Starting phenix.real_space_refine on Wed Jan 14 10:02:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ud3_64060/01_2026/9ud3_64060.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ud3_64060/01_2026/9ud3_64060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ud3_64060/01_2026/9ud3_64060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ud3_64060/01_2026/9ud3_64060.map" model { file = "/net/cci-nas-00/data/ceres_data/9ud3_64060/01_2026/9ud3_64060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ud3_64060/01_2026/9ud3_64060.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.053 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 3 5.49 5 S 92 5.16 5 C 9496 2.51 5 N 2405 2.21 5 O 2679 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14680 Number of models: 1 Model: "" Number of chains: 10 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': 1, 'PTRANS': 22, 'TRANS': 422} Chain: "B" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2969 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 14, 'TRANS': 372} 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: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1562 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 9, 'TRANS': 194} 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: 3165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3165 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 24, 'TRANS': 383} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'LMT': 1, 'RBF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9093 SG CYS D 112 46.672 78.120 37.228 1.00 66.55 S ATOM 10059 SG CYS E 26 45.362 78.956 40.311 1.00 53.34 S ATOM 8454 SG CYS D 29 46.549 83.659 41.816 1.00 53.55 S ATOM 10781 SG CYS E 120 47.877 83.088 38.291 1.00 62.87 S ATOM 11907 SG CYS F 79 50.617 47.001 36.228 1.00195.54 S ATOM 12146 SG CYS F 111 49.836 50.134 36.453 1.00180.97 S ATOM 11860 SG CYS F 70 44.631 48.072 33.482 1.00193.83 S ATOM 11888 SG CYS F 76 45.801 45.466 35.780 1.00198.68 S Time building chain proxies: 3.33, per 1000 atoms: 0.23 Number of scatterers: 14680 At special positions: 0 Unit cell: (92.4, 148.72, 115.28, 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 3 15.00 O 2679 8.00 N 2405 7.00 C 9496 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: 1.30 Conformation dependent library (CDL) restraints added in 505.7 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 26 " pdb="FE2 FES E 301 " - pdb=" SG CYS D 29 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 120 " pdb="FE1 FES E 301 " - pdb=" SG CYS D 112 " pdb=" FES F 501 " pdb="FE1 FES F 501 " - pdb=" SG CYS F 79 " pdb="FE1 FES F 501 " - pdb=" SG CYS F 111 " pdb="FE2 FES F 501 " - pdb=" SG CYS F 70 " pdb="FE2 FES F 501 " - pdb=" SG CYS F 76 " Number of angles added : 14 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3420 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 15 sheets defined 52.9% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... 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 107 through 112 removed outlier: 3.862A pdb=" N ALA A 111 " --> pdb=" O ASN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 162 through 171 removed outlier: 3.781A pdb=" N VAL A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN A 168 " --> pdb=" O THR A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 182 removed outlier: 3.692A pdb=" N VAL A 175 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 219 through 226 removed outlier: 3.793A pdb=" N HIS A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE A 226 " --> pdb=" O THR A 222 " (cutoff:3.500A) 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 removed outlier: 3.848A pdb=" N HIS A 313 " --> pdb=" O THR A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.975A pdb=" N HIS A 354 " --> pdb=" O PHE A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 389 through 400 removed outlier: 3.696A pdb=" N LEU A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ARG A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 410 through 413 removed outlier: 3.637A pdb=" N LEU A 413 " --> pdb=" O ALA A 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 410 through 413' Processing helix chain 'A' and resid 414 through 424 removed outlier: 3.868A pdb=" N ALA A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LEU A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N CYS A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 424 " --> pdb=" O LEU A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 446 removed outlier: 3.675A pdb=" N ARG A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 29 No H-bonds generated for 'chain 'B' and resid 27 through 29' Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'B' and resid 52 through 62 Processing helix chain 'B' and resid 64 through 87 removed outlier: 4.225A pdb=" N TRP B 70 " --> pdb=" O PRO B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 97 removed outlier: 3.519A pdb=" N LEU B 92 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 106 Processing helix chain 'B' and resid 117 through 152 removed outlier: 4.297A pdb=" N LEU B 123 " --> pdb=" O GLY B 119 " (cutoff:3.500A) Proline residue: B 131 - end of helix removed outlier: 3.573A pdb=" N ILE B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 168 removed outlier: 4.178A pdb=" N THR B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 189 removed outlier: 3.518A pdb=" N ALA B 179 " --> pdb=" O PRO B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.620A pdb=" N LEU B 212 " --> pdb=" O GLY B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 221 removed outlier: 3.582A pdb=" N ILE B 220 " --> pdb=" O TYR B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 244 removed outlier: 3.660A pdb=" N ALA B 242 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 248 Processing helix chain 'B' and resid 259 through 266 Processing helix chain 'B' and resid 276 through 290 removed outlier: 4.088A pdb=" N GLY B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE B 287 " --> pdb=" O GLY B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 316 removed outlier: 4.097A pdb=" N ILE B 298 " --> pdb=" O SER B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 325 Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 336 through 342 Processing helix chain 'B' and resid 353 through 374 removed outlier: 4.185A pdb=" N TRP B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 369 " --> pdb=" O GLY B 365 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG B 372 " --> pdb=" O CYS B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 410 removed outlier: 3.943A pdb=" N LEU B 387 " --> pdb=" O MET B 383 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Proline residue: B 394 - end of helix removed outlier: 3.860A pdb=" N ASP B 397 " --> pdb=" O ALA B 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 33 removed outlier: 3.876A pdb=" N VAL C 14 " --> pdb=" O LYS C 10 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE C 24 " --> pdb=" O LEU C 20 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE C 25 " --> pdb=" O VAL C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 41 Processing helix chain 'C' and resid 42 through 54 removed outlier: 4.191A pdb=" N LYS C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 71 Processing helix chain 'C' and resid 79 through 81 No H-bonds generated for 'chain 'C' and resid 79 through 81' Processing helix chain 'C' and resid 92 through 97 removed outlier: 