Starting phenix.real_space_refine on Fri Jul 3 16:05:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uda_64066/07_2026/9uda_64066.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uda_64066/07_2026/9uda_64066.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uda_64066/07_2026/9uda_64066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uda_64066/07_2026/9uda_64066.map" model { file = "/net/cci-nas-00/data/ceres_data/9uda_64066/07_2026/9uda_64066.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uda_64066/07_2026/9uda_64066.cif" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.152 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 4 7.16 5 P 4 5.49 5 S 92 5.16 5 C 9657 2.51 5 N 2447 2.21 5 O 2758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14963 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3416 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 422} Chain: "B" Number of atoms: 3178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3178 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 15, 'TRANS': 396} Chain: "C" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1902 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain: "D" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1580 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "E" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1511 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "F" Number of atoms: 3157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3157 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 383} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {'FMN': 1, 'IQT': 1, 'RBF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'FAD': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9320 SG CYS D 112 44.608 74.534 66.739 1.00105.32 S ATOM 10286 SG CYS E 26 46.297 71.712 67.912 1.00 98.28 S ATOM 8681 SG CYS D 29 45.001 68.668 63.451 1.00 95.72 S ATOM 11008 SG CYS E 120 43.577 71.677 61.953 1.00100.32 S ATOM 12130 SG CYS F 79 41.398 89.379 96.084 1.00258.20 S ATOM 12369 SG CYS F 111 40.170 89.481 92.761 1.00242.43 S Time building chain proxies: 3.22, per 1000 atoms: 0.22 Number of scatterers: 14963 At special positions: 0 Unit cell: (90.64, 124.08, 154, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 Ca 1 19.99 S 92 16.00 P 4 15.00 O 2758 8.00 N 2447 7.00 C 9657 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: 1.06 Conformation dependent library (CDL) restraints added in 620.4 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 26 " pdb="FE1 FES E 301 " - pdb=" SG CYS D 112 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 120 " pdb="FE2 FES E 301 " - pdb=" SG CYS D 29 " pdb=" FES F 501 " pdb="FE1 FES F 501 " - pdb=" SG CYS F 111 " pdb="FE1 FES F 501 " - pdb=" SG CYS F 79 " Number of angles added : 9 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3470 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 12 sheets defined 54.9% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 106 through 113 removed outlier: 3.587A pdb=" N LEU A 110 " --> pdb=" O ALA A 107 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA A 111 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 113 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.538A pdb=" N PHE A 131 " --> pdb=" O TRP A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 168 removed outlier: 3.627A pdb=" N VAL A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 219 through 228 Processing helix chain 'A' and resid 241 through 254 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 335 through 339 removed outlier: 3.670A pdb=" N MET A 339 " --> pdb=" O GLY A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.874A pdb=" N HIS A 354 " --> pdb=" O PHE A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 384 removed outlier: 4.042A pdb=" N LYS A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 383 " --> pdb=" O ASN A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 401 through 409 Processing helix chain 'A' and resid 410 through 413 Processing helix chain 'A' and resid 414 through 417 Processing helix chain 'A' and resid 418 through 424 Processing helix chain 'A' and resid 430 through 446 removed outlier: 3.933A pdb=" N LEU A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 10 removed outlier: 3.632A pdb=" N GLU B 8 " --> pdb=" O LYS B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 removed outlier: 4.134A pdb=" N PHE B 14 " --> pdb=" O ILE B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 23 through 35 Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.870A pdb=" N VAL B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 87 Processing helix chain 'B' and resid 89 through 98 Processing helix chain 'B' and resid 99 through 108 removed outlier: 3.722A pdb=" N THR B 105 " --> pdb=" O HIS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 152 removed outlier: 3.682A pdb=" N TYR B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 158 through 168 removed outlier: 4.166A pdb=" N ILE B 164 " --> pdb=" O PHE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 191 removed outlier: 3.541A pdb=" N ALA B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 195 Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 236 through 245 Processing helix chain 'B' and resid 246 through 249 Processing helix chain 'B' and resid 259 through 266 Processing helix chain 'B' and resid 276 through 290 removed outlier: 3.718A pdb=" N PHE B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 287 " --> pdb=" O GLY B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 316 Processing helix chain 'B' and resid 320 through 325 removed outlier: 3.573A pdb=" N ASN B 324 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET B 325 " --> pdb=" O MET B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 333 removed outlier: 4.072A pdb=" N VAL B 332 " --> pdb=" O HIS B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 353 through 375 removed outlier: 3.768A pdb=" N TRP B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN B 375 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 410 removed outlier: 3.843A pdb=" N LEU B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Proline residue: B 394 - end of helix Processing helix chain 'C' and resid 7 through 33 removed outlier: 3.621A pdb=" N LEU C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 53 removed outlier: 3.629A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 70 removed outlier: 4.176A pdb=" N GLN C 62 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS C 69 " --> pdb=" O GLU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 177 through 181 removed outlier: 3.542A pdb=" N VAL C 180 " --> pdb=" O GLY C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 188 removed outlier: 3.811A pdb=" N GLN C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 239 removed outlier: 3.727A pdb=" N GLY C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE C 235 " --> pdb=" O VAL C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 253 removed outlier: 3.634A pdb=" N LYS C 250 " --> pdb=" O PRO C 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 17 Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 