Starting phenix.real_space_refine on Fri Jul 3 14:32:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ud3_64060/07_2026/9ud3_64060.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ud3_64060/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ud3_64060/07_2026/9ud3_64060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ud3_64060/07_2026/9ud3_64060.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ud3_64060/07_2026/9ud3_64060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ud3_64060/07_2026/9ud3_64060.map" } 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-dev-6108/lib/python3.11/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, 31 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'FAD': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 2.93, per 1000 atoms: 0.20 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: 1.31 Conformation dependent library (CDL) restraints added in 729.4 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: 0.25 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: 1.60 Time building geometry restraints manager: 1.75 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: 2.920 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.960 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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/Z covalent geometry : bond 0.00427 / 0.19 (15018) covalent geometry : angle 0.70736 / 0.37 (20379) hydrogen bonds : bond 0.16157 / 10.95 ( 669) hydrogen bonds : angle 5.82593 / 4.16 ( 1878) metal coordination : bond 0.01635 / 0.81 ( 8) metal coordination : angle 11.00217 / 5.40 ( 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 : 0.614 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: 0.7509 (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: 0.8052 (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: 0.0914 time to fit residues: 36.3223 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 : 0.447 ------------------------------------------------------------------------------- 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... ** 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 = 0.4140 r_free = 0.4140 target = 0.171346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.131089 restraints weight = 24639.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.130634 restraints weight = 16645.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.133386 restraints weight = 11687.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.134103 restraints weight = 8380.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.134434 restraints weight = 7420.589| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.0776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15026 Z= 0.210 Angle : 0.712 19.569 20393 Z= 0.339 Chirality : 0.045 0.174 2306 Planarity : 0.005 0.061 2566 Dihedral : 8.712 70.665 2239 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 5.89 % Allowed : 19.81 % Favored : 74.30 % 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: 0.18 (0.19), residues: 813 sheet: -0.42 (0.37), residues: 181 loop : -1.05 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 151 TYR 0.018 0.001 TYR B 236 PHE 0.019 0.002 PHE F 267 TRP 0.013 0.002 TRP F 250 HIS 0.011 0.002 HIS F 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.21 (15018) covalent geometry : angle 0.65880 / 0.34 (20379) hydrogen bonds : bond 0.04957 / 3.33 ( 669) hydrogen bonds : angle 5.11714 / 3.61 ( 1878) metal coordination : bond 0.02590 / 1.24 ( 8) metal coordination : angle 10.27909 / 4.92 ( 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 316 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 225 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 ASP cc_start: 0.7416 (t0) cc_final: 0.6573 (p0) REVERT: B 151 ARG cc_start: 0.7932 (ptp-110) cc_final: 0.7442 (mmp-170) REVERT: B 221 SER cc_start: 0.9158 (t) cc_final: 0.8301 (p) REVERT: B 390 ASN cc_start: 0.7817 (m-40) cc_final: 0.7266 (m-40) REVERT: C 62 GLN cc_start: 0.8285 (mp10) cc_final: 0.7754 (tt0) REVERT: C 204 LYS cc_start: 0.8302 (mmtt) cc_final: 0.7947 (mtmt) REVERT: D 115 MET cc_start: 0.8493 (mmm) cc_final: 0.7985 (mmp) REVERT: D 175 TYR cc_start: 0.9048 (t80) cc_final: 0.8563 (t80) REVERT: E 50 THR cc_start: 0.8377 (OUTLIER) cc_final: 0.7842 (t) REVERT: E 75 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8383 (mm) REVERT: E 100 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.5903 (tmm160) REVERT: F 1 MET cc_start: 0.7379 (mmm) cc_final: 0.7164 (tpt) REVERT: F 163 ARG cc_start: 0.8083 (mtp180) cc_final: 0.7822 (tpp80) REVERT: F 214 MET cc_start: 0.7574 (ptp) cc_final: 0.7264 (ptp) REVERT: F 276 MET cc_start: 0.7661 (mtm) cc_final: 0.7039 (mpp) REVERT: F 288 MET cc_start: 0.8715 (mmm) cc_final: 0.7982 (mmt) REVERT: F 305 MET cc_start: 0.8372 (pmm) cc_final: 0.8073 (pmm) REVERT: F 317 MET cc_start: 0.7042 (ttt) cc_final: 0.6835 (ptt) REVERT: F 345 GLU cc_start: 0.7888 (pt0) cc_final: 0.7289 (pm20) REVERT: F 383 MET cc_start: 0.7107 (mmm) cc_final: 0.6497 (ttt) outliers start: 91 outliers final: 60 residues processed: 295 average time/residue: 0.1081 time to fit residues: 49.8899 Evaluate side-chains 273 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 210 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 363 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 164 ILE 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 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 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 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 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: 2.9990 chunk 130 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN D 75 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 = 0.4098 r_free = 0.4098 target = 0.168388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.126774 restraints weight = 24968.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.126376 restraints weight = 16655.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.128508 restraints weight = 12611.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.129736 restraints weight = 8921.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.129944 restraints weight = 7703.819| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 15026 Z= 0.250 Angle : 0.751 23.695 20393 Z= 0.354 Chirality : 0.046 0.162 2306 Planarity : 0.005 0.066 2566 Dihedral : 8.162 71.502 2189 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 8.22 % Allowed : 19.42 % Favored : 72.36 % 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: -0.87 (0.19), residues: 1882 helix: 0.06 (0.19), residues: 807 sheet: -0.59 (0.36), residues: 193 loop : -1.11 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 151 TYR 0.022 0.002 TYR B 236 PHE 0.020 0.002 PHE C 67 TRP 0.014 0.002 TRP B 226 HIS 0.006 0.002 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.25 (15018) covalent geometry : angle 0.69227 / 0.35 (20379) hydrogen bonds : bond 0.04963 / 3.34 ( 669) hydrogen bonds : angle 5.09747 / 3.59 ( 1878) metal coordination : bond 0.02886 / 1.39 ( 8) metal coordination : angle 11.13044 / 5.31 ( 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 343 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 216 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 MET cc_start: 0.7803 (mmt) cc_final: 0.7589 (mmt) REVERT: B 115 ASP cc_start: 0.7495 (t0) cc_final: 0.6610 (p0) REVERT: B 151 ARG cc_start: 0.8073 (ptp-110) cc_final: 0.7242 (mmm160) REVERT: B 221 SER cc_start: 0.9206 (t) cc_final: 0.8372 (p) REVERT: B 390 ASN cc_start: 0.7845 (m-40) cc_final: 0.7386 (m110) REVERT: C 62 GLN cc_start: 0.8298 (mp10) cc_final: 0.7846 (tt0) REVERT: D 115 MET cc_start: 0.8454 (mmm) cc_final: 0.8014 (mmp) REVERT: D 175 TYR cc_start: 0.9088 (t80) cc_final: 0.8612 (t80) REVERT: E 75 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8331 (mm) REVERT: E 190 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8204 (t80) REVERT: F 154 ILE cc_start: 0.5203 (OUTLIER) cc_final: 0.4961 (mp) REVERT: F 163 ARG cc_start: 0.8094 (mtp180) cc_final: 0.7850 (tpp80) REVERT: F 214 MET cc_start: 0.7596 (ptp) cc_final: 0.7001 (ptp) REVERT: F 276 MET cc_start: 0.7848 (mtm) cc_final: 0.7272 (mpp) REVERT: F 288 MET cc_start: 0.8721 (mmm) cc_final: 0.7996 (mmt) REVERT: F 305 MET cc_start: 0.8447 (pmm) cc_final: 0.8055 (pmm) REVERT: F 317 MET cc_start: 0.7108 (ttt) cc_final: 0.6873 (ptt) REVERT: F 345 GLU cc_start: 0.7948 (pt0) cc_final: 0.7302 (pm20) REVERT: F 383 MET cc_start: 0.7128 (mmm) cc_final: 0.6511 (ttt) outliers start: 127 outliers final: 83 residues processed: 318 average time/residue: 0.1060 time to fit residues: 52.4470 Evaluate side-chains 290 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 204 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 155 ASP 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 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 A residue 434 LEU 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 95 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 282 ILE Chi-restraints excluded: chain B residue 294 SER 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 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 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 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 66 VAL Chi-restraints excluded: chain F residue 98 ILE 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 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: 8.