_start: 0.8456 (m-80) cc_final: 0.8077 (m-80) REVERT: I 249 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7638 (mm-30) REVERT: I 290 TYR cc_start: 0.8366 (p90) cc_final: 0.8048 (p90) REVERT: J 6 ILE cc_start: 0.9286 (mm) cc_final: 0.9034 (mt) REVERT: J 29 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8490 (tt0) REVERT: K 58 LYS cc_start: 0.9122 (tttm) cc_final: 0.8563 (tttp) outliers start: 72 outliers final: 44 residues processed: 347 average time/residue: 0.1703 time to fit residues: 92.0936 Evaluate side-chains 304 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 256 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 59 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 263 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 211 LEU Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 304 TYR Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain J residue 29 GLN Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 50 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 160 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 chunk 110 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 284 optimal weight: 6.9990 chunk 128 optimal weight: 0.0470 chunk 183 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 chunk 262 optimal weight: 6.9990 overall best weight: 1.9284 ------------------------------------------------------------------------------- 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 A 396 ASN B 306 HIS D 329 ASN F 260 GLN F 342 GLN G 260 GLN H 96 GLN I 94 ASN I 342 GLN ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.136426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.100044 restraints weight = 49725.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.099424 restraints weight = 31248.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.099635 restraints weight = 37231.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.101801 restraints weight = 23579.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.102094 restraints weight = 18286.073| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 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 = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25143 Z= 0.185 Angle : 0.718 14.515 34412 Z= 0.338 Chirality : 0.056 0.710 3885 Planarity : 0.004 0.057 4315 Dihedral : 11.549 155.981 4030 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.29 % Allowed : 17.00 % Favored : 79.71 % 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: -1.46 (0.14), residues: 2995 helix: 0.80 (0.17), residues: 906 sheet: -0.58 (0.22), residues: 518 loop : -2.27 (0.14), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 69 TYR 0.016 0.002 TYR G 324 PHE 0.014 0.001 PHE G 114 TRP 0.024 0.001 TRP A 394 HIS 0.005 0.001 HIS D 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (25143) covalent geometry : angle 0.71797 / 0.34 (34412) hydrogen bonds : bond 0.03420 / 2.29 ( 991) hydrogen bonds : angle 4.56843 / 3.21 ( 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 365 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 288 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.7915 (p0) REVERT: A 287 PHE cc_start: 0.6312 (OUTLIER) cc_final: 0.5768 (t80) REVERT: A 397 ARG cc_start: 0.7096 (OUTLIER) cc_final: 0.6544 (mtm110) REVERT: B 124 GLN cc_start: 0.7806 (mm-40) cc_final: 0.7593 (pm20) REVERT: C 117 MET cc_start: 0.4047 (mmp) cc_final: 0.3831 (mtp) REVERT: D 146 ASN cc_start: 0.8037 (t0) cc_final: 0.7723 (t0) REVERT: D 195 PHE cc_start: 0.8046 (m-80) cc_final: 0.7768 (m-80) REVERT: D 206 LYS cc_start: 0.7872 (tptt) cc_final: 0.7667 (tptp) REVERT: D 212 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.7901 (m-30) REVERT: D 294 ASP cc_start: 0.7555 (t70) cc_final: 0.7190 (t70) REVERT: E 74 ASN cc_start: 0.8141 (p0) cc_final: 0.7819 (p0) REVERT: E 146 ASN cc_start: 0.8933 (t0) cc_final: 0.8721 (t0) REVERT: F 203 ARG cc_start: 0.7748 (ptp-110) cc_final: 0.7320 (ttm110) REVERT: F 212 ASP cc_start: 0.7979 (m-30) cc_final: 0.7770 (m-30) REVERT: F 249 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7929 (mt-10) REVERT: G 155 ARG cc_start: 0.7991 (ttp80) cc_final: 0.7691 (ttp80) REVERT: H 146 ASN cc_start: 0.8316 (t0) cc_final: 0.7926 (t0) REVERT: H 269 ARG cc_start: 0.8633 (ptp-170) cc_final: 0.8392 (ptp90) REVERT: H 304 TYR cc_start: 0.8494 (m-80) cc_final: 0.8123 (m-80) REVERT: I 249 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7633 (mm-30) REVERT: I 290 TYR cc_start: 0.8348 (p90) cc_final: 0.8038 (p90) REVERT: I 321 LEU cc_start: 0.8400 (mt) cc_final: 0.7897 (mp) outliers start: 77 outliers final: 51 residues processed: 351 