27 through 34 removed outlier: 3.872A pdb=" N ALA D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 62 Processing helix chain 'D' and resid 67 through 69 No H-bonds generated for 'chain 'D' and resid 67 through 69' Processing helix chain 'D' and resid 70 through 94 Processing helix chain 'D' and resid 94 through 102 Processing helix chain 'D' and resid 103 through 109 Processing helix chain 'D' and resid 111 through 121 removed outlier: 3.919A pdb=" N MET D 115 " --> pdb=" O ASN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 125 Processing helix chain 'D' and resid 126 through 158 removed outlier: 3.641A pdb=" N VAL D 144 " --> pdb=" O GLY D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'D' and resid 183 through 202 removed outlier: 3.878A pdb=" N ALA D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 206 Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 24 through 31 Processing helix chain 'E' and resid 34 through 63 Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 75 through 77 No H-bonds generated for 'chain 'E' and resid 75 through 77' Processing helix chain 'E' and resid 78 through 102 Processing helix chain 'E' and resid 102 through 109 Processing helix chain 'E' and resid 110 through 116 Proline residue: E 114 - end of helix Processing helix chain 'E' and resid 119 through 133 removed outlier: 3.813A pdb=" N PHE E 123 " --> pdb=" O ASN E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 164 Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 175 through 191 removed outlier: 3.528A pdb=" N MET E 191 " --> pdb=" O ALA E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 194 No H-bonds generated for 'chain 'E' and resid 192 through 194' Processing helix chain 'F' and resid 2 through 30 Processing helix chain 'F' and resid 54 through 62 removed outlier: 4.118A pdb=" N ALA F 58 " --> pdb=" O LYS F 54 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY F 61 " --> pdb=" O THR F 57 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 105 Processing helix chain 'F' and resid 123 through 130 removed outlier: 3.817A pdb=" N GLU F 126 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE F 127 " --> pdb=" O PRO F 124 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N PHE F 128 " --> pdb=" O GLU F 125 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY F 129 " --> pdb=" O GLU F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 158 Processing helix chain 'F' and resid 180 through 182 No H-bonds generated for 'chain 'F' and resid 180 through 182' Processing helix chain 'F' and resid 185 through 196 removed outlier: 3.524A pdb=" N GLY F 190 " --> pdb=" O GLU F 186 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ASP F 191 " --> pdb=" O LYS F 187 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TRP F 192 " --> pdb=" O TYR F 188 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS F 194 " --> pdb=" O GLY F 190 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'F' and resid 244 through 252 removed outlier: 3.839A pdb=" N LEU F 252 " --> pdb=" O TYR F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 298 removed outlier: 3.798A pdb=" N MET F 288 " --> pdb=" O GLY F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 330 removed outlier: 3.935A pdb=" N GLY F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 363 Processing helix chain 'F' and resid 364 through 367 Processing helix chain 'F' and resid 369 through 373 Processing helix chain 'F' and resid 380 through 393 Processing helix chain 'F' and resid 397 through 399 No H-bonds generated for 'chain 'F' and resid 397 through 399' Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 6.399A pdb=" N ILE A 2 " --> pdb=" O ASP A 212 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 22 removed outlier: 3.841A pdb=" N LEU A 274 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VAL A 19 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ARG A 276 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N SER A 21 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 9.778A pdb=" N VAL A 278 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N VAL A 323 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N SER A 263 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL A 325 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA A 265 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 9.293A pdb=" N ARG A 327 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N GLN A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 32 removed outlier: 6.777A pdb=" N LEU A 87 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ARG A 81 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N SER A 89 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE A 79 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL A 91 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 43 removed outlier: 7.007A pdb=" N PHE A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 83 through 84 removed outlier: 4.586A pdb=" N LEU C 75 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 14.922A pdb=" N VAL C 121 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 11.611A pdb=" N VAL C 140 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N VAL C 123 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU C 138 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TYR C 125 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL C 136 " --> pdb=" O TYR C 125 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL C 127 " --> pdb=" O SER C 134 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N MET C 148 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLU C 169 " --> pdb=" O MET C 148 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N TYR C 150 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N TYR C 167 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N PHE C 152 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU C 165 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA C 154 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 103 through 105 Processing sheet with id=AA7, first strand: chain 'C' and resid 204 through 206 Processing sheet with id=AA8, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AA9, first strand: chain 'F' and resid 47 through 49 removed outlier: 6.629A pdb=" N THR F 36 " --> pdb=" O MET F 119 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N LEU F 121 " --> pdb=" O THR F 36 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N SER F 38 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS F 82 " --> pdb=" O GLU F 122 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 208 through 213 removed outlier: 6.379A pdb=" N TYR F 167 " --> pdb=" O PRO F 263 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU F 171 " --> pdb=" O THR F 259 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N THR F 259 " --> pdb=" O GLU F 171 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR F 136 " --> pdb=" O ALA F 153 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 175 through 178 Processing sheet with id=AB3, first strand: chain 'F' and resid 335 through 339 removed outlier: 6.984A pdb=" N MET F 276 " --> pdb=" O SER F 306 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N TRP F 308 " --> pdb=" O MET F 276 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N PHE F 278 " --> pdb=" O TRP F 308 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N GLY F 310 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLY F 280 " --> pdb=" O GLY F 310 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N CYS F 378 " --> pdb=" O ILE F 279 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR F 375 " --> pdb=" O LEU F 402 " (cutoff:3.500A) 743 hydrogen bonds defined for protein. 