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 15 optimal weight: 0.3980 chunk 154 optimal weight: 20.0000 chunk 147 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 GLN A 242 GLN B 74 ASN C 37 GLN C 51 GLN D 75 GLN F 112 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.171294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.129348 restraints weight = 24636.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.130242 restraints weight = 15718.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.132111 restraints weight = 11317.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.133111 restraints weight = 8160.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.133524 restraints weight = 7126.844| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15026 Z= 0.168 Angle : 0.676 18.157 20393 Z= 0.318 Chirality : 0.044 0.162 2306 Planarity : 0.004 0.061 2566 Dihedral : 8.004 72.824 2187 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 6.80 % Allowed : 22.07 % Favored : 71.13 % 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: 0.21 (0.19), residues: 804 sheet: -0.54 (0.37), residues: 193 loop : -1.05 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 117 TYR 0.016 0.001 TYR B 236 PHE 0.019 0.001 PHE C 67 TRP 0.013 0.001 TRP B 177 HIS 0.005 0.001 HIS B 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (15018) covalent geometry : angle 0.62568 / 0.32 (20379) hydrogen bonds : bond 0.04414 / 2.98 ( 669) hydrogen bonds : angle 4.81234 / 3.38 ( 1878) metal coordination : bond 0.02232 / 1.07 ( 8) metal coordination : angle 9.73920 / 4.69 ( 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 333 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 228 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LEU cc_start: 0.8236 (tp) cc_final: 0.8018 (tt) REVERT: B 42 LYS cc_start: 0.8402 (mmmm) cc_final: 0.8177 (mmmm) REVERT: B 115 ASP cc_start: 0.7362 (t0) cc_final: 0.6609 (p0) REVERT: B 151 ARG cc_start: 0.8042 (ptp-110) cc_final: 0.7490 (mmp-170) REVERT: B 221 SER cc_start: 0.9099 (OUTLIER) cc_final: 0.8276 (p) REVERT: B 330 HIS cc_start: 0.7390 (OUTLIER) cc_final: 0.6515 (t-90) REVERT: B 390 ASN cc_start: 0.7734 (m-40) cc_final: 0.7282 (m-40) REVERT: C 62 GLN cc_start: 0.8154 (mp10) cc_final: 0.7886 (tt0) REVERT: D 35 THR cc_start: 0.8613 (p) cc_final: 0.8314 (t) REVERT: D 119 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6103 (tm-30) REVERT: D 175 TYR cc_start: 0.8958 (t80) cc_final: 0.8601 (t80) REVERT: E 56 ASN cc_start: 0.8044 (t0) cc_final: 0.7664 (t0) REVERT: E 75 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8380 (mm) REVERT: E 190 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8292 (t80) REVERT: F 154 ILE cc_start: 0.5332 (OUTLIER) cc_final: 0.5054 (mp) REVERT: F 214 MET cc_start: 0.7454 (ptp) cc_final: 0.7198 (ptp) REVERT: F 276 MET cc_start: 0.7864 (mtm) cc_final: 0.7395 (mpp) REVERT: F 288 MET cc_start: 0.8564 (mmm) cc_final: 0.7764 (mmt) REVERT: F 305 MET cc_start: 0.8419 (pmm) cc_final: 0.8004 (pmm) REVERT: F 383 MET cc_start: 0.7201 (mmm) cc_final: 0.6737 (ttp) outliers start: 105 outliers final: 70 residues processed: 310 average time/residue: 0.1061 time to fit residues: 51.4559 Evaluate side-chains 286 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 210 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 69 THR Chi-restraints excluded: chain A residue 137 SER 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 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 348 THR 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 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 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 148 CYS 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 221 SER 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 312 PHE Chi-restraints excluded: chain B residue 325 MET 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 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 28 VAL 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 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 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 59 LEU 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 252 LEU Chi-restraints excluded: chain F residue 257 LYS 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: 9.9990 chunk 97 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 GLN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN C 51 GLN F 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.173765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.133416 restraints weight = 24697.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.132949 restraints weight = 17073.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.135319 restraints weight = 11987.