average time/residue: 0.1723 time to fit residues: 94.1227 Evaluate side-chains 318 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 262 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain 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 105 SER Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 262 SER Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 331 VAL Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 304 TYR Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 50 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 131 optimal weight: 5.9990 chunk 219 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 223 optimal weight: 0.9990 chunk 232 optimal weight: 0.0870 chunk 229 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 269 optimal weight: 0.8980 chunk 228 optimal weight: 0.9990 chunk 280 optimal weight: 0.8980 chunk 243 optimal weight: 1.9990 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 A 335 GLN C 82 HIS D 329 ASN ** F 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 94 ASN I 227 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.139319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.103587 restraints weight = 49795.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.101878 restraints weight = 34269.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.103226 restraints weight = 33089.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.104063 restraints weight = 21780.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.105735 restraints weight = 19374.944| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25143 Z= 0.120 Angle : 0.667 14.082 34412 Z= 0.315 Chirality : 0.051 0.569 3885 Planarity : 0.003 0.058 4315 Dihedral : 11.298 157.822 4027 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.68 % Favored : 94.29 % Rotamer: Outliers : 3.08 % Allowed : 18.80 % Favored : 78.13 % 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: -1.10 (0.15), residues: 2995 helix: 1.22 (0.17), residues: 899 sheet: -0.34 (0.23), residues: 514 loop : -2.15 (0.14), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 169 TYR 0.025 0.001 TYR I 144 PHE 0.009 0.001 PHE C 143 TRP 0.023 0.001 TRP A 394 HIS 0.006 0.001 HIS D 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (25143) covalent geometry : angle 0.66746 / 0.31 (34412) hydrogen bonds : bond 0.03102 / 2.07 ( 991) hydrogen bonds : angle 4.32913 / 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 373 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 301 time to evaluate : 0.937 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 235 TYR cc_start: 0.8586 (m-80) cc_final: 0.8275 (m-80) REVERT: A 397 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6648 (mtm110) REVERT: B 281 GLU cc_start: 0.8100 (pp20) cc_final: 0.7457 (pp20) REVERT: C 56 GLU cc_start: 0.6234 (tp30) cc_final: 0.5983 (tp30) REVERT: D 146 ASN cc_start: 0.8063 (t0) cc_final: 0.7734 (t0) REVERT: D 195 PHE cc_start: 0.7850 (m-80) cc_final: 0.7580 (m-80) REVERT: D 206 LYS cc_start: 0.7870 (tptt) cc_final: 0.7634 (tptp) REVERT: D 278 LYS cc_start: 0.8580 (tttp) cc_final: 0.8306 (tttt) REVERT: D 294 ASP cc_start: 0.7475 (t70) cc_final: 0.7115 (t70) REVERT: E 74 ASN cc_start: 0.8108 (p0) cc_final: 0.7816 (p0) REVERT: E 146 ASN cc_start: 0.8892 (t0) cc_final: 0.8683 (t0) REVERT: F 203 ARG cc_start: 0.7635 (ptp-110) cc_final: 0.7200 (ttm110) REVERT: H 146 ASN cc_start: 0.8239 (t0) cc_final: 0.7856 (t0) REVERT: H 269 ARG cc_start: 0.8510 (ptp-170) cc_final: 0.8274 (ptp90) REVERT: H 285 THR cc_start: 0.8799 (m) cc_final: 0.8553 (p) REVERT: H 304 TYR cc_start: 0.8404 (m-80) cc_final: 0.8034 (m-80) REVERT: I 249 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7579 (mm-30) REVERT: I 290 TYR cc_start: 0.8287 (p90) cc_final: 0.8025 (p90) REVERT: I 321 LEU cc_start: 0.8463 (mt) cc_final: 0.7965 (mp) REVERT: K 47 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8137 (mm) outliers start: 72 outliers final: 47 residues processed: 352 average time/residue: 0.1671 time to fit residues: 92.4115 Evaluate side-chains 317 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 268 time to evaluate : 1.109 ------------------------------------------------------------------------------- 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 397 ARG Chi-restraints excluded: chain A residue 414 TRP Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 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 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 189 VAL Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain 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 26 SER 