2106 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.21 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.40: 6094 1.40 - 1.60: 9011 1.60 - 1.80: 86 1.80 - 2.00: 75 2.00 - 2.20: 8 Bond restraints: 15274 Sorted by residual: bond pdb=" C12 IQT B 503 " pdb=" C13 IQT B 503 " ideal model delta sigma weight residual 1.454 1.278 0.176 2.00e-02 2.50e+03 7.77e+01 bond pdb=" C1 IQT B 503 " pdb=" C7 IQT B 503 " ideal model delta sigma weight residual 1.479 1.376 0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" C4 FMN C 301 " pdb=" C4A FMN C 301 " ideal model delta sigma weight residual 1.485 1.404 0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C4 FMN B 501 " pdb=" C4A FMN B 501 " ideal model delta sigma weight residual 1.485 1.405 0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" C6 IQT B 503 " pdb=" C7 IQT B 503 " ideal model delta sigma weight residual 1.333 1.398 -0.065 2.00e-02 2.50e+03 1.05e+01 ... (remaining 15269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 20344 2.12 - 4.23: 366 4.23 - 6.35: 19 6.35 - 8.47: 0 8.47 - 10.58: 1 Bond angle restraints: 20730 Sorted by residual: angle pdb=" N PHE A 136 " pdb=" CA PHE A 136 " pdb=" CB PHE A 136 " ideal model delta sigma weight residual 114.17 110.10 4.07 1.14e+00 7.69e-01 1.28e+01 angle pdb=" CB MET F 317 " pdb=" CG MET F 317 " pdb=" SD MET F 317 " ideal model delta sigma weight residual 112.70 123.28 -10.58 3.00e+00 1.11e-01 1.24e+01 angle pdb=" C VAL D 34 " pdb=" CA VAL D 34 " pdb=" CB VAL D 34 " ideal model delta sigma weight residual 112.19 108.48 3.71 1.15e+00 7.56e-01 1.04e+01 angle pdb=" C ILE D 62 " pdb=" CA ILE D 62 " pdb=" CB ILE D 62 " ideal model delta sigma weight residual 112.19 108.59 3.60 1.15e+00 7.56e-01 9.78e+00 angle pdb=" CA TRP B 103 " pdb=" CB TRP B 103 " pdb=" CG TRP B 103 " ideal model delta sigma weight residual 113.60 119.14 -5.54 1.90e+00 2.77e-01 8.51e+00 ... (remaining 20725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.66: 8791 34.66 - 69.31: 189 69.31 - 103.97: 20 103.97 - 138.63: 0 138.63 - 173.28: 3 Dihedral angle restraints: 9003 sinusoidal: 3564 harmonic: 5439 Sorted by residual: dihedral pdb=" CA PHE E 112 " pdb=" C PHE E 112 " pdb=" N LEU E 113 " pdb=" CA LEU E 113 " ideal model delta harmonic sigma weight residual -180.00 -154.00 -26.00 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" C14 IQT B 503 " pdb=" C15 IQT B 503 " pdb=" C16 IQT B 503 " pdb=" C17 IQT B 503 " ideal model delta sinusoidal sigma weight residual 87.07 -99.65 -173.28 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C14 IQT B 503 " pdb=" C15 IQT B 503 " pdb=" C16 IQT B 503 " pdb=" O4 IQT B 503 " ideal model delta sinusoidal sigma weight residual 157.21 -29.57 -173.22 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 9000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1386 0.029 - 0.059: 542 0.059 - 0.088: 210 0.088 - 0.117: 164 0.117 - 0.146: 31 Chirality restraints: 2333 Sorted by residual: chirality pdb=" CB THR B 127 " pdb=" CA THR B 127 " pdb=" OG1 THR B 127 " pdb=" CG2 THR B 127 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CB THR C 249 " pdb=" CA THR C 249 " pdb=" OG1 THR C 249 " pdb=" CG2 THR C 249 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA ILE A 79 " pdb=" N ILE A 79 " pdb=" C ILE A 79 " pdb=" CB ILE A 79 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-01 ... (remaining 2330 not shown) Planarity restraints: 2612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 IQT B 503 " 0.205 2.00e-02 2.50e+03 1.88e-01 3.52e+02 pdb=" C13 IQT B 503 " -0.210 2.00e-02 2.50e+03 pdb=" C14 IQT B 503 " -0.163 2.00e-02 2.50e+03 pdb=" C15 IQT B 503 " 0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 IQT B 503 " -0.084 2.00e-02 2.50e+03 1.84e-01 3.39e+02 pdb=" C11 IQT B 503 " 0.234 2.00e-02 2.50e+03 pdb=" C12 IQT B 503 " -0.252 2.00e-02 2.50e+03 pdb=" C13 IQT B 503 " 0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7 IQT B 503 " 0.086 2.00e-02 2.50e+03 6.95e-02 6.04e+01 pdb=" C8 IQT B 503 " -0.040 2.00e-02 2.50e+03 pdb=" C9 IQT B 503 " 0.064 2.00e-02 2.50e+03 pdb=" N1 IQT B 503 " -0.105 2.00e-02 2.50e+03 pdb=" O5 IQT B 503 " -0.006 2.00e-02 2.50e+03 ... (remaining 2609 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 9 2.22 - 2.89: 5786 2.89 - 3.56: 20831 3.56 - 4.23: 35084 4.23 - 4.90: 61192 Nonbonded interactions: 122902 Sorted by model distance: nonbonded pdb=" O ASN B 375 " pdb=" O HOH B 601 " model vdw 1.545 3.040 nonbonded pdb=" O THR D 110 " pdb=" O HOH D 301 " model vdw 1.721 3.040 nonbonded pdb=" O VAL E 118 " pdb=" O HOH E 401 " model vdw 1.988 3.040 nonbonded pdb=" N GLU E 71 " pdb=" OE1 GLU E 71 " model vdw 2.113 3.120 nonbonded pdb=" NZ LYS F 392 " pdb=" O VAL F 396 " model vdw 2.121 3.120 ... (remaining 122897 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.220 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:6.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.176 15280 Z= 0.195 Angle : 0.637 10.585 20739 Z= 0.355 Chirality : 0.044 0.146 2333 Planarity : 0.007 0.188 2612 Dihedral : 14.610 173.282 5533 Min Nonbonded Distance : 1.545 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.38 % Allowed : 10.09 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.19), residues: 1909 helix: 1.34 (0.18), residues: 877 sheet: -0.09 (0.36), residues: 177 loop : -0.26 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 104 TYR 0.016 0.001 TYR D 141 PHE 0.015 0.001 PHE E 102 TRP 0.018 0.001 TRP B 103 HIS 0.003 0.001 HIS B 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.20 (15274) covalent geometry : angle 0.62890 / 0.35 (20730) hydrogen bonds : bond 0.14012 / 9.62 ( 743) hydrogen bonds : angle 5.52824 / 3.86 ( 2106) metal coordination : bond 0.00494 / 0.23 ( 6) metal coordination : angle 4.87015 / 2.19 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 280 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 THR cc_start: 0.6877 (m) cc_final: 0.6671 (t) REVERT: A 46 ARG cc_start: 0.6446 (ptp90) cc_final: 0.6156 (ptp-170) REVERT: A 75 LYS cc_start: 0.6975 (ttmt) cc_final: 0.6509 (ttpt) REVERT: A 93 GLU cc_start: 0.6932 (tt0) cc_final: 0.6715 (tt0) REVERT: A 103 ASP cc_start: 0.7360 (m-30) cc_final: 0.6926 (m-30) REVERT: A 104 LYS cc_start: 0.7313 (ptmt) cc_final: 0.6890 (ptmm) REVERT: A 143 ASP cc_start: 0.6741 (p0) cc_final: 0.6475 (p0) REVERT: A 147 GLU cc_start: 0.7007 (mt-10) cc_final: 0.6760 (mt-10) REVERT: A 200 ARG cc_start: 0.7258 (mtm-85) cc_final: 0.6272 (mtp-110) REVERT: A 202 GLN cc_start: 0.7425 (mm-40) cc_final: 0.7221 (mm110) REVERT: A 233 ASP cc_start: 0.6260 (p0) cc_final: 0.5606 (m-30) REVERT: A 259 GLN cc_start: 0.6203 (mm110) cc_final: 