3.694A pdb=" N ALA C 97 " --> pdb=" O GLN C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 101 removed outlier: 6.979A pdb=" N SER C 101 " --> pdb=" O LYS C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 98 through 101' Processing helix chain 'C' and resid 178 through 181 removed outlier: 4.072A pdb=" N GLU C 181 " --> pdb=" O GLY C 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 178 through 181' Processing helix chain 'C' and resid 182 through 188 Processing helix chain 'C' and resid 224 through 239 Processing helix chain 'C' and resid 244 through 254 removed outlier: 3.572A pdb=" N LYS C 250 " --> pdb=" O PRO C 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 11 removed outlier: 3.740A pdb=" N SER D 10 " --> pdb=" O LEU D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 35 removed outlier: 3.952A pdb=" N THR D 35 " --> pdb=" O ALA D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 62 removed outlier: 3.957A pdb=" N VAL D 43 " --> pdb=" O GLU D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 94 removed outlier: 3.959A pdb=" N LEU D 82 " --> pdb=" O ILE D 78 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL D 85 " --> pdb=" O SER D 81 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN D 88 " --> pdb=" O ILE D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 102 removed outlier: 4.330A pdb=" N GLN D 100 " --> pdb=" O ASP D 96 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 101 " --> pdb=" O ILE D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 107 removed outlier: 4.297A pdb=" N GLY D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 111 through 121 removed outlier: 4.091A pdb=" N MET D 115 " --> pdb=" O ASN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 158 removed outlier: 3.710A pdb=" N VAL D 144 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU D 155 " --> pdb=" O PHE D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 179 through 183 Processing helix chain 'D' and resid 184 through 202 removed outlier: 3.882A pdb=" N PHE D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 206 Processing helix chain 'E' and resid 2 through 14 removed outlier: 4.317A pdb=" N LEU E 8 " --> pdb=" O TYR E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 29 Processing helix chain 'E' and resid 34 through 64 removed outlier: 4.843A pdb=" N GLY E 40 " --> pdb=" O LYS E 36 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU E 41 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) 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 101 Processing helix chain 'E' and resid 102 through 107 removed outlier: 3.574A pdb=" N ASN E 107 " --> pdb=" O PRO E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 133 removed outlier: 3.877A pdb=" N GLY E 125 " --> pdb=" O ALA E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 164 removed outlier: 4.017A pdb=" N VAL E 141 " --> pdb=" O ALA E 137 " (cutoff:3.500A) 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 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 removed outlier: 3.701A pdb=" N PHE F 6 " --> pdb=" O SER F 2 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS F 28 " --> pdb=" O PHE F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 61 Processing helix chain 'F' and resid 93 through 97 removed outlier: 3.507A pdb=" N ASP F 96 " --> pdb=" O THR F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 104 removed outlier: 3.904A pdb=" N ARG F 104 " --> pdb=" O LYS F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 113 No H-bonds generated for 'chain 'F' and resid 111 through 113' Processing helix chain 'F' and resid 124 through 130 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 195 removed outlier: 3.945A pdb=" N ASP F 191 " --> pdb=" O LYS F 187 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 199 Processing helix chain 'F' and resid 243 through 252 Processing helix chain 'F' and resid 284 through 298 removed outlier: 4.042A pdb=" N GLN F 295 " --> pdb=" O HIS F 291 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU F 296 " --> pdb=" O ILE F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 317 Processing helix chain 'F' and resid 319 through 330 removed outlier: 4.049A pdb=" N GLY F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA F 328 " --> pdb=" O ASP F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 347 removed outlier: 3.671A pdb=" N ASN F 347 " --> pdb=" O PRO F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 363 removed outlier: 3.733A pdb=" N VAL F 358 " --> pdb=" O PHE F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 373 removed outlier: 4.039A pdb=" N CYS F 373 " --> pdb=" O PRO F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 395 removed outlier: 4.436A pdb=" N ALA F 386 " --> pdb=" O MET F 382 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 21 Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 32 removed outlier: 6.895A pdb=" N LEU A 87 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ARG A 81 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N SER A 89 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ILE A 79 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL A 91 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 43 removed outlier: 7.150A pdb=" N PHE A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 133 removed outlier: 3.556A pdb=" N ILE A 149 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL A 189 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N HIS A 209 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL A 191 " --> pdb=" O HIS A 209 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 296 through 300 removed outlier: 3.559A pdb=" N LEU A 326 " --> pdb=" O ARG A 297 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 250 through 251 Processing sheet with id=AA7, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.510A pdb=" N VAL C 76 " --> pdb=" O GLY C 122 " (cutoff:3.500A) removed outlier: 14.216A pdb=" N VAL C 121 " --> pdb=" O HIS C 141 " (cutoff:3.500A) removed outlier: 12.667A pdb=" N HIS C 141 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL C 123 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS C 135 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N MET C 148 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N GLU C 169 " --> pdb=" O MET C 148 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N TYR C 150 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYR C 167 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N PHE C 152 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU C 165 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA C 154 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 103 through 105 removed outlier: 3.576A pdb=" N ARG C 118 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 204 through 206 Processing sheet with id=AB1, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AB2, first strand: chain 'F' and resid 46 through 49 removed outlier: 3.603A pdb=" N ILE F 35 " --> pdb=" O THR F 49 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET F 119 " --> pdb=" O THR F 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 80 through 82 Processing sheet with id=AB4, first strand: chain 'F' and resid 208 through 213 removed outlier: 6.179A pdb=" N TYR F 167 " --> pdb=" O PRO F 263 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU F 171 " --> pdb=" O THR F 259 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N THR F 259 " --> pdb=" O GLU F 171 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL F 137 " --> pdb=" O ALA F 153 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ALA F 153 " --> pdb=" O VAL F 137 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER F 139 " --> pdb=" O LYS F 151 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 175 through 178 Processing sheet with id=AB6, first strand: chain 'F' and resid 333 through 339 removed outlier: 6.642A pdb=" N MET F 305 " --> pdb=" O VAL F 334 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N HIS F 336 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N TYR F 307 " --> pdb=" O HIS F 336 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ALA F 338 " --> pdb=" O TYR F 307 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TYR F 309 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N MET F 276 " --> pdb=" O SER F 306 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N TRP F 308 " --> pdb=" O MET F 276 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE F 278 " --> pdb=" O TRP F 308 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N GLY F 310 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N GLY F 280 " --> pdb=" O GLY F 310 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR F 375 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ASP F 404 " --> pdb=" O TYR F 375 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N MET F 377 " --> pdb=" O ASP F 404 " (cutoff:3.500A) 669 hydrogen bonds defined for protein. 1878 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: 2.51 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.41: 6078 1.41 - 1.61: 8772 1.61 - 1.80: 140 1.80 - 2.00: 20 2.00 - 2.20: 8 Bond restraints: 15018 Sorted by residual: bond pdb=" C4 FMN C 301 " pdb=" C4A FMN C 301 " ideal model delta sigma weight residual 1.485 1.381 0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" C4A FMN C 301 " pdb=" N5 FMN C 301 " ideal model delta sigma weight residual 1.300 1.373 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" O5' FMN C 301 " pdb=" P FMN C 301 " ideal model delta sigma weight residual 1.676 1.609 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C10 FMN C 301 " pdb=" C4A FMN C 301 " ideal model delta sigma weight residual 1.443 1.381 0.062 2.00e-02 2.50e+03 9.54e+00 bond pdb=" C10 FMN C 301 " pdb=" N1 FMN C 301 " ideal model delta sigma weight residual 1.317 1.376 -0.059 2.00e-02 2.50e+03 8.76e+00 ... (remaining 15013 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 20062 2.44 - 4.89: 275 4.89 - 7.33: 39 7.33 - 9.77: 2 9.77 - 12.22: 1 Bond angle restraints: 20379 Sorted by residual: angle pdb=" N THR B 254 " pdb=" CA THR B 254 " pdb=" C THR B 254 " ideal model delta sigma weight residual 114.75 108.86 5.89 1.26e+00 6.30e-01 2.19e+01 angle pdb=" N GLY F 350 " pdb=" CA GLY F 350 " pdb=" C GLY F 350 " ideal model delta sigma weight residual 111.21 115.05 -3.84 1.04e+00 9.25e-01 1.36e+01 angle pdb=" C ASN C 79 " pdb=" N THR C 80 " pdb=" CA THR C 80 " ideal model delta sigma weight residual 121.54 128.49 -6.95 1.91e+00 2.74e-01 1.32e+01 angle pdb=" CA LYS C 69 " pdb=" CB LYS C 69 " pdb=" CG LYS C 69 " ideal model delta sigma weight residual 114.10 121.37 -7.27 2.00e+00 2.50e-01 1.32e+01 angle pdb=" C ALA B 215 " pdb=" N TYR B 216 " pdb=" CA TYR B 216 " ideal model delta sigma weight residual 122.85 118.94 3.91 1.10e+00 8.26e-01 1.26e+01 ... (remaining 20374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 7752 17.89 - 35.79: 869 35.79 - 53.68: 207 53.68 - 71.58: 30 71.58 - 89.47: 28 Dihedral angle restraints: 8886 sinusoidal: 3523 harmonic: 5363 Sorted by residual: dihedral pdb=" CA ASN D 111 " pdb=" C ASN D 111 " pdb=" N CYS D 112 " pdb=" CA CYS D 112 " ideal model delta harmonic sigma weight residual -180.00 -159.98 -20.02 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA LYS C 69 " pdb=" C LYS C 69 " pdb=" N SER C 70 " pdb=" CA SER C 70 " ideal model delta harmonic sigma weight residual -180.00 -161.15 -18.85 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA SER C 70 " pdb=" C SER C 70 " pdb=" N ILE C 71 " pdb=" CA ILE C 71 " ideal model delta harmonic sigma weight residual -180.00 -163.35 -16.65 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 8883 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1420 0.034 - 0.068: 605 0.068 - 0.101: 194 0.101 - 0.135: 80 0.135 - 0.169: 7 Chirality restraints: 2306 Sorted by residual: chirality pdb=" CG LEU C 66 " pdb=" CB LEU C 66 " pdb=" CD1 LEU C 66 " pdb=" CD2 LEU C 66 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.13e-01 chirality pdb=" CA LEU C 66 " pdb=" N LEU C 66 " pdb=" C LEU C 66 " pdb=" CB LEU C 66 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.76e-01 chirality pdb=" CB VAL F 64 " pdb=" CA VAL F 64 " pdb=" CG1 VAL F 64 " pdb=" CG2 VAL F 64 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.19e-01 ... (remaining 2303 not shown) Planarity restraints: 2566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 153 " 0.022 2.00e-02 2.50e+03 2.35e-02 8.28e+00 pdb=" CG HIS B 153 " -0.050 2.00e-02 2.50e+03 pdb=" ND1 HIS B 153 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS B 153 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 HIS B 153 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS B 153 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 126 " 0.041 5.00e-02 4.00e+02 6.23e-02 6.21e+00 pdb=" N PRO D 127 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 127 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 127 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 67 " -0.010 2.00e-02 2.50e+03 1.30e-02 2.96e+00 pdb=" CG PHE C 67 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE C 67 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE C 67 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE C 67 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 67 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 67 " -0.000 2.00e-02 2.50e+03 ... (remaining 2563 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1931 2.75 - 3.29: 15034 3.29 - 3.82: 24117 3.82 - 4.36: 26647 4.36 - 4.90: 46447 Nonbonded interactions: 114176 Sorted by model distance: nonbonded pdb=" OG1 THR B 353 " pdb=" OD1 ASP B 397 " model vdw 2.210 3.040 nonbonded pdb=" NH1 ARG E 161 " pdb=" OG1 THR E 179 " model vdw 2.229 3.120 nonbonded pdb=" O GLY F 243 " pdb=" OG SER F 247 " model vdw 2.235 3.040 nonbonded pdb=" NH2 ARG A 81 " pdb=" OE2 GLU F 371 " model vdw 2.243 3.120 nonbonded pdb=" OG1 THR C 225 " pdb=" O3P FMN C 301 " model vdw 2.249 3.040 ... (remaining 114171 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.310 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.480 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 20.