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 304 TYR Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 260 GLN 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 J residue 49 THR Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 50 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 62 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 115 optimal weight: 0.0370 chunk 165 optimal weight: 2.9990 chunk 272 optimal weight: 1.9990 chunk 268 optimal weight: 0.8980 chunk 148 optimal weight: 0.0030 chunk 145 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 288 optimal weight: 9.9990 chunk 296 optimal weight: 0.7980 overall best weight: 0.5470 ------------------------------------------------------------------------------- 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 D 329 ASN E 51 GLN E 342 GLN G 183 HIS H 148 GLN I 94 ASN ** I 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 227 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.140886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.103488 restraints weight = 47483.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.104913 restraints weight = 35130.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.105473 restraints weight = 29980.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.105883 restraints weight = 22162.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.107255 restraints weight = 18966.795| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25143 Z= 0.108 Angle : 0.654 13.576 34412 Z= 0.305 Chirality : 0.049 0.387 3885 Planarity : 0.003 0.060 4315 Dihedral : 11.108 158.624 4027 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.90 % Allowed : 19.01 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.15), residues: 2995 helix: 1.52 (0.17), residues: 901 sheet: -0.26 (0.23), residues: 514 loop : -2.05 (0.14), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 46 TYR 0.018 0.001 TYR C 97 PHE 0.034 0.001 PHE A 425 TRP 0.026 0.001 TRP A 394 HIS 0.005 0.001 HIS D 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (25143) covalent geometry : angle 0.65383 / 0.30 (34412) hydrogen bonds : bond 0.02926 / 1.96 ( 991) hydrogen bonds : angle 4.18665 / 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 391 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 323 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 281 GLU cc_start: 0.8137 (pp20) cc_final: 0.7487 (pp20) REVERT: D 146 ASN cc_start: 0.8120 (t0) cc_final: 0.7821 (t0) REVERT: D 195 PHE cc_start: 0.7866 (m-80) cc_final: 0.7624 (m-80) REVERT: D 278 LYS cc_start: 0.8539 (tttp) cc_final: 0.8300 (tttt) REVERT: D 294 ASP cc_start: 0.7457 (t70) cc_final: 0.7094 (t70) REVERT: E 74 ASN cc_start: 0.8028 (p0) cc_final: 0.7756 (p0) REVERT: E 146 ASN cc_start: 0.8898 (t0) cc_final: 0.8682 (t0) REVERT: F 51 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7260 (pt0) REVERT: F 203 ARG cc_start: 0.7581 (ptp-110) cc_final: 0.7154 (ttm110) REVERT: G 73 SER cc_start: 0.8303 (t) cc_final: 0.7982 (t) REVERT: H 146 ASN cc_start: 0.8230 (t0) cc_final: 0.7817 (t0) REVERT: H 304 TYR cc_start: 0.8270 (m-80) cc_final: 0.7967 (m-80) REVERT: H 321 LEU cc_start: 0.8487 (tp) cc_final: 0.8262 (tp) REVERT: I 249 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7545 (mm-30) REVERT: I 269 ARG cc_start: 0.7310 (mtm-85) cc_final: 0.6744 (mtm-85) REVERT: I 290 TYR cc_start: 0.8244 (p90) cc_final: 0.8031 (p90) REVERT: I 321 LEU cc_start: 0.8376 (mt) cc_final: 0.7929 (mp) REVERT: I 333 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7857 (mtt90) REVERT: J 9 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7518 (tt0) REVERT: K 57 TYR cc_start: 0.8131 (p90) cc_final: 0.7780 (p90) outliers start: 68 outliers final: 50 residues processed: 372 average time/residue: 0.1707 time to fit residues: 99.7965 Evaluate side-chains 334 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 282 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 414 TRP Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 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 204 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain 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 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 E residue 78 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 143 THR 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 262 SER Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 348 ASN 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 297 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 231 optimal weight: 0.7980 chunk 244 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 17 optimal weight: 0.4980 chunk 177 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN F 159 HIS I 94 ASN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.138338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.100026 restraints weight = 40027.