0.5822 (mp10) REVERT: A 279 MET cc_start: 0.7967 (mtp) cc_final: 0.7663 (mtp) REVERT: A 333 GLU cc_start: 0.6219 (mm-30) cc_final: 0.5628 (mp0) REVERT: A 359 GLN cc_start: 0.7029 (tt0) cc_final: 0.6641 (tt0) REVERT: A 384 MET cc_start: 0.6987 (tpp) cc_final: 0.6180 (tmm) REVERT: A 403 ASP cc_start: 0.6550 (m-30) cc_final: 0.6183 (m-30) REVERT: B 28 GLU cc_start: 0.5390 (pt0) cc_final: 0.5039 (pt0) REVERT: B 42 LYS cc_start: 0.7308 (mtpt) cc_final: 0.6158 (mmpt) REVERT: B 152 LYS cc_start: 0.6657 (mttp) cc_final: 0.6332 (mttp) REVERT: B 154 GLU cc_start: 0.4945 (pm20) cc_final: 0.4606 (pp20) REVERT: B 236 THR cc_start: 0.7180 (OUTLIER) cc_final: 0.6902 (p) REVERT: B 281 MET cc_start: 0.6303 (mtp) cc_final: 0.5965 (mtt) REVERT: C 39 GLU cc_start: 0.5121 (mt-10) cc_final: 0.4791 (tt0) REVERT: C 44 ASP cc_start: 0.6699 (t0) cc_final: 0.6431 (t0) REVERT: C 56 GLU cc_start: 0.6854 (mm-30) cc_final: 0.6299 (mp0) REVERT: C 61 LYS cc_start: 0.6392 (ttmm) cc_final: 0.6149 (ttpp) REVERT: C 72 GLU cc_start: 0.7361 (tt0) cc_final: 0.7130 (tt0) REVERT: C 116 GLN cc_start: 0.5942 (mt0) cc_final: 0.5456 (mp10) REVERT: C 131 ASP cc_start: 0.5871 (t0) cc_final: 0.4866 (p0) REVERT: C 200 LYS cc_start: 0.6044 (mppt) cc_final: 0.5378 (ptmt) REVERT: C 204 LYS cc_start: 0.5459 (mptp) cc_final: 0.4939 (mtpt) REVERT: D 72 ILE cc_start: 0.6275 (mm) cc_final: 0.5946 (tt) REVERT: D 99 LYS cc_start: 0.5817 (mtpt) cc_final: 0.5141 (tptp) REVERT: D 102 SER cc_start: 0.6269 (t) cc_final: 0.5922 (p) REVERT: E 32 SER cc_start: 0.7523 (m) cc_final: 0.7206 (p) REVERT: E 50 THR cc_start: 0.6135 (t) cc_final: 0.5900 (m) REVERT: F 119 MET cc_start: 0.4812 (ptp) cc_final: 0.2130 (tpt) REVERT: F 189 ARG cc_start: 0.3118 (ttm-80) cc_final: 0.2856 (ttm-80) REVERT: F 270 LYS cc_start: 0.6489 (mtmt) cc_final: 0.6187 (mttt) REVERT: F 273 ASP cc_start: 0.5169 (t70) cc_final: 0.4902 (m-30) REVERT: F 285 MET cc_start: 0.3910 (mmm) cc_final: 0.3375 (mmm) REVERT: F 295 GLN cc_start: 0.3063 (OUTLIER) cc_final: 0.2768 (mp10) REVERT: F 298 ARG cc_start: 0.5244 (ttp80) cc_final: 0.5041 (tmm160) REVERT: F 366 ASP cc_start: 0.7257 (m-30) cc_final: 0.7038 (t0) REVERT: F 382 MET cc_start: 0.1368 (pp-130) cc_final: 0.0714 (ttt) REVERT: F 399 GLU cc_start: 0.4983 (pt0) cc_final: 0.4363 (mp0) REVERT: F 402 LEU cc_start: 0.4268 (mt) cc_final: 0.3973 (mm) outliers start: 6 outliers final: 1 residues processed: 285 average time/residue: 0.6525 time to fit residues: 202.3516 Evaluate side-chains 196 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 193 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 295 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.0060 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 0.9980 overall best weight: 2.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 91 GLN B 252 ASN B 330 HIS C 37 GLN C 46 GLN C 182 ASN C 198 ASN E 3 HIS E 92 GLN F 356 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.185926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.149543 restraints weight = 12569.974| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.26 r_work: 0.3238 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15280 Z= 0.189 Angle : 0.640 8.908 20739 Z= 0.337 Chirality : 0.047 0.176 2333 Planarity : 0.005 0.053 2612 Dihedral : 7.367 107.324 2166 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.04 % Allowed : 10.41 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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 (0.19), residues: 1909 helix: 1.18 (0.18), residues: 876 sheet: 0.21 (0.37), residues: 165 loop : -0.28 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 372 TYR 0.023 0.002 TYR F 319 PHE 0.020 0.002 PHE F 318 TRP 0.022 0.002 TRP B 103 HIS 0.004 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (15274) covalent geometry : angle 0.63355 / 0.34 (20730) hydrogen bonds : bond 0.06455 / 4.46 ( 743) hydrogen bonds : angle 4.80006 / 3.35 ( 2106) metal coordination : bond 0.01266 / 0.65 ( 6) metal coordination : angle 4.40135 / 1.86 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8269 (ptp90) cc_final: 0.7439 (ptp90) REVERT: A 75 LYS cc_start: 0.8782 (ttmt) cc_final: 0.8562 (tttt) REVERT: A 93 GLU cc_start: 0.8443 (tt0) cc_final: 0.8161 (tt0) REVERT: A 143 ASP cc_start: 0.8062 (p0) cc_final: 0.7822 (p0) REVERT: A 200 ARG cc_start: 0.8478 (mtm-85) cc_final: 0.8166 (mtp-110) REVERT: A 233 ASP cc_start: 0.8307 (p0) cc_final: 0.7608 (m-30) REVERT: A 260 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8043 (mmt180) REVERT: A 279 MET cc_start: 0.8710 (mtp) cc_final: 0.8390 (mtp) REVERT: A 384 MET cc_start: 0.8675 (tpp) cc_final: 0.8407 (tmm) REVERT: A 403 ASP cc_start: 0.8712 (m-30) cc_final: 0.8376 (m-30) REVERT: B 28 GLU cc_start: 0.8178 (pt0) cc_final: 0.7963 (pt0) REVERT: B 42 LYS cc_start: 0.8639 (mtpt) cc_final: 0.7963 (mmpt) REVERT: B 152 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8156 (mmtm) REVERT: B 154 GLU cc_start: 0.7353 (pm20) cc_final: 0.7019 (pp20) REVERT: B 281 MET cc_start: 0.8854 (mtp) cc_final: 0.8464 (mtt) REVERT: C 39 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7202 (tt0) REVERT: C 44 ASP cc_start: 0.7833 (t0) cc_final: 0.7563 (t70) REVERT: C 56 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7338 (mp0) REVERT: C 69 LYS cc_start: 0.7878 (ptmm) cc_final: 0.7500 (pttt) REVERT: C 200 LYS cc_start: 0.7551 (mppt) cc_final: 0.6815 (ptmt) REVERT: C 204 LYS cc_start: 0.7751 (mptp) cc_final: 0.7044 (mtpt) REVERT: D 72 ILE cc_start: 0.8274 (mm) cc_final: 0.8032 (tt) REVERT: D 99 LYS cc_start: 0.8197 (mtpt) cc_final: 0.7574 (tptp) REVERT: D 124 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.7041 (mptt) REVERT: E 116 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.7383 (pt) REVERT: F 119 MET cc_start: 0.4997 (ptp) cc_final: 0.2558 (tpt) REVERT: F 170 ILE cc_start: 0.2569 (OUTLIER) cc_final: 0.2322 (tp) REVERT: F 270 LYS cc_start: 0.7106 (mtmt) cc_final: 0.6901 (mttt) REVERT: F 298 ARG cc_start: 0.5513 (ttp80) cc_final: 0.5211 (tmm160) REVERT: F 382 MET cc_start: 0.2101 (pp-130) cc_final: 0.1448 (ttt) REVERT: F 399 GLU cc_start: 0.6026 (pt0) cc_final: 0.5591 (mp0) REVERT: F 402 LEU cc_start: 0.5478 (mt) cc_final: 0.5136 (mm) outliers start: 32 outliers final: 11 residues processed: 224 average time/residue: 0.6095 time to fit residues: 149.8212 Evaluate side-chains 194 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 170 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 42 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 172 optimal weight: 0.0070 chunk 85 optimal weight: 0.0970 chunk 159 optimal weight: 30.0000 chunk 79 optimal weight: 2.9990 chunk 155 optimal weight: 30.0000 chunk 48 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 overall best weight: 2.