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.136444 restraints weight = 8501.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.137998 restraints weight = 7429.425| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15026 Z= 0.167 Angle : 0.676 17.408 20393 Z= 0.319 Chirality : 0.044 0.157 2306 Planarity : 0.004 0.063 2566 Dihedral : 7.709 73.816 2181 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 7.83 % Allowed : 22.14 % 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: -0.68 (0.19), residues: 1882 helix: 0.27 (0.19), residues: 804 sheet: -0.55 (0.36), residues: 193 loop : -1.05 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 289 TYR 0.017 0.001 TYR E 166 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/Z covalent geometry : bond 0.00399 / 0.17 (15018) covalent geometry : angle 0.63090 / 0.32 (20379) hydrogen bonds : bond 0.04267 / 2.88 ( 669) hydrogen bonds : angle 4.73344 / 3.31 ( 1878) metal coordination : bond 0.02158 / 1.04 ( 8) metal coordination : angle 9.32711 / 4.49 ( 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 336 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 215 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LEU cc_start: 0.8220 (tp) cc_final: 0.8004 (tt) REVERT: A 374 MET cc_start: 0.9009 (ppp) cc_final: 0.7899 (ptt) REVERT: B 42 LYS cc_start: 0.8213 (mmmm) cc_final: 0.7975 (mmmm) REVERT: B 115 ASP cc_start: 0.7409 (t0) cc_final: 0.6616 (p0) REVERT: B 151 ARG cc_start: 0.8049 (ptp-110) cc_final: 0.7343 (mmm160) REVERT: B 221 SER cc_start: 0.9095 (OUTLIER) cc_final: 0.8249 (p) REVERT: B 330 HIS cc_start: 0.7437 (OUTLIER) cc_final: 0.6543 (t-90) REVERT: B 390 ASN cc_start: 0.7778 (m-40) cc_final: 0.7272 (m-40) REVERT: C 62 GLN cc_start: 0.8215 (mp10) cc_final: 0.7905 (tt0) REVERT: D 35 THR cc_start: 0.8628 (p) cc_final: 0.8313 (t) REVERT: D 175 TYR cc_start: 0.8997 (t80) cc_final: 0.8622 (t80) REVERT: E 56 ASN cc_start: 0.7997 (t0) cc_final: 0.7612 (t0) REVERT: E 75 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8346 (mm) REVERT: E 190 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.8255 (t80) REVERT: F 154 ILE cc_start: 0.5424 (OUTLIER) cc_final: 0.5115 (mp) REVERT: F 214 MET cc_start: 0.7528 (ptp) cc_final: 0.7313 (ptp) REVERT: F 276 MET cc_start: 0.7843 (mtm) cc_final: 0.7549 (mpp) REVERT: F 288 MET cc_start: 0.8585 (mmm) cc_final: 0.7548 (mmt) REVERT: F 305 MET cc_start: 0.8451 (pmm) cc_final: 0.8212 (pmm) REVERT: F 307 TYR cc_start: 0.7642 (t80) cc_final: 0.7192 (t80) REVERT: F 308 TRP cc_start: 0.8236 (m100) cc_final: 0.7853 (m100) REVERT: F 345 GLU cc_start: 0.7964 (pt0) cc_final: 0.7263 (pm20) REVERT: F 383 MET cc_start: 0.7190 (mmm) cc_final: 0.6670 (ttp) REVERT: F 389 ASN cc_start: 0.9281 (t0) cc_final: 0.8988 (t0) outliers start: 121 outliers final: 87 residues processed: 314 average time/residue: 0.1042 time to fit residues: 51.8721 Evaluate side-chains 302 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 210 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 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 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 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 135 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 221 SER 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 312 PHE Chi-restraints excluded: chain B residue 325 MET 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 B residue 395 LEU Chi-restraints excluded: chain B residue 412 TYR 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 C residue 231 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 48 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 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 47 VAL 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 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 F residue 5 ILE Chi-restraints excluded: chain F residue 55 LEU 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 257 LYS Chi-restraints excluded: chain F residue 322 ASP 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: 5.9990 chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 183 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 chunk 170 optimal weight: 20.0000 chunk 132 optimal weight: 1.9990 chunk 47 optimal weight: 0.2980 chunk 129 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN C 51 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.173903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.133304 restraints weight = 24640.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.134535 restraints weight = 16663.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.136399 restraints weight = 10934.