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.101632 restraints weight = 33383.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.102155 restraints weight = 23493.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.102836 restraints weight = 19089.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.102874 restraints weight = 17028.571| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 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 = 0.3095 r_free = 0.3095 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: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25143 Z= 0.152 Angle : 0.676 14.090 34412 Z= 0.317 Chirality : 0.050 0.403 3885 Planarity : 0.003 0.060 4315 Dihedral : 11.091 153.446 4026 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.82 % Allowed : 19.56 % 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: -0.79 (0.15), residues: 2995 helix: 1.64 (0.17), residues: 900 sheet: -0.19 (0.23), residues: 510 loop : -2.05 (0.14), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 32 TYR 0.016 0.001 TYR C 97 PHE 0.016 0.001 PHE A 425 TRP 0.028 0.001 TRP A 394 HIS 0.004 0.001 HIS H 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (25143) covalent geometry : angle 0.67572 / 0.32 (34412) hydrogen bonds : bond 0.03041 / 2.04 ( 991) hydrogen bonds : angle 4.20669 / 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: 66 poor density : 291 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: symmetry clash REVERT: B 82 ASN cc_start: 0.9309 (m-40) cc_final: 0.9024 (m-40) REVERT: B 281 GLU cc_start: 0.8169 (pp20) cc_final: 0.7509 (pp20) REVERT: D 146 ASN cc_start: 0.8124 (t0) cc_final: 0.7802 (t0) REVERT: D 195 PHE cc_start: 0.7873 (m-80) cc_final: 0.7618 (m-80) REVERT: D 212 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7686 (m-30) REVERT: D 294 ASP cc_start: 0.7442 (t70) cc_final: 0.7131 (t70) REVERT: E 348 ASN cc_start: 0.9027 (t0) cc_final: 0.8587 (t0) REVERT: F 203 ARG cc_start: 0.7630 (ptp-110) cc_final: 0.7181 (ttm110) REVERT: G 73 SER cc_start: 0.8495 (t) cc_final: 0.8133 (t) REVERT: H 128 CYS cc_start: 0.8534 (p) cc_final: 0.8278 (t) REVERT: H 146 ASN cc_start: 0.8316 (t0) cc_final: 0.7883 (t0) REVERT: H 339 VAL cc_start: 0.8162 (t) cc_final: 0.7835 (p) REVERT: I 249 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7556 (mm-30) REVERT: I 290 TYR cc_start: 0.8264 (p90) cc_final: 0.7987 (p90) REVERT: I 321 LEU cc_start: 0.8423 (mt) cc_final: 0.7956 (mp) REVERT: I 333 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7889 (mtt90) outliers start: 66 outliers final: 58 residues processed: 343 average time/residue: 0.1703 time to fit residues: 92.6175 Evaluate side-chains 335 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 275 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 41 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 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 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 277 GLN Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 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 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 260 GLN Chi-restraints excluded: chain G residue 262 SER Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain H residue 331 VAL Chi-restraints excluded: chain 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 2 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 205 optimal weight: 0.8980 chunk 240 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 242 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 chunk 198 optimal weight: 0.9980 chunk 239 optimal weight: 5.9990 chunk 225 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 251 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 ASN D 329 ASN I 227 HIS ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.139478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.101630 restraints weight = 40535.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.103871 restraints weight = 33729.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.104035 restraints weight = 23674.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.104467 restraints weight = 18855.