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 91 GLN B 252 ASN ** F 176 HIS ** 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 = 0.3977 r_free = 0.3977 target = 0.185231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.149523 restraints weight = 12657.449| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.27 r_work: 0.3270 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15280 Z= 0.186 Angle : 0.621 8.618 20739 Z= 0.327 Chirality : 0.046 0.162 2333 Planarity : 0.005 0.051 2612 Dihedral : 6.997 93.783 2160 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.81 % Allowed : 11.37 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 0.43 (0.19), residues: 1909 helix: 1.02 (0.18), residues: 881 sheet: 0.35 (0.38), residues: 164 loop : -0.42 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 372 TYR 0.019 0.002 TYR F 319 PHE 0.019 0.002 PHE F 11 TRP 0.021 0.002 TRP B 103 HIS 0.004 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (15274) covalent geometry : angle 0.61447 / 0.33 (20730) hydrogen bonds : bond 0.06415 / 4.42 ( 743) hydrogen bonds : angle 4.70019 / 3.28 ( 2106) metal coordination : bond 0.01160 / 0.57 ( 6) metal coordination : angle 4.42506 / 1.90 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 183 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: A 93 GLU cc_start: 0.7974 (tt0) cc_final: 0.7742 (tt0) REVERT: A 259 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7235 (mp10) REVERT: A 444 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7006 (mtmt) REVERT: B 28 GLU cc_start: 0.8137 (pt0) cc_final: 0.7913 (pt0) REVERT: B 42 LYS cc_start: 0.8500 (mtpt) cc_final: 0.7944 (mmpt) REVERT: B 130 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8622 (mp) REVERT: B 281 MET cc_start: 0.8535 (mtp) cc_final: 0.8171 (mtt) REVERT: B 406 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8018 (mppt) REVERT: C 44 ASP cc_start: 0.7414 (t0) cc_final: 0.7186 (t70) REVERT: C 204 LYS cc_start: 0.7978 (mptp) cc_final: 0.7664 (mtpt) REVERT: D 99 LYS cc_start: 0.8133 (mtpt) cc_final: 0.7855 (tptp) REVERT: D 124 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7323 (mttt) REVERT: E 49 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8343 (tt) REVERT: E 116 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7358 (pt) REVERT: F 84 LYS cc_start: 0.4849 (mttm) cc_final: 0.4176 (tppp) REVERT: F 90 ILE cc_start: 0.5443 (OUTLIER) cc_final: 0.4825 (tt) REVERT: F 119 MET cc_start: 0.4540 (ptp) cc_final: 0.3187 (tpt) REVERT: F 295 GLN cc_start: 0.6098 (OUTLIER) cc_final: 0.5824 (mp10) REVERT: F 382 MET cc_start: 0.2809 (pp-130) cc_final: 0.2081 (ttt) REVERT: F 388 ILE cc_start: 0.6893 (OUTLIER) cc_final: 0.6532 (tt) outliers start: 44 outliers final: 17 residues processed: 215 average time/residue: 0.6223 time to fit residues: 146.7344 Evaluate side-chains 195 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 295 GLN Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 366 ASP Chi-restraints excluded: chain F residue 388 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 154 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 137 optimal weight: 0.0070 chunk 92 optimal weight: 0.0770 chunk 47 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 145 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 overall best weight: 1.4160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 91 GLN B 252 ASN C 120 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.188045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.151638 restraints weight = 12615.288| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.26 r_work: 0.3337 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15280 Z= 0.141 Angle : 0.558 7.989 20739 Z= 0.295 Chirality : 0.044 0.153 2333 Planarity : 0.005 0.046 2612 Dihedral : 6.815 88.712 2160 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.81 % Allowed : 12.32 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 0.56 (0.19), residues: 1909 helix: 1.20 (0.18), residues: 881 sheet: 0.39 (0.38), residues: 162 loop : -0.43 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 63 TYR 0.018 0.002 TYR D 141 PHE 0.017 0.002 PHE D 50 TRP 0.022 0.002 TRP B 103 HIS 0.007 0.001 HIS F 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (15274) covalent geometry : angle 0.55129 / 0.29 (20730) hydrogen bonds : bond 0.05607 / 3.87 ( 743) hydrogen bonds : angle 4.53789 / 3.17 ( 2106) metal coordination : bond 0.00825 / 0.41 ( 6) metal coordination : angle 4.09992 / 1.74 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 176 time to evaluate : 0.575 Fit side-chains REVERT: A 93 GLU cc_start: 0.8044 (tt0) cc_final: 0.7819 (mt-10) REVERT: A 259 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.7443 (mp10) REVERT: A 260 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8061 (mmt180) REVERT: A 444 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.6966 (mtmt) REVERT: B 28 GLU cc_start: 0.8306 (pt0) cc_final: 0.8098 (pt0) REVERT: B 42 LYS cc_start: 0.8639 (mtpt) cc_final: 0.8076 (mmpt) REVERT: B 281 MET cc_start: 0.8738 (mtp) cc_final: 0.8352 (mtt) REVERT: B 406 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8114 (mppt) REVERT: C 44 ASP cc_start: 0.7506 (t0) cc_final: 0.7268 (t70) REVERT: C 204 LYS cc_start: 0.8017 (mptp) cc_final: 0.7648 (mtpt) REVERT: D 99 LYS cc_start: 0.8214 (mtpt) cc_final: 0.7924 (tptp) REVERT: D 124 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7321 (mttt) REVERT: E 49 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8287 (tt) REVERT: E 116 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7348 (pt) REVERT: F 84 LYS cc_start: 0.4838 (mttm) cc_final: 0.4167 (tppp) REVERT: F 90 ILE cc_start: 0.5407 (OUTLIER) cc_final: 0.4713 (tt) REVERT: F 119 MET cc_start: 0.4550 (ptp) cc_final: 0.3201 (tpt) REVERT: F 295 GLN cc_start: 0.6100 (OUTLIER) cc_final: 0.5858 (mp10) REVERT: F 382 MET cc_start: 0.2763 (pp-130) cc_final: 0.1982 (ttt) REVERT: F 388 ILE cc_start: 0.6979 (OUTLIER) cc_final: 0.6591 (tt) outliers start: 44 outliers final: 18 residues processed: 210 average time/residue: 0.5900 time to fit residues: 136.3362 Evaluate side-chains 197 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 295 GLN Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 388 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 126 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 186 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 66 optimal weight: 0.0040 chunk 91 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 252 ASN C 120 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.190146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.130832 restraints weight = 12730.427| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.60 r_work: 0.3091 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15280 Z= 0.116 Angle : 0.513 7.580 20739 Z= 0.272 Chirality : 0.042 0.147 2333 Planarity : 0.004 0.043 2612 Dihedral : 6.597 83.852 2160 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.23 % Allowed : 13.60 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 0.75 (0.19), residues: 1909 helix: 1.41 (0.18), residues: 885 sheet: 0.57 (0.38), residues: 160 loop : -0.42 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 63 TYR 0.023 0.001 TYR F 309 PHE 0.015 0.001 PHE F 11 TRP 0.022 0.001 TRP B 103 HIS 0.008 0.001 HIS F 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (15274) covalent geometry : angle 0.50691 / 0.27 (20730) hydrogen bonds : bond 0.04905 / 3.39 ( 743) hydrogen bonds : angle 4.36973 / 3.05 ( 2106) metal coordination : bond 0.00636 / 0.32 ( 6) metal coordination : angle 3.84647 / 1.64 