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 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 0.104 15026 Z= 0.191 Angle : 0.764 23.665 20393 Z= 0.373 Chirality : 0.044 0.169 2306 Planarity : 0.004 0.062 2566 Dihedral : 16.309 89.469 5466 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.43 % Allowed : 22.39 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.19), residues: 1882 helix: 0.20 (0.19), residues: 820 sheet: -0.23 (0.38), residues: 179 loop : -1.12 (0.20), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 199 TYR 0.028 0.001 TYR E 166 PHE 0.030 0.002 PHE C 67 TRP 0.022 0.002 TRP B 226 HIS 0.026 0.002 HIS B 153 Details of bonding type rmsd covalent geometry : bond 0.00427 (15018) covalent geometry : angle 0.70736 (20379) hydrogen bonds : bond 0.16157 ( 669) hydrogen bonds : angle 5.82593 ( 1878) metal coordination : bond 0.01635 ( 8) metal coordination : angle 11.00217 ( 14) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 220 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 ARG cc_start: 0.7810 (ptp90) cc_final: 0.7508 (ptt90) REVERT: B 390 ASN cc_start: 0.7753 (m-40) cc_final: 0.7269 (m110) REVERT: C 161 THR cc_start: 0.8527 (m) cc_final: 0.7926 (p) REVERT: C 204 LYS cc_start: 0.8327 (mmtt) cc_final: 0.8053 (mtmt) REVERT: D 18 ASN cc_start: 0.7942 (t0) cc_final: 0.7559 (t0) REVERT: D 35 THR cc_start: 0.8658 (p) cc_final: 0.8445 (t) REVERT: D 175 TYR cc_start: 0.9054 (t80) cc_final: 0.8541 (t80) REVERT: E 100 ARG cc_start: 0.6810 (tmt170) cc_final: 0.5623 (tmm160) REVERT: F 1 MET cc_start: 0.7313 (mmm) cc_final: 0.7052 (tpt) REVERT: F 163 ARG cc_start: 0.8067 (mtp180) cc_final: 0.7789 (tpp80) REVERT: F 214 MET cc_start: 0.7503 (ptp) cc_final: 0.7233 (ptp) REVERT: F 288 MET cc_start: 0.8631 (mmm) cc_final: 0.7907 (mmt) REVERT: F 315 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7169 (mmm160) REVERT: F 317 MET cc_start: 0.7081 (ttt) cc_final: 0.6866 (ptt) REVERT: F 345 GLU cc_start: 0.7867 (pt0) cc_final: 0.7218 (pm20) outliers start: 53 outliers final: 46 residues processed: 255 average time/residue: 0.1023 time to fit residues: 40.2818 Evaluate side-chains 254 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 207 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain D residue 93 TYR Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 151 PHE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 92 GLN Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 186 MET Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 225 MET Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 315 ARG Chi-restraints excluded: chain F residue 394 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.0170 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 20.0000 overall best weight: 2.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN C 37 GLN D 111 ASN F 176 HIS F 295 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.171145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.130908 restraints weight = 24633.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.130704 restraints weight = 16769.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.133773 restraints weight = 11670.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.134183 restraints weight = 8188.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.134521 restraints weight = 7383.463| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15026 Z= 0.207 Angle : 0.712 19.591 20393 Z= 0.339 Chirality : 0.045 0.165 2306 Planarity : 0.005 0.063 2566 Dihedral : 8.758 73.110 2239 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 6.02 % Allowed : 19.42 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.73 (0.19), residues: 1882 helix: 0.18 (0.19), residues: 804 sheet: -0.43 (0.37), residues: 181 loop : -1.05 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 199 TYR 0.019 0.002 TYR B 236 PHE 0.020 0.002 PHE F 267 TRP 0.014 0.002 TRP F 250 HIS 0.010 0.002 HIS F 336 Details of bonding type rmsd covalent geometry : bond 0.00496 (15018) covalent geometry : angle 0.66031 (20379) hydrogen bonds : bond 0.04820 ( 669) hydrogen bonds : angle 5.08095 ( 1878) metal coordination : bond 0.02614 ( 8) metal coordination : angle 10.14131 ( 14) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 229 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 ASP cc_start: 0.7420 (t0) cc_final: 0.6575 (p0) REVERT: B 151 ARG cc_start: 0.8069 (ptp-110) cc_final: 0.7413 (mmm160) REVERT: B 221 SER cc_start: 0.9132 (t) cc_final: 0.8282 (p) REVERT: B 302 MET cc_start: 0.8444 (tpp) cc_final: 0.8173 (tpp) REVERT: B 390 ASN cc_start: 0.7823 (m-40) cc_final: 0.7278 (m-40) REVERT: C 62 GLN cc_start: 0.8239 (mp10) cc_final: 0.7732 (tt0) REVERT: C 204 LYS cc_start: 0.8279 (mmtt) cc_final: 0.7938 (mtmt) REVERT: D 137 ASN cc_start: 0.8718 (m-40) cc_final: 0.8501 (m-40) REVERT: D 145 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7245 (tm) REVERT: D 175 TYR cc_start: 0.9033 (t80) cc_final: 0.8549 (t80) REVERT: E 75 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8383 (mm) REVERT: F 163 ARG cc_start: 0.8066 (mtp180) cc_final: 0.7850 (tpp80) REVERT: F 214 MET cc_start: 0.7554 (ptp) cc_final: 0.7250 (ptp) REVERT: F 288 MET cc_start: 0.8679 (mmm) cc_final: 0.7938 (mmt) REVERT: F 317 MET cc_start: 0.7002 (ttt) cc_final: 0.6632 (ptm) REVERT: F 345 GLU cc_start: 0.7908 (pt0) cc_final: 0.7299 (pm20) REVERT: F 383 MET cc_start: 0.7090 (mmm) cc_final: 0.6554 (ttt) outliers start: 93 outliers final: 61 residues processed: 303 average time/residue: 0.0987 time to fit residues: 46.5221 Evaluate side-chains 275 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 212 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 151 PHE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 186 MET Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 257 LYS Chi-restraints excluded: chain F residue 322 ASP Chi-restraints excluded: chain F residue 394 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 85 optimal weight: 7.9990 chunk 176 optimal weight: 10.0000 chunk 130 optimal weight: 0.0970 chunk 3 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 chunk 133 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN F 112 GLN F 295 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.170443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.128632 restraints weight = 24869.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.129843 restraints weight = 15971.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.131688 restraints weight = 11417.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.132741 restraints weight = 8011.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.133002 restraints weight = 7077.332| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15026 Z= 0.195 Angle : 0.705 21.682 20393 Z= 0.331 Chirality : 0.044 0.156 2306 Planarity : 0.004 0.067 2566 Dihedral : 7.955 70.966 2187 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 7.77 % Allowed : 19.81 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 1882 helix: 0.22 (0.19), residues: 804 sheet: -0.53 (0.36), residues: 193 loop : -1.03 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 407 TYR 0.018 0.001 TYR B 236 PHE 0.019 0.002 PHE C 67 TRP 0.013 0.001 TRP B 226 HIS 0.006 0.001 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00468 (15018) covalent geometry : angle 0.64956 (20379) hydrogen bonds : bond 0.04630 ( 669) hydrogen bonds : angle 4.94128 ( 1878) metal coordination : bond 0.02349 ( 8) metal coordination : angle 10.51948 ( 14) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 218 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 MET cc_start: 0.7710 (mmt) cc_final: 0.7435 (mmt) REVERT: B 115 ASP cc_start: 0.7434 (t0) cc_final: 0.6599 (p0) REVERT: B 151 ARG cc_start: 0.8065 (ptp-110) cc_final: 0.7463 (mmp-170) REVERT: B 221 SER cc_start: 0.9145 (t) cc_final: 0.8315 (p) REVERT: B 302 MET cc_start: 0.8466 (tpp) cc_final: 0.8158 (tpp) REVERT: B 390 ASN cc_start: 0.7786 (m-40) cc_final: 0.7271 (m-40) REVERT: C 62 GLN cc_start: 0.8205 (mp10) cc_final: 0.7822 (tt0) REVERT: D 175 TYR cc_start: 0.9025 (t80) cc_final: 0.8626 (t80) REVERT: E 50 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.7839 (t) REVERT: E 75 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8382 (mm) REVERT: E 190 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8247 (t80) REVERT: F 154 ILE cc_start: 0.5167 (OUTLIER) cc_final: 0.4930 (mp) REVERT: F 163 ARG cc_start: 0.8092 (mtp180) cc_final: 0.7871 (tpp80) REVERT: F 214 MET cc_start: 0.7563 (ptp) cc_final: 0.6997 (ptp) REVERT: F 288 MET cc_start: 0.8677 (mmm) cc_final: 0.7964 (mmt) REVERT: F 317 MET cc_start: 0.7077 (ttt) cc_final: 0.6866 (ptt) REVERT: F 345 GLU cc_start: 0.7925 (pt0) cc_final: 0.7285 (pm20) REVERT: F 383 MET cc_start: 0.7147 (mmm) cc_final: 0.6595 (ttt) outliers start: 120 outliers final: 79 residues processed: 312 average time/residue: 0.0955 time to fit residues: 46.5725 Evaluate side-chains 290 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 207 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 151 PHE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 186 MET Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 322 ASP Chi-restraints excluded: chain F residue 394 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 159 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 154 optimal weight: 20.0000 chunk 147 optimal weight: 0.9980 chunk 160 optimal weight: 20.0000 chunk 41 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 242 GLN B 74 ASN C 37 GLN C 51 GLN F 112 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.170880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.128974 restraints weight = 24624.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.128608 restraints weight = 16460.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.130732 restraints weight = 12364.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.132023 restraints weight = 8782.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.132494 restraints weight = 7467.908| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15026 Z= 0.179 Angle : 0.681 17.991 20393 Z= 0.321 Chirality : 0.044 0.163 2306 Planarity : 0.004 0.060 2566 Dihedral : 7.882 72.510 2183 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 7.38 % Allowed : 21.10 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.69 (0.20), residues: 1882 helix: 0.22 (0.19), residues: 804 sheet: -0.50 (0.37), residues: 193 loop : -1.03 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 117 TYR 0.017 0.001 TYR B 236 PHE 0.020 0.002 PHE C 67 TRP 0.013 0.001 TRP B 226 HIS 0.005 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00430 (15018) covalent geometry : angle 0.63059 (20379) hydrogen bonds : bond 0.04427 ( 669) hydrogen bonds : angle 4.80026 ( 1878) metal coordination : bond 0.02281 ( 8) metal coordination : angle 9.78704 ( 14) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 223 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LEU cc_start: 0.8276 (tp) cc_final: 0.8036 (tt) REVERT: A 374 MET cc_start: 0.9021 (ppp) cc_final: 0.7930 (ptt) REVERT: B 42 LYS cc_start: 0.8431 (mmmm) cc_final: 0.8172 (mmmm) REVERT: B 115 ASP cc_start: 0.7488 (t0) cc_final: 0.6618 (p0) REVERT: B 151 ARG cc_start: 0.8056 (ptp-110) cc_final: 0.7384 (mmp-170) REVERT: B 221 SER cc_start: 0.9112 (t) cc_final: 0.8286 (p) REVERT: B 330 HIS cc_start: 0.7424 (OUTLIER) cc_final: 0.6467 (t-90) REVERT: B 390 ASN cc_start: 0.7790 (m-40) cc_final: 0.7275 (m-40) REVERT: C 62 GLN cc_start: 0.8253 (mp10) cc_final: 0.7904 (tt0) REVERT: D 35 THR cc_start: 0.8574 (p) cc_final: 0.8233 (t) REVERT: D 119 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6101 (tm-30) REVERT: D 175 TYR cc_start: 0.9054 (t80) cc_final: 0.8635 (t80) REVERT: E 56 ASN cc_start: 0.8070 (t0) cc_final: 0.7683 (t0) REVERT: E 75 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8350 (mm) REVERT: E 166 TYR cc_start: 0.8790 (t80) cc_final: 0.8587 (t80) REVERT: E 168 ASP cc_start: 0.8231 (t70) cc_final: 0.8000 (t70) REVERT: E 190 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.8254 (t80) REVERT: F 154 ILE cc_start: 0.5372 (OUTLIER) cc_final: 0.5085 (mp) REVERT: F 163 ARG cc_start: 0.8104 (mtp180) cc_final: 0.7859 (tpp80) REVERT: F 214 MET cc_start: 0.7598 (ptp) cc_final: 0.7323 (ptp) REVERT: F 276 MET cc_start: 0.8618 (ptp) cc_final: 0.8341 (pmm) REVERT: F 288 MET cc_start: 0.8604 (mmm) cc_final: 0.7775 (mmt) REVERT: F 317 MET cc_start: 0.7195 (ttt) cc_final: 0.6889 (ptt) REVERT: F 383 MET cc_start: 0.7149 (mmm) cc_final: 0.6608 (ttp) outliers start: 114 outliers final: 83 residues processed: 312 average time/residue: 0.0972 time to fit residues: 47.6519 Evaluate side-chains 298 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 210 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 330 HIS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 151 PHE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 186 MET Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 257 LYS Chi-restraints excluded: chain F residue 322 ASP Chi-restraints excluded: chain F residue 394 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 chunk 120 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 159 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 104 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN C 51 GLN E 61 ASN F 112 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.173286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.131963 restraints weight = 24499.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.131828 restraints weight = 16217.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.134236 restraints weight = 11856.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.135420 restraints weight = 8062.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.135659 restraints weight = 7070.655| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15026 Z= 0.125 Angle : 0.633 16.610 20393 Z= 0.298 Chirality : 0.043 0.154 2306 Planarity : 0.004 0.060 2566 Dihedral : 7.682 73.298 2183 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 6.15 % Allowed : 23.37 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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 (0.20), residues: 1882 helix: 0.44 (0.19), residues: 804 sheet: -0.43 (0.37), residues: 193 loop : -0.94 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 71 TYR 0.012 0.001 TYR B 236 PHE 0.022 0.001 PHE C 67 TRP 0.013 0.001 TRP B 226 HIS 0.011 0.001 HIS F 336 Details of bonding type rmsd covalent geometry : bond 0.00287 (15018) covalent geometry : angle 0.58818 (20379) hydrogen bonds : bond 0.03903 ( 669) hydrogen bonds : angle 4.57523 ( 1878) metal coordination : bond 0.01694 ( 8) metal coordination : angle 8.89894 ( 14) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 226 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 MET cc_start: 0.8896 (ppp) cc_final: 0.7765 (ptt) REVERT: B 42 LYS cc_start: 0.8249 (mmmm) cc_final: 0.8034 (mmmm) REVERT: B 115 ASP cc_start: 0.7348 (t0) cc_final: 0.6583 (p0) REVERT: B 151 ARG cc_start: 0.7997 (ptp-110) cc_final: 0.7351 (mmm160) REVERT: B 221 SER cc_start: 0.9025 (t) cc_final: 0.8199 (p) REVERT: B 330 HIS cc_start: 0.7365 (OUTLIER) cc_final: 0.6450 (t-90) REVERT: B 390 ASN cc_start: 0.7753 (m-40) cc_final: 0.7326 (m-40) REVERT: C 62 GLN cc_start: 0.8080 (mp10) cc_final: 0.7870 (tt0) REVERT: D 115 MET cc_start: 0.8285 (mmm) cc_final: 0.7953 (mmp) REVERT: D 119 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6092 (tm-30) REVERT: D 175 TYR cc_start: 0.8927 (t80) cc_final: 0.8571 (t80) REVERT: E 75 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8390 (mm) REVERT: E 168 ASP cc_start: 0.8163 (t70) cc_final: 0.7860 (t70) REVERT: E 190 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8340 (t80) REVERT: F 154 ILE cc_start: 0.5354 (OUTLIER) cc_final: 0.5051 (mp) REVERT: F 225 MET cc_start: 0.4577 (ptt) cc_final: 0.4361 (tpp) REVERT: F 288 MET cc_start: 0.8515 (mmm) cc_final: 0.8204 (mmt) REVERT: F 308 TRP cc_start: 0.8258 (m100) cc_final: 0.7945 (m100) REVERT: F 383 MET cc_start: 0.7147 (mmm) cc_final: 0.6690 (ttp) REVERT: F 389 ASN cc_start: 0.9248 (t0) cc_final: 0.8961 (t0) outliers start: 95 outliers final: 66 residues processed: 295 average time/residue: 0.0989 time to fit residues: 45.2425 Evaluate side-chains 283 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 212 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 330 HIS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 93 TYR Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 151 PHE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 92 GLN Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 186 MET Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 257 LYS Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain F residue 406 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 19 optimal weight: 0.0020 chunk 13 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 183 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 99 optimal weight: 0.1980 chunk 170 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 GLN C 51 GLN E 57 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.175067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.133308 restraints weight = 24372.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.134042 restraints weight = 18185.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.136694 restraints weight = 11138.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.138011 restraints weight = 7858.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.138289 restraints weight = 6772.028| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15026 Z= 0.114 Angle : 0.632 17.536 20393 Z= 0.295 Chirality : 0.042 0.158 2306 Planarity : 0.004 0.063 2566 Dihedral : 7.330 73.598 2176 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 5.89 % Allowed : 24.08 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.36 (0.20), residues: 1882 helix: 0.55 (0.19), residues: 806 sheet: -0.30 (0.37), residues: 193 loop : -0.91 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 117 TYR 0.024 0.001 TYR F 200 PHE 0.023 0.001 PHE C 67 TRP 0.012 0.001 TRP B 226 HIS 0.008 0.001 HIS F 336 Details of bonding type rmsd covalent geometry : bond 0.00256 (15018) covalent geometry : angle 0.59201 (20379) hydrogen bonds : bond 0.03612 ( 669) hydrogen bonds : angle 4.42548 ( 1878) metal coordination : bond 0.01387 ( 8) metal coordination : angle 8.50358 ( 14) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 225 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7699 (mp) REVERT: A 374 MET cc_start: 0.8924 (ppp) cc_final: 0.7941 (ptt) REVERT: B 115 ASP cc_start: 0.7406 (t0) cc_final: 0.6579 (p0) REVERT: B 151 ARG cc_start: 0.7966 (ptp-110) cc_final: 0.7191 (mmm160) REVERT: B 221 SER cc_start: 0.8957 (t) cc_final: 0.8079 (p) REVERT: B 330 HIS cc_start: 0.7379 (OUTLIER) cc_final: 0.6461 (t-90) REVERT: B 390 ASN cc_start: 0.7838 (m-40) cc_final: 0.7352 (m110) REVERT: D 119 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6192 (tm-30) REVERT: D 175 TYR cc_start: 0.8964 (t80) cc_final: 0.8591 (t80) REVERT: E 57 ASN cc_start: 0.6875 (OUTLIER) cc_final: 0.6486 (m110) REVERT: E 168 ASP cc_start: 0.8262 (t70) cc_final: 0.7869 (t70) REVERT: E 186 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.7481 (mtp) REVERT: E 190 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.8297 (t80) REVERT: F 154 ILE cc_start: 0.5406 (OUTLIER) cc_final: 0.5107 (mp) REVERT: F 214 MET cc_start: 0.7694 (ptp) cc_final: 0.7315 (ptp) REVERT: F 288 MET cc_start: 0.8480 (mmm) cc_final: 0.8246 (mmt) REVERT: F 295 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7735 (pm20) REVERT: F 308 TRP cc_start: 0.8132 (m100) cc_final: 0.7705 (m100) REVERT: F 382 MET cc_start: 0.8457 (mpp) cc_final: 0.8195 (mtm) REVERT: F 383 MET cc_start: 0.7121 (mmm) cc_final: 0.6614 (ttp) REVERT: F 389 ASN cc_start: 0.9273 (t0) cc_final: 0.9070 (t0) outliers start: 91 outliers final: 60 residues processed: 294 average time/residue: 0.0938 time to fit residues: 43.8130 Evaluate side-chains 275 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 207 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 330 HIS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 93 TYR Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 151 PHE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 92 GLN Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 186 MET Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 257 LYS Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 295 GLN Chi-restraints excluded: chain F residue 394 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 111 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN D 75 GLN E 57 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.174808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.133263 restraints weight = 24470.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.134071 restraints weight = 16490.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.136212 restraints weight = 10989.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.137162 restraints weight = 8060.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.137451 restraints weight = 7022.136| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15026 Z= 0.163 Angle : 0.677 16.488 20393 Z= 0.316 Chirality : 0.044 0.192 2306 Planarity : 0.004 0.064 2566 Dihedral : 7.371 73.618 2174 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 6.34 % Allowed : 23.95 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.47 (0.19), residues: 1882 helix: 0.46 (0.19), residues: 807 sheet: -0.31 (0.37), residues: 193 loop : -0.97 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 117 TYR 0.016 0.001 TYR B 236 PHE 0.026 0.001 PHE C 67 TRP 0.013 0.001 TRP B 226 HIS 0.005 0.001 HIS F 336 Details of bonding type rmsd covalent geometry : bond 0.00387 (15018) covalent geometry : angle 0.63399 (20379) hydrogen bonds : bond 0.03947 ( 669) hydrogen bonds : angle 4.50770 ( 1878) metal coordination : bond 0.02008 ( 8) metal coordination : angle 9.03646 ( 14) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 218 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7677 (mp) REVERT: A 92 ILE cc_start: 0.7669 (OUTLIER) cc_final: 0.7318 (pt) REVERT: A 374 MET cc_start: 0.8978 (ppp) cc_final: 0.8010 (ptt) REVERT: B 42 LYS cc_start: 0.8413 (mmmm) cc_final: 0.8157 (mmmm) REVERT: B 115 ASP cc_start: 0.7464 (t0) cc_final: 0.6616 (p0) REVERT: B 151 ARG cc_start: 0.8073 (ptp-110) cc_final: 0.7145 (mmm160) REVERT: B 221 SER cc_start: 0.9020 (t) cc_final: 0.8130 (p) REVERT: B 330 HIS cc_start: 0.7429 (OUTLIER) cc_final: 0.6505 (t-90) REVERT: B 390 ASN cc_start: 0.7851 (m-40) cc_final: 0.7327 (m110) REVERT: D 107 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8616 (tt) REVERT: D 119 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6223 (tm-30) REVERT: D 175 TYR cc_start: 0.9019 (t80) cc_final: 0.8622 (t80) REVERT: E 56 ASN cc_start: 0.7780 (t0) cc_final: 0.7469 (t0) REVERT: E 168 ASP cc_start: 0.8346 (t70) cc_final: 0.7949 (t70) REVERT: E 190 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8351 (t80) REVERT: F 214 MET cc_start: 0.7727 (ptp) cc_final: 0.7314 (ptp) REVERT: F 285 MET cc_start: 0.7904 (tpp) cc_final: 0.7649 (tpp) REVERT: F 295 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7687 (pm20) REVERT: F 382 MET cc_start: 0.8445 (mpp) cc_final: 0.8123 (mtm) REVERT: F 383 MET cc_start: 0.7118 (mmm) cc_final: 0.6593 (ttp) REVERT: F 389 ASN cc_start: 0.9250 (t0) cc_final: 0.9037 (t0) outliers start: 98 outliers final: 76 residues processed: 292 average time/residue: 0.0964 time to fit residues: 44.2923 Evaluate side-chains 284 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 201 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 330 HIS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 93 TYR Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 151 PHE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 92 GLN Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 186 MET Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 257 LYS Chi-restraints excluded: chain F residue 295 GLN Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain F residue 394 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 179 optimal weight: 0.0670 chunk 144 optimal weight: 0.1980 chunk 97 optimal weight: 6.9990 chunk 158 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 171 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 overall best weight: 1.0524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 GLN E 57 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.174350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.132862 restraints weight = 24587.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.133232 restraints weight = 15666.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.135413 restraints weight = 10825.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.136360 restraints weight = 8083.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.136687 restraints weight = 7019.432| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15026 Z= 0.129 Angle : 0.664 16.775 20393 Z= 0.308 Chirality : 0.043 0.194 2306 Planarity : 0.004 0.065 2566 Dihedral : 7.344 74.160 2174 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 5.37 % Allowed : 25.31 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.44 (0.19), residues: 1882 helix: 0.47 (0.19), residues: 807 sheet: -0.27 (0.37), residues: 193 loop : -0.96 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 71 TYR 0.012 0.001 TYR B 236 PHE 0.026 0.001 PHE C 67 TRP 0.020 0.001 TRP B 100 HIS 0.006 0.001 HIS F 336 Details of bonding type rmsd covalent geometry : bond 0.00300 (15018) covalent geometry : angle 0.62265 (20379) hydrogen bonds : bond 0.03755 ( 669) hydrogen bonds : angle 4.44516 ( 1878) metal coordination : bond 0.01678 ( 8) metal coordination : angle 8.84891 ( 14) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 207 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LEU cc_start: 0.8185 (tp) cc_final: 0.7985 (tt) REVERT: A 31 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7750 (mp) REVERT: A 374 MET cc_start: 0.8916 (ppp) cc_final: 0.7950 (ptt) REVERT: B 42 LYS cc_start: 0.8417 (mmmm) cc_final: 0.8177 (mmmm) REVERT: B 115 ASP cc_start: 0.7395 (t0) cc_final: 0.6600 (p0) REVERT: B 151 ARG cc_start: 0.8038 (ptp-110) cc_final: 0.7208 (mmm160) REVERT: B 221 SER cc_start: 0.8976 (t) cc_final: 0.8117 (p) REVERT: B 302 MET cc_start: 0.8346 (tpp) cc_final: 0.8051 (tpp) REVERT: B 330 HIS cc_start: 0.7399 (OUTLIER) cc_final: 0.6468 (t-90) REVERT: B 390 ASN cc_start: 0.7804 (m-40) cc_final: 0.7301 (m-40) REVERT: D 107 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8438 (tt) REVERT: D 119 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6200 (tm-30) REVERT: D 175 TYR cc_start: 0.8958 (t80) cc_final: 0.8601 (t80) REVERT: E 56 ASN cc_start: 0.7815 (t0) cc_final: 0.7530 (t0) REVERT: E 168 ASP cc_start: 0.8295 (t70) cc_final: 0.7953 (t70) REVERT: E 186 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7469 (mtp) REVERT: E 190 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.8348 (t80) REVERT: F 112 GLN cc_start: 0.7721 (mm110) cc_final: 0.7204 (mp10) REVERT: F 154 ILE cc_start: 0.5414 (OUTLIER) cc_final: 0.5144 (mp) REVERT: F 214 MET cc_start: 0.7789 (ptp) cc_final: 0.7375 (ptp) REVERT: F 285 MET cc_start: 0.7811 (tpp) cc_final: 0.7575 (tpp) REVERT: F 288 MET cc_start: 0.9041 (mmt) cc_final: 0.8416 (mtp) REVERT: F 295 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7682 (pm20) REVERT: F 307 TYR cc_start: 0.7224 (t80) cc_final: 0.6874 (t80) REVERT: F 383 MET cc_start: 0.7112 (mmm) cc_final: 0.6592 (ttp) REVERT: F 389 ASN cc_start: 0.9248 (t0) cc_final: 0.9046 (t0) outliers start: 83 outliers final: 62 residues processed: 270 average time/residue: 0.0969 time to fit residues: 41.1355 Evaluate side-chains 273 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 203 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 330 HIS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 93 TYR Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 151 PHE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 92 GLN Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 186 MET Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 257 LYS Chi-restraints excluded: chain F residue 295 GLN Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain F residue 406 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 27 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 14 optimal weight: 0.0040 chunk 184 optimal weight: 7.9990 chunk 168 optimal weight: 20.0000 chunk 157 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 chunk 146 optimal weight: 6.9990 overall best weight: 2.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN E 56 ASN E 57 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.172261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.131545 restraints weight = 24702.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.131236 restraints weight = 16037.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.133592 restraints weight = 11478.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.134352 restraints weight = 8614.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.134603 restraints weight = 7548.895| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 15026 Z= 0.235 Angle : 0.758 16.722 20393 Z= 0.357 Chirality : 0.046 0.195 2306 Planarity : 0.005 0.068 2566 Dihedral : 7.561 75.676 2172 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 6.15 % Allowed : 24.27 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.19), residues: 1882 helix: 0.17 (0.19), residues: 812 sheet: -0.39 (0.37), residues: 195 loop : -1.12 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 71 TYR 0.022 0.002 TYR B 236 PHE 0.031 0.002 PHE C 67 TRP 0.021 0.002 TRP B 100 HIS 0.006 0.002 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00567 (15018) covalent geometry : angle 0.71284 (20379) hydrogen bonds : bond 0.04515 ( 669) hydrogen bonds : angle 4.72143 ( 1878) metal coordination : bond 0.02444 ( 8) metal coordination : angle 9.88659 ( 14) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 200 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7865 (mp) REVERT: B 42 LYS cc_start: 0.8564 (mmmm) cc_final: 0.8344 (mmmm) REVERT: B 115 ASP cc_start: 0.7534 (t0) cc_final: 0.6807 (p0) REVERT: B 151 ARG cc_start: 0.8246 (ptp-110) cc_final: 0.7156 (mmm160) REVERT: B 