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.104696 restraints weight = 16955.001| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3004 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= 0.128 Angle : 0.665 14.105 34412 Z= 0.310 Chirality : 0.049 0.399 3885 Planarity : 0.003 0.059 4315 Dihedral : 11.055 151.531 4026 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.90 % Allowed : 19.52 % Favored : 77.57 % 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: -0.76 (0.15), residues: 2995 helix: 1.67 (0.17), residues: 901 sheet: -0.23 (0.23), residues: 522 loop : -2.02 (0.14), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 32 TYR 0.014 0.001 TYR C 97 PHE 0.015 0.001 PHE A 425 TRP 0.036 0.001 TRP A 394 HIS 0.004 0.001 HIS H 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (25143) covalent geometry : angle 0.66515 / 0.31 (34412) hydrogen bonds : bond 0.02929 / 1.96 ( 991) hydrogen bonds : angle 4.16049 / 2.95 ( 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 353 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 285 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 ARG cc_start: 0.6700 (tmm-80) cc_final: 0.6392 (ptt-90) REVERT: B 48 VAL cc_start: 0.7903 (OUTLIER) cc_final: 0.7677 (p) REVERT: B 281 GLU cc_start: 0.8146 (pp20) cc_final: 0.7508 (pp20) REVERT: D 146 ASN cc_start: 0.8083 (t0) cc_final: 0.7785 (t0) REVERT: D 195 PHE cc_start: 0.7838 (m-80) cc_final: 0.7630 (m-80) REVERT: D 206 LYS cc_start: 0.7785 (tptp) cc_final: 0.7461 (pttt) REVERT: D 212 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7633 (m-30) REVERT: D 294 ASP cc_start: 0.7326 (t70) cc_final: 0.7059 (t0) REVERT: E 348 ASN cc_start: 0.8959 (t0) cc_final: 0.8558 (t0) REVERT: F 203 ARG cc_start: 0.7598 (ptp-110) cc_final: 0.7153 (ttm110) REVERT: G 73 SER cc_start: 0.8461 (t) cc_final: 0.8092 (t) REVERT: H 128 CYS cc_start: 0.8500 (p) cc_final: 0.8257 (t) REVERT: H 146 ASN cc_start: 0.8273 (t0) cc_final: 0.7835 (t0) REVERT: H 321 LEU cc_start: 0.8452 (tp) cc_final: 0.8247 (tp) REVERT: H 339 VAL cc_start: 0.8187 (t) cc_final: 0.7868 (p) REVERT: I 249 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7509 (mm-30) REVERT: I 290 TYR cc_start: 0.8237 (p90) cc_final: 0.8005 (p90) REVERT: I 321 LEU cc_start: 0.8380 (mt) cc_final: 0.7934 (mp) REVERT: I 333 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7817 (mtt90) outliers start: 68 outliers final: 57 residues processed: 336 average time/residue: 0.1626 time to fit residues: 87.0831 Evaluate side-chains 336 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 276 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 320 GLN Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 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 189 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 244 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 143 THR 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 260 GLN Chi-restraints excluded: chain G residue 262 SER Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 348 ASN Chi-restraints excluded: chain H residue 348 ASN Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 44 MET 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: 0.9980 chunk 248 optimal weight: 2.9990 chunk 264 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 270 optimal weight: 0.7980 chunk 197 optimal weight: 0.6980 chunk 202 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 285 optimal weight: 5.9990 chunk 43 optimal weight: 0.4980 chunk 299 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 GLN ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN I 227 HIS ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.142404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.105142 restraints weight = 40257.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.106584 restraints weight = 32975.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.107037 restraints weight = 23758.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.107479 restraints weight = 19610.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.107753 restraints weight = 17976.401| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25143 Z= 0.115 Angle : 0.651 14.089 34412 Z= 0.303 Chirality : 0.048 0.389 3885 Planarity : 0.003 0.059 4315 Dihedral : 10.948 149.605 4026 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.64 % Favored : 94.32 % Rotamer: Outliers : 2.69 % Allowed : 19.69 % 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: -0.65 (0.15), residues: 2995 helix: 1.77 (0.17), residues: 902 sheet: -0.12 (0.23), residues: 514 loop : -1.97 (0.14), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 32 TYR 0.016 0.001 TYR C 97 PHE 0.012 0.001 PHE A 425 TRP 0.029 0.001 TRP A 394 HIS 0.003 0.001 HIS D 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (25143) covalent