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: A 4 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8105 (mp) REVERT: A 46 ARG cc_start: 0.8224 (ptp-170) cc_final: 0.6882 (ptp90) REVERT: A 93 GLU cc_start: 0.8282 (tt0) cc_final: 0.8009 (mt-10) REVERT: A 233 ASP cc_start: 0.8189 (p0) cc_final: 0.7407 (m-30) REVERT: A 259 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.7383 (mp10) REVERT: A 260 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8103 (mmt180) REVERT: B 28 GLU cc_start: 0.8043 (pt0) cc_final: 0.7787 (pt0) REVERT: B 42 LYS cc_start: 0.8640 (mtpt) cc_final: 0.7882 (mmpt) REVERT: B 281 MET cc_start: 0.8683 (mtp) cc_final: 0.8234 (mtt) REVERT: C 44 ASP cc_start: 0.7773 (t0) cc_final: 0.7547 (t70) REVERT: C 58 LYS cc_start: 0.7600 (mmmm) cc_final: 0.6817 (mptt) REVERT: C 204 LYS cc_start: 0.7511 (mptp) cc_final: 0.6845 (mtpt) REVERT: D 99 LYS cc_start: 0.8058 (mtpt) cc_final: 0.7363 (tptp) REVERT: E 49 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.7999 (tt) REVERT: F 40 ASN cc_start: 0.4823 (m-40) cc_final: 0.4527 (t0) REVERT: F 84 LYS cc_start: 0.5236 (mttm) cc_final: 0.4364 (tppp) REVERT: F 90 ILE cc_start: 0.4460 (OUTLIER) cc_final: 0.4246 (tt) REVERT: F 119 MET cc_start: 0.5076 (ptp) cc_final: 0.2658 (tpt) REVERT: F 293 PHE cc_start: 0.5642 (m-80) cc_final: 0.5268 (m-80) REVERT: F 295 GLN cc_start: 0.4113 (OUTLIER) cc_final: 0.3761 (mp10) REVERT: F 319 TYR cc_start: 0.5815 (m-80) cc_final: 0.5333 (m-80) REVERT: F 366 ASP cc_start: 0.7847 (t0) cc_final: 0.7607 (t0) REVERT: F 382 MET cc_start: 0.1799 (pp-130) cc_final: 0.1021 (ttt) REVERT: F 388 ILE cc_start: 0.6208 (OUTLIER) cc_final: 0.5838 (tt) outliers start: 35 outliers final: 16 residues processed: 209 average time/residue: 0.6016 time to fit residues: 138.8644 Evaluate side-chains 196 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 295 GLN Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 388 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 188 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 167 optimal weight: 30.0000 chunk 3 optimal weight: 0.9990 chunk 155 optimal weight: 0.0470 chunk 132 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 144 optimal weight: 7.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 252 ASN C 120 ASN C 182 ASN C 198 ASN D 178 ASN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.187344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.126724 restraints weight = 12569.374| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.64 r_work: 0.3067 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15280 Z= 0.183 Angle : 0.611 7.850 20739 Z= 0.320 Chirality : 0.046 0.167 2333 Planarity : 0.005 0.054 2612 Dihedral : 6.817 80.379 2160 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.00 % Allowed : 13.22 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 0.48 (0.19), residues: 1909 helix: 1.10 (0.17), residues: 882 sheet: 0.57 (0.38), residues: 162 loop : -0.49 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 63 TYR 0.029 0.002 TYR F 309 PHE 0.021 0.002 PHE F 11 TRP 0.021 0.002 TRP B 103 HIS 0.009 0.001 HIS F 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (15274) covalent geometry : angle 0.60506 / 0.32 (20730) hydrogen bonds : bond 0.06290 / 4.34 ( 743) hydrogen bonds : angle 4.58986 / 3.21 ( 2106) metal coordination : bond 0.01071 / 0.52 ( 6) metal coordination : angle 4.12038 / 1.76 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 176 time to evaluate : 0.573 Fit side-chains REVERT: A 4 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8206 (mp) REVERT: A 93 GLU cc_start: 0.8310 (tt0) cc_final: 0.7976 (mt-10) REVERT: A 259 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.7395 (mp10) REVERT: A 260 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8053 (mmt180) REVERT: A 384 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8354 (tmm) REVERT: A 433 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8131 (mm-40) REVERT: A 444 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.6696 (mtmt) REVERT: B 28 GLU cc_start: 0.8000 (pt0) cc_final: 0.7749 (pt0) REVERT: B 42 LYS cc_start: 0.8656 (mtpt) cc_final: 0.7894 (mmpt) REVERT: B 281 MET cc_start: 0.8695 (mtp) cc_final: 0.8258 (mtt) REVERT: B 406 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8135 (mppt) REVERT: C 44 ASP cc_start: 0.7731 (t0) cc_final: 0.7483 (t70) REVERT: C 48 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.7073 (mmtp) REVERT: C 58 LYS cc_start: 0.7578 (mmmm) cc_final: 0.6894 (mptt) REVERT: C 204 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.6847 (mtpt) REVERT: D 99 LYS cc_start: 0.8089 (mtpt) cc_final: 0.7401 (tptp) REVERT: D 124 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.6861 (mttt) REVERT: E 49 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8107 (tt) REVERT: E 116 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7403 (pt) REVERT: F 84 LYS cc_start: 0.5187 (mttm) cc_final: 0.4319 (tppp) REVERT: F 90 ILE cc_start: 0.4497 (OUTLIER) cc_final: 0.4277 (tt) REVERT: F 119 MET cc_start: 0.5107 (ptp) cc_final: 0.2638 (tpt) REVERT: F 285 MET cc_start: 0.4881 (OUTLIER) cc_final: 0.4501 (mmm) REVERT: F 319 TYR cc_start: 0.6037 (m-80) cc_final: 0.5386 (m-80) REVERT: F 366 ASP cc_start: 0.7851 (t0) cc_final: 0.7605 (t0) REVERT: F 382 MET cc_start: 0.1881 (pp-130) cc_final: 0.1072 (ttt) REVERT: F 388 ILE cc_start: 0.6362 (OUTLIER) cc_final: 0.5983 (tt) outliers start: 47 outliers final: 18 residues processed: 210 average time/residue: 0.5751 time to fit residues: 133.2951 Evaluate side-chains 206 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 173 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 388 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 179 optimal weight: 10.0000 chunk 135 optimal weight: 0.0050 chunk 2 optimal weight: 0.0870 chunk 142 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 164 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.8574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 252 ASN C 182 ASN C 198 ASN D 178 ASN ** F 176 HIS ** 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 = 0.4063 r_free = 0.4063 target = 0.192491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.148308 restraints weight = 12312.382| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.46 r_work: 0.3199 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15280 Z= 0.114 Angle : 0.515 7.672 20739 Z= 0.271 Chirality : 0.042 0.149 2333 Planarity : 0.004 0.043 2612 Dihedral : 6.578 79.996 2160 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.43 % Allowed : 14.18 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 0.75 (0.19), residues: 1909 helix: 1.39 (0.18), residues: 884 sheet: 0.62 (0.38), residues: 160 loop : -0.42 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 63 TYR 0.030 0.001 TYR F 309 PHE 0.015 0.001 PHE D 50 TRP 0.021 0.001 TRP B 103 HIS 0.007 0.001 HIS F 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (15274) covalent geometry : angle 0.50872 / 0.27 (20730) hydrogen bonds : bond 0.04935 / 3.41 ( 743) hydrogen bonds : angle 4.38619 / 3.06 ( 2106) metal coordination : bond 0.00577 / 0.29 ( 6) metal coordination : angle 3.84976 / 