221 SER cc_start: 0.9095 (t) cc_final: 0.8287 (p) REVERT: B 330 HIS cc_start: 0.7397 (OUTLIER) cc_final: 0.6542 (t-90) REVERT: B 390 ASN cc_start: 0.7840 (m-40) cc_final: 0.7335 (m-40) REVERT: D 107 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8493 (tt) REVERT: D 175 TYR cc_start: 0.9028 (t80) cc_final: 0.8662 (t80) REVERT: E 168 ASP cc_start: 0.8344 (t70) cc_final: 0.8097 (t70) REVERT: E 190 PHE cc_start: 0.9116 (OUTLIER) cc_final: 0.8276 (t80) REVERT: F 154 ILE cc_start: 0.5547 (OUTLIER) cc_final: 0.5293 (mp) REVERT: F 285 MET cc_start: 0.7785 (tpp) cc_final: 0.7559 (tpp) REVERT: F 288 MET cc_start: 0.9045 (mmt) cc_final: 0.8368 (mtp) REVERT: F 295 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7726 (pm20) REVERT: F 382 MET cc_start: 0.8457 (mtm) cc_final: 0.8209 (mpp) REVERT: F 383 MET cc_start: 0.7216 (mmm) cc_final: 0.6714 (ttp) REVERT: F 389 ASN cc_start: 0.9262 (t0) cc_final: 0.9055 (t0) outliers start: 95 outliers final: 68 residues processed: 274 average time/residue: 0.0959 time to fit residues: 41.8327 Evaluate side-chains 269 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 195 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 330 HIS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 93 TYR Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 151 PHE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 186 MET Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 257 LYS Chi-restraints excluded: chain F residue 295 GLN Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain F residue 394 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 9 optimal weight: 0.7980 chunk 59 optimal weight: 0.3980 chunk 119 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 44 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 98 optimal weight: 0.3980 chunk 65 optimal weight: 0.9980 chunk 183 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN F 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.174785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.132872 restraints weight = 24399.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.133085 restraints weight = 15681.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.135638 restraints weight = 10870.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.136577 restraints weight = 7682.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.136948 restraints weight = 6809.894| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15026 Z= 0.120 Angle : 0.704 19.621 20393 Z= 0.320 Chirality : 0.043 0.178 2306 Planarity : 0.004 0.067 2566 Dihedral : 7.336 75.604 2172 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.82 % Allowed : 26.67 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 1882 helix: 0.43 (0.19), residues: 809 sheet: -0.27 (0.38), residues: 193 loop : -0.99 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 71 TYR 0.013 0.001 TYR B 360 PHE 0.027 0.001 PHE C 67 TRP 0.020 0.001 TRP F 335 HIS 0.007 0.001 HIS F 336 Details of bonding type rmsd covalent geometry : bond 0.00274 (15018) covalent geometry : angle 0.65219 (20379) hydrogen bonds : bond 0.03707 ( 669) hydrogen bonds : angle 4.43702 ( 1878) metal coordination : bond 0.01758 ( 8) metal coordination : angle 10.15780 ( 14) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3764 Ramachandran restraints generated. 1882 Oldfield, 0 Emsley, 1882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 214 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7794 (mp) REVERT: B 42 LYS cc_start: 0.8449 (mmmm) cc_final: 0.8194 (mmmm) REVERT: B 115 ASP cc_start: 0.7394 (t0) cc_final: 0.6613 (p0) REVERT: B 151 ARG cc_start: 0.8146 (ptp-110) cc_final: 0.7126 (mmm160) REVERT: B 221 SER cc_start: 0.8974 (t) cc_final: 0.8110 (p) REVERT: B 306 ILE cc_start: 0.8442 (tt) cc_final: 0.8076 (pt) REVERT: B 330 HIS cc_start: 0.7312 (OUTLIER) cc_final: 0.6451 (t-90) REVERT: B 390 ASN cc_start: 0.7820 (m-40) cc_final: 0.7357 (m110) REVERT: D 107 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8433 (tt) REVERT: D 175 TYR cc_start: 0.8921 (t80) cc_final: 0.8575 (t80) REVERT: E 100 ARG cc_start: 0.6768 (tmt170) cc_final: 0.5883 (tmm160) REVERT: E 168 ASP cc_start: 0.8228 (t70) cc_final: 0.7991 (t70) REVERT: E 186 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.7511 (mtp) REVERT: E 190 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.8342 (t80) REVERT: F 1 MET cc_start: 0.7253 (tpt) cc_final: 0.6688 (mpp) REVERT: F 154 ILE cc_start: 0.5432 (OUTLIER) cc_final: 0.5146 (mp) REVERT: F 214 MET cc_start: 0.7798 (ptp) cc_final: 0.7436 (ptp) REVERT: F 285 MET cc_start: 0.7778 (tpp) cc_final: 0.7499 (tpp) REVERT: F 288 MET cc_start: 0.9112 (mmt) cc_final: 0.8670 (mtp) REVERT: F 295 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7683 (pm20) REVERT: F 307 TYR cc_start: 0.7343 (t80) cc_final: 0.7056 (t80) REVERT: F 308 TRP cc_start: 0.7938 (m100) cc_final: 0.7536 (m100) REVERT: F 382 MET cc_start: 0.8421 (mtm) cc_final: 0.8147 (mpp) REVERT: F 383 MET cc_start: 0.7176 (mmm) cc_final: 0.6680 (ttp) REVERT: F 390 MET cc_start: 0.7977 (ttm) cc_final: 0.7685 (ttt) outliers start: 59 outliers final: 48 residues processed: 260 average time/residue: 0.0978 time to fit residues: 39.8142 Evaluate side-chains 258 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 203 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 330 HIS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 151 PHE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 92 GLN Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 186 MET Chi-restraints excluded: chain E residue 190 PHE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 257 LYS Chi-restraints excluded: chain F residue 295 GLN Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain F residue 394 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 32 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 chunk 149 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 GLN F 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.176482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.134605 restraints weight = 24400.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.135809 restraints weight = 16859.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.136317 restraints weight = 11699.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.137319 restraints weight = 10080.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.137654 restraints weight = 8504.101| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15026 Z= 0.140 Angle : 0.692 23.566 20393 Z= 0.321 Chirality : 0.043 0.177 2306 Planarity : 0.004 0.068 2566 Dihedral : 7.290 75.896 2172 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.27 % Allowed : 26.54 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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 (0.20), residues: 1882 helix: 0.43 (0.19), residues: 806 sheet: -0.24 (0.38), residues: 195 loop : -0.99 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 34 TYR 0.014 0.001 TYR B 236 PHE 0.028 0.001 PHE C 67 TRP 0.018 0.001 TRP B 100 HIS 0.006 0.001 HIS F 336 Details of bonding type rmsd covalent geometry : bond 0.00333 (15018) covalent geometry : angle 0.64922 (20379) hydrogen bonds : bond 0.03767 ( 669) hydrogen bonds : angle 4.44940 ( 1878) metal coordination : bond 0.01478 ( 8) metal coordination : angle 9.13131 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2226.00 seconds wall clock time: 39 minutes 21.59 seconds (2361.59 seconds total)