geometry : angle 0.65079 / 0.30 (34412) hydrogen bonds : bond 0.02811 / 1.88 ( 991) hydrogen bonds : angle 4.06260 / 2.88 ( 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 363 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 300 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 ARG cc_start: 0.6546 (tmm-80) cc_final: 0.6275 (ptt-90) REVERT: B 48 VAL cc_start: 0.7929 (OUTLIER) cc_final: 0.7716 (p) REVERT: B 82 ASN cc_start: 0.9198 (m-40) cc_final: 0.8967 (m-40) REVERT: B 156 ASN cc_start: 0.7044 (m110) cc_final: 0.6678 (m-40) REVERT: B 281 GLU cc_start: 0.8121 (pp20) cc_final: 0.7626 (pp20) REVERT: D 44 MET cc_start: 0.8187 (ptp) cc_final: 0.7910 (ptp) REVERT: D 57 GLU cc_start: 0.8046 (pm20) cc_final: 0.7631 (tm-30) REVERT: D 146 ASN cc_start: 0.8004 (t0) cc_final: 0.7712 (t0) REVERT: D 206 LYS cc_start: 0.7725 (tptp) cc_final: 0.7400 (pttt) REVERT: D 212 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7484 (m-30) REVERT: D 348 ASN cc_start: 0.9198 (t0) cc_final: 0.8910 (t0) REVERT: E 348 ASN cc_start: 0.8932 (t0) cc_final: 0.8471 (t0) REVERT: F 44 MET cc_start: 0.8756 (mtt) cc_final: 0.8538 (mtt) REVERT: F 203 ARG cc_start: 0.7520 (ptp-110) cc_final: 0.7085 (ttm110) REVERT: G 73 SER cc_start: 0.8453 (t) cc_final: 0.8081 (t) REVERT: H 25 LEU cc_start: 0.8500 (tp) cc_final: 0.8081 (tp) REVERT: H 128 CYS cc_start: 0.8487 (p) cc_final: 0.8242 (t) REVERT: H 146 ASN cc_start: 0.8229 (t0) cc_final: 0.7776 (t0) REVERT: H 206 LYS cc_start: 0.8839 (mmmt) cc_final: 0.8403 (mmtt) REVERT: H 339 VAL cc_start: 0.8177 (t) cc_final: 0.7857 (p) REVERT: I 249 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7497 (mm-30) REVERT: I 290 TYR cc_start: 0.8193 (p90) cc_final: 0.7984 (p90) REVERT: I 321 LEU cc_start: 0.8387 (mt) cc_final: 0.8017 (mp) REVERT: I 333 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7823 (mtt90) REVERT: K 57 TYR cc_start: 0.8186 (p90) cc_final: 0.7785 (p90) outliers start: 63 outliers final: 53 residues processed: 348 average time/residue: 0.1664 time to fit residues: 92.5903 Evaluate side-chains 338 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 282 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 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 320 GLN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain 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 189 VAL Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 143 THR 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 260 GLN Chi-restraints excluded: chain G residue 262 SER Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 348 ASN Chi-restraints excluded: chain H residue 331 VAL Chi-restraints excluded: chain H residue 348 ASN Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 304 TYR Chi-restraints excluded: chain I residue 333 ARG Chi-restraints excluded: chain 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: 0.8980 chunk 29 optimal weight: 0.9990 chunk 301 optimal weight: 9.9990 chunk 132 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 254 optimal weight: 0.0270 chunk 215 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 115 optimal weight: 0.8980 chunk 229 optimal weight: 2.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.142706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.106014 restraints weight = 42455.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.108595 restraints weight = 31784.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.108705 restraints weight = 24762.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.109106 restraints weight = 18764.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.109401 restraints weight = 17006.418| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25143 Z= 0.113 Angle : 0.652 14.113 34412 Z= 0.303 Chirality : 0.048 0.384 3885 Planarity : 0.003 0.063 4315 Dihedral : 10.905 148.852 4025 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.56 % Allowed : 20.08 % Favored : 77.36 % 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: -0.60 (0.15), residues: 2995 helix: 1.82 (0.17), residues: 903 sheet: -0.15 (0.23), residues: 520 loop : -1.94 (0.14), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 32 TYR 0.016 0.001 TYR A 179 PHE 0.043 0.001 PHE A 425 TRP 0.035 0.001 TRP A 394 HIS 0.009 0.001 HIS I 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (25143) covalent geometry : angle 0.65218 / 0.30 (34412) hydrogen bonds : bond 0.02779 / 1.86 ( 991) hydrogen bonds : angle 4.02559 / 2.85 ( 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 358 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 298 time to evaluate : 0.944 