1.61 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 0.588 Fit side-chains REVERT: A 93 GLU cc_start: 0.8414 (tt0) cc_final: 0.8157 (mt-10) REVERT: A 143 ASP cc_start: 0.8003 (p0) cc_final: 0.7761 (p0) REVERT: A 259 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.7558 (mp10) REVERT: A 260 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8110 (mmt180) REVERT: A 433 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8266 (mm-40) REVERT: A 444 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.6822 (mtmt) REVERT: B 28 GLU cc_start: 0.8293 (pt0) cc_final: 0.8067 (pt0) REVERT: B 42 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8002 (mmpt) REVERT: B 152 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8056 (mppt) REVERT: B 281 MET cc_start: 0.8756 (mtp) cc_final: 0.8324 (mtt) REVERT: C 44 ASP cc_start: 0.7956 (t0) cc_final: 0.7717 (t70) REVERT: C 58 LYS cc_start: 0.7565 (mmmm) cc_final: 0.6856 (mptt) REVERT: C 204 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.6994 (mtpt) REVERT: D 12 LEU cc_start: 0.8439 (mm) cc_final: 0.8214 (mm) REVERT: D 99 LYS cc_start: 0.8246 (mtpt) cc_final: 0.7575 (tptp) REVERT: E 116 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7206 (pt) REVERT: E 122 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.7579 (mm) REVERT: E 186 MET cc_start: 0.8888 (mtp) cc_final: 0.8383 (mtp) REVERT: F 40 ASN cc_start: 0.5371 (m-40) cc_final: 0.4976 (t0) REVERT: F 90 ILE cc_start: 0.4877 (OUTLIER) cc_final: 0.4503 (tt) REVERT: F 119 MET cc_start: 0.5006 (ptp) cc_final: 0.2798 (tpt) REVERT: F 295 GLN cc_start: 0.5246 (OUTLIER) cc_final: 0.4833 (mp10) REVERT: F 319 TYR cc_start: 0.6332 (m-80) cc_final: 0.5879 (m-80) REVERT: F 366 ASP cc_start: 0.7890 (t0) cc_final: 0.7614 (t0) REVERT: F 382 MET cc_start: 0.2176 (pp-130) cc_final: 0.1298 (ttt) REVERT: F 388 ILE cc_start: 0.6613 (OUTLIER) cc_final: 0.6200 (tt) outliers start: 38 outliers final: 14 residues processed: 204 average time/residue: 0.5571 time to fit residues: 125.4409 Evaluate side-chains 198 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 295 GLN Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 388 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 24 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 135 optimal weight: 0.7980 chunk 180 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 182 ASN C 198 ASN D 178 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.187530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.126382 restraints weight = 12641.626| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.70 r_work: 0.3072 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15280 Z= 0.179 Angle : 0.601 7.939 20739 Z= 0.314 Chirality : 0.046 0.171 2333 Planarity : 0.005 0.052 2612 Dihedral : 6.766 76.912 2160 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.62 % Allowed : 13.98 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 0.51 (0.19), residues: 1909 helix: 1.12 (0.17), residues: 883 sheet: 0.62 (0.38), residues: 160 loop : -0.48 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 63 TYR 0.027 0.002 TYR F 309 PHE 0.020 0.002 PHE F 11 TRP 0.021 0.002 TRP B 103 HIS 0.007 0.001 HIS F 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (15274) covalent geometry : angle 0.59527 / 0.31 (20730) hydrogen bonds : bond 0.06172 / 4.26 ( 743) hydrogen bonds : angle 4.57916 / 3.20 ( 2106) metal coordination : bond 0.01007 / 0.49 ( 6) metal coordination : angle 4.13036 / 1.76 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 0.567 Fit side-chains REVERT: A 93 GLU cc_start: 0.8314 (tt0) cc_final: 0.7987 (mt-10) REVERT: A 143 ASP cc_start: 0.7822 (p0) cc_final: 0.7560 (p0) REVERT: A 212 ASP cc_start: 0.8792 (m-30) cc_final: 0.8576 (m-30) REVERT: A 259 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.7367 (mp10) REVERT: A 260 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8062 (mmt180) REVERT: A 384 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8394 (tmm) REVERT: A 433 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8105 (mm-40) REVERT: A 444 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.6697 (mtmt) REVERT: B 42 LYS cc_start: 0.8640 (mtpt) cc_final: 0.7872 (mmpt) REVERT: B 152 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8085 (mppt) REVERT: B 281 MET cc_start: 0.8689 (mtp) cc_final: 0.8242 (mtt) REVERT: C 44 ASP cc_start: 0.7750 (t0) cc_final: 0.7493 (t70) REVERT: C 58 LYS cc_start: 0.7670 (mmmm) cc_final: 0.7016 (mptt) REVERT: C 204 LYS cc_start: 0.7588 (OUTLIER) cc_final: 0.6884 (mtpt) REVERT: D 99 LYS cc_start: 0.8077 (mtpt) cc_final: 0.7396 (tptp) REVERT: D 124 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.6830 (mttt) REVERT: E 49 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8100 (tt) REVERT: E 116 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7403 (pt) REVERT: E 122 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.7429 (mm) REVERT: F 90 ILE cc_start: 0.4380 (OUTLIER) cc_final: 0.4159 (tt) REVERT: F 119 MET cc_start: 0.4974 (ptp) cc_final: 0.2607 (tpt) REVERT: F 285 MET cc_start: 0.5167 (mmm) cc_final: 0.4652 (mmm) REVERT: F 319 TYR cc_start: 0.6266 (m-80) cc_final: 0.5592 (m-80) REVERT: F 366 ASP cc_start: 0.7900 (t0) cc_final: 0.7640 (t0) REVERT: F 382 MET cc_start: 0.2072 (pp-130) cc_final: 0.1179 (ttt) REVERT: F 388 ILE cc_start: 0.6257 (OUTLIER) cc_final: 0.5886 (tt) outliers start: 41 outliers final: 18 residues processed: 198 average time/residue: 0.6126 time to fit residues: 133.1372 Evaluate side-chains 196 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 388 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 86 optimal weight: 1.9990 chunk 92 optimal weight: 0.0170 chunk 83 optimal weight: 2.9990 chunk 152 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 169 optimal weight: 20.0000 overall best weight: 1.4022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 182 ASN C 198 ASN C 216 HIS D 178 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.188715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.127750 restraints weight = 12641.301| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.74 r_work: 0.3096 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15280 Z= 0.137 Angle : 0.543 7.569 20739 Z= 0.286 Chirality : 0.043 0.163 2333 Planarity : 0.005 0.045 2612 Dihedral : 6.632 76.402 2160 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.55 % Allowed : 14.05 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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 (0.19), residues: 1909 helix: 1.29 (0.18), residues: 882 sheet: 0.66 (0.38), residues: 160 loop : -0.46 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 63 TYR 0.025 0.002 TYR F 309 PHE 0.017 0.002 PHE F 11 TRP 0.021 0.002 TRP B 103 HIS 0.006 0.001 HIS F 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (15274) covalent geometry : angle 0.53786 / 0.29 (20730) hydrogen bonds : bond 0.05384 / 3.72 ( 743) hydrogen bonds : angle 4.45915 / 3.12 ( 2106) metal coordination : bond 0.00769 / 0.38 ( 6) metal coordination : angle 3.73794 / 1.57 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 169 time to evaluate : 0.490 Fit side-chains REVERT: A 4 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8155 (mp) REVERT: A 93 GLU cc_start: 0.8267 (tt0) cc_final: 0.8002 (mt-10) REVERT: A 143 ASP cc_start: 0.7861 (p0) cc_final: 0.7609 (p0) REVERT: A 233 ASP cc_start: 0.8149 (p0) cc_final: 0.7349 (m-30) REVERT: A 259 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.7369 (mp10) REVERT: A 260 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8057 (mmt180) REVERT: A 444 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.6625 (mtmt) REVERT: B 42 LYS cc_start: 0.8635 (mtpt) cc_final: 0.7869 (mmpt) REVERT: B 152 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7974 (mppt) REVERT: B 281 MET cc_start: 0.8686 (mtp) cc_final: 0.8229 (mtt) REVERT: B 406 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8107 (mppt) REVERT: C 44 ASP cc_start: 0.7761 (t0) cc_final: 0.7506 (t70) REVERT: C 58 LYS cc_start: 0.7596 (mmmm) cc_final: 0.6863 (mptt) REVERT: C 204 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.6814 (mtpt) REVERT: D 99 LYS cc_start: 0.8088 (mtpt) cc_final: 0.7410 (tptp) REVERT: D 124 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.6822 (mttt) REVERT: E 49 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8054 (tt) REVERT: E 116 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7276 (pt) REVERT: E 122 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.7461 (mm) REVERT: F 40 ASN cc_start: 0.4798 (m-40) cc_final: 0.4596 (t0) REVERT: F 90 ILE cc_start: 0.4508 (OUTLIER) cc_final: 0.4294 (tt) REVERT: F 119 MET cc_start: 0.5024 (ptp) cc_final: 0.2739 (tpt) REVERT: F 285 MET cc_start: 0.5038 (mmm) cc_final: 0.4465 (mmm) REVERT: F 319 TYR cc_start: 0.6290 (m-80) cc_final: 0.5542 (m-80) REVERT: F 366 ASP cc_start: 0.7866 (t0) cc_final: 0.7588 (t0) REVERT: F 382 MET cc_start: 0.2163 (pp-130) cc_final: 0.1243 (ttt) REVERT: F 388 ILE cc_start: 0.6328 (OUTLIER) cc_final: 0.5948 (tt) outliers start: 40 outliers final: 16 residues processed: 200 average time/residue: 0.6065 time to fit residues: 133.7225 Evaluate side-chains 200 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 388 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 94 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 91 GLN C 182 ASN C 198 ASN D 178 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.189426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.131031 restraints weight = 12734.169| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.57 r_work: 0.3079 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15280 Z= 0.123 Angle : 0.523 7.448 20739 Z= 0.275 Chirality : 0.042 0.169 2333 Planarity : 0.004 0.045 2612 Dihedral : 6.533 75.745 2160 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.17 % Allowed : 14.30 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 0.78 (0.19), residues: 1909 helix: 1.45 (0.18), residues: 876 sheet: 0.69 (0.38), residues: 160 loop : -0.44 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 63 TYR 0.022 0.001 TYR F 309 PHE 0.016 0.001 PHE F 11 TRP 0.022 0.002 TRP B 103 HIS 0.006 0.001 HIS F 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (15274) covalent geometry : angle 0.51679 / 0.27 (20730) hydrogen bonds : bond 0.05076 / 3.51 ( 743) hydrogen bonds : angle 4.38939 / 3.07 ( 2106) metal coordination : bond 0.00599 / 0.30 ( 6) metal coordination : angle 3.79147 / 1.62 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3818 Ramachandran restraints generated. 1909 Oldfield, 0 Emsley, 1909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 0.507 Fit side-chains REVERT: A 93 GLU cc_start: 0.8344 (tt0) cc_final: 0.8085 (mt-10) REVERT: A 143 ASP cc_start: 0.7895 (p0) cc_final: 0.7645 (p0) REVERT: A 233 ASP cc_start: 0.8184 (p0) cc_final: 0.7377 (m-30) REVERT: A 259 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.7412 (mp10) REVERT: A 260 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8107 (mmt180) REVERT: A 444 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.6640 (mtmt) REVERT: B 42 LYS cc_start: 0.8634 (mtpt) cc_final: 0.7846 (mmpt) REVERT: B 152 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7968 (mppt) REVERT: B 281 MET cc_start: 0.8689 (mtp) cc_final: 0.8247 (mtt) REVERT: C 44 ASP cc_start: 0.7850 (t0) cc_final: 0.7608 (t70) REVERT: C 58 LYS cc_start: 0.7574 (mmmm) cc_final: 0.6804 (mptt) REVERT: C 204 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.6795 (mtpt) REVERT: D 99 LYS cc_start: 0.8095 (mtpt) cc_final: 0.7414 (tptp) REVERT: D 124 LYS cc_start: 0.7341 (OUTLIER) cc_final: 0.6856 (mttt) REVERT: E 49 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8022 (tt) REVERT: E 116 ILE cc_start: 0.7720 (OUTLIER) cc_final: 0.7241 (pt) REVERT: E 122 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.7470 (mm) REVERT: F 40 ASN cc_start: 0.4847 (m-40) cc_final: 0.4647 (t0) REVERT: F 90 ILE cc_start: 0.4428 (OUTLIER) cc_final: 0.4195 (tt) REVERT: F 119 MET cc_start: 0.5057 (ptp) cc_final: 0.2717 (tpt) REVERT: F 224 ILE cc_start: 0.2784 (mp) cc_final: 0.2236 (tt) REVERT: F 285 MET cc_start: 0.5212 (mmm) cc_final: 0.4709 (mmm) REVERT: F 295 GLN cc_start: 0.4552 (OUTLIER) cc_final: 0.4149 (mp10) REVERT: F 319 TYR cc_start: 0.6252 (m-80) cc_final: 0.5536 (m-80) REVERT: F 366 ASP cc_start: 0.7877 (t0) cc_final: 0.7585 (t0) REVERT: F 382 MET cc_start: 0.2090 (pp-130) cc_final: 0.1253 (ttt) REVERT: F 388 ILE cc_start: 0.6392 (OUTLIER) cc_final: 0.6028 (tt) outliers start: 34 outliers final: 15 residues processed: 201 average time/residue: 0.5729 time to fit residues: 126.9452 Evaluate side-chains 194 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 295 GLN Chi-restraints excluded: chain F residue 388 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 177 optimal weight: 20.0000 chunk 167 optimal weight: 8.9990 chunk 61 optimal weight: 0.0870 chunk 185 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 160 optimal weight: 0.0670 chunk 109 optimal weight: 3.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 182 ASN C 198 ASN D 178 ASN E 3 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.193351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.132380 restraints weight = 12689.869| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.11 r_work: 0.3111 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15280 Z= 0.098 Angle : 0.478 8.056 20739 Z= 0.251 Chirality : 0.041 0.148 2333 Planarity : 0.004 0.045 2612 Dihedral : 6.320 75.953 2160 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.34 % Allowed : 15.45 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 1.00 (0.19), residues: 1909 helix: 1.67 (0.18), residues: 879 sheet: 0.44 (0.39), residues: 164 loop : -0.29 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 63 TYR 0.019 0.001 TYR F 309 PHE 0.013 0.001 PHE D 50 TRP 0.023 0.001 TRP B 103 HIS 0.005 0.001 HIS F 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.10 (15274) covalent geometry : angle 0.47160 / 0.25 (20730) hydrogen bonds : bond 0.04234 / 2.92 ( 743) hydrogen bonds : angle 4.21586 / 2.94 ( 2106) metal coordination : bond 0.00549 / 0.29 ( 6) metal coordination : angle 3.78175 / 1.65 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5738.36 seconds wall clock time: 98 minutes 17.81 seconds (5897.81 seconds total)