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 397 ARG cc_start: 0.6635 (tmm-80) cc_final: 0.6057 (ptt-90) REVERT: B 48 VAL cc_start: 0.7952 (OUTLIER) cc_final: 0.7710 (p) REVERT: B 156 ASN cc_start: 0.7080 (m110) cc_final: 0.6593 (m-40) REVERT: B 281 GLU cc_start: 0.7985 (pp20) cc_final: 0.7776 (pp20) REVERT: D 57 GLU cc_start: 0.8031 (pm20) cc_final: 0.7578 (tm-30) REVERT: D 146 ASN cc_start: 0.7995 (t0) cc_final: 0.7713 (t0) REVERT: D 206 LYS cc_start: 0.7718 (tptp) cc_final: 0.7366 (pttt) REVERT: D 212 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7497 (m-30) REVERT: D 348 ASN cc_start: 0.9188 (t0) cc_final: 0.8894 (t0) REVERT: E 348 ASN cc_start: 0.8935 (t0) cc_final: 0.8472 (t0) REVERT: F 44 MET cc_start: 0.8885 (mtt) cc_final: 0.8679 (mtt) REVERT: F 51 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7170 (pt0) REVERT: F 203 ARG cc_start: 0.7541 (ptp-110) cc_final: 0.7132 (ttm110) REVERT: G 73 SER cc_start: 0.8464 (t) cc_final: 0.8073 (t) REVERT: H 25 LEU cc_start: 0.8518 (tp) cc_final: 0.8109 (tp) REVERT: H 128 CYS cc_start: 0.8528 (p) cc_final: 0.8290 (t) REVERT: H 146 ASN cc_start: 0.8229 (t0) cc_final: 0.7775 (t0) REVERT: H 206 LYS cc_start: 0.8806 (mmmt) cc_final: 0.8402 (mmtt) REVERT: H 339 VAL cc_start: 0.8163 (t) cc_final: 0.7847 (p) REVERT: I 249 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7524 (mm-30) REVERT: I 290 TYR cc_start: 0.8187 (p90) cc_final: 0.7952 (p90) REVERT: I 321 LEU cc_start: 0.8410 (mt) cc_final: 0.8039 (mp) REVERT: I 333 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7788 (mtt90) REVERT: K 57 TYR cc_start: 0.8113 (p90) cc_final: 0.7732 (p90) outliers start: 60 outliers final: 51 residues processed: 346 average time/residue: 0.1667 time to fit residues: 91.7658 Evaluate side-chains 336 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 281 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 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 320 GLN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain 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 189 VAL Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 143 THR 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 260 GLN Chi-restraints excluded: chain G residue 262 SER Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 348 ASN Chi-restraints excluded: chain H residue 331 VAL Chi-restraints excluded: chain H residue 348 ASN Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 304 TYR Chi-restraints excluded: chain I residue 333 ARG Chi-restraints excluded: chain 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: 4.9990 chunk 219 optimal weight: 2.9990 chunk 223 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 271 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 185 optimal weight: 0.0570 chunk 60 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 278 optimal weight: 6.9990 overall best weight: 1.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN D 329 ASN ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 227 HIS ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.142846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.106330 restraints weight = 42546.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.108254 restraints weight = 32505.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.108452 restraints weight = 25808.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.108866 restraints weight = 19851.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.109172 restraints weight = 17747.788| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3255 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3255 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.227 25143 Z= 0.170 Angle : 0.800 59.200 34412 Z= 0.411 Chirality : 0.050 0.906 3885 Planarity : 0.003 0.064 4315 Dihedral : 10.896 148.840 4024 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.43 % Allowed : 20.16 % Favored : 77.40 % Cbeta Deviations : 0.04 % 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: -0.61 (0.15), residues: 2995 helix: 1.81 (0.17), residues: 903 sheet: -0.14 (0.23), residues: 520 loop : -1.94 (0.14), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG I 203 TYR 0.013 0.001 TYR C 97 PHE 0.033 0.001 PHE A 425 TRP 0.031 0.001 TRP A 394 HIS 0.005 0.001 HIS I 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (25143) covalent geometry : angle 0.80015 / 0.41 (34412) hydrogen bonds : bond 0.02785 / 1.86 ( 991) hydrogen bonds : angle 4.02761 / 2.85 ( 2911) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4092.63 seconds wall clock time: 71 minutes 34.57 seconds (4294.57 seconds total)