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.137697 restraints weight = 8143.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.138092 restraints weight = 6956.232| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15026 Z= 0.171 Angle : 0.686 17.050 20393 Z= 0.321 Chirality : 0.044 0.163 2306 Planarity : 0.004 0.063 2566 Dihedral : 7.676 74.955 2179 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 7.25 % Allowed : 22.65 % Favored : 70.10 % 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 (0.19), residues: 1882 helix: 0.26 (0.19), residues: 804 sheet: -0.50 (0.36), residues: 193 loop : -1.06 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 71 TYR 0.017 0.001 TYR B 236 PHE 0.023 0.001 PHE C 67 TRP 0.014 0.001 TRP B 226 HIS 0.008 0.001 HIS F 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (15018) covalent geometry : angle 0.64165 / 0.32 (20379) hydrogen bonds : bond 0.04248 / 2.87 ( 669) hydrogen bonds : angle 4.67894 / 3.26 ( 1878) metal coordination : bond 0.02140 / 1.03 ( 8) metal coordination : angle 9.23780 / 4.47 ( 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 326 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 214 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7730 (mp) REVERT: A 374 MET cc_start: 0.8992 (ppp) cc_final: 0.7967 (ptt) REVERT: B 42 LYS cc_start: 0.8279 (mmmm) cc_final: 0.8010 (mmmm) REVERT: B 115 ASP cc_start: 0.7459 (t0) cc_final: 0.6616 (p0) REVERT: B 151 ARG cc_start: 0.8044 (ptp-110) cc_final: 0.7317 (mmm160) REVERT: B 221 SER cc_start: 0.9050 (OUTLIER) cc_final: 0.8213 (p) REVERT: B 330 HIS cc_start: 0.7435 (OUTLIER) cc_final: 0.6511 (t-90) REVERT: B 390 ASN cc_start: 0.7800 (m-40) cc_final: 0.7271 (m-40) REVERT: C 62 GLN cc_start: 0.8163 (mp10) cc_final: 0.7898 (tt0) REVERT: D 175 TYR cc_start: 0.9031 (t80) cc_final: 0.8689 (t80) REVERT: E 75 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8350 (mm) REVERT: E 190 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8331 (t80) REVERT: F 154 ILE cc_start: 0.5222 (OUTLIER) cc_final: 0.4941 (mp) REVERT: F 276 MET cc_start: 0.7951 (mtm) cc_final: 0.7603 (mpp) REVERT: F 288 MET cc_start: 0.8537 (mmm) cc_final: 0.7551 (mmt) REVERT: F 307 TYR cc_start: 0.7721 (t80) cc_final: 0.7307 (t80) REVERT: F 383 MET cc_start: 0.7213 (mmm) cc_final: 0.6744 (ttp) REVERT: F 389 ASN cc_start: 0.9269 (t0) cc_final: 0.9038 (t0) outliers start: 112 outliers final: 87 residues processed: 301 average time/residue: 0.1019 time to fit residues: 48.9901 Evaluate side-chains 294 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 201 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 31 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 69 THR 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 252 LEU 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 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 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 135 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 148 CYS 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 221 SER 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 312 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 330 HIS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 412 TYR 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 C residue 169 GLU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 28 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 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 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 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 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 322 ASP 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: 2.9990 chunk 31 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 136 optimal weight: 8.9990 chunk 63 optimal weight: 0.4980 chunk 27 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 GLN D 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.172173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.130521 restraints weight = 24571.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.130325 restraints weight = 16401.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.132561 restraints weight = 12239.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.134196 restraints weight = 8548.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.134291 restraints weight = 7231.084| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15026 Z= 0.187 Angle : 0.707 16.678 20393 Z= 0.331 Chirality : 0.044 0.164 2306 Planarity : 0.004 0.065 2566 Dihedral : 7.698 76.068 2179 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 6.93 % Allowed : 23.11 % Favored : 69.97 % 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: 0.20 (0.19), residues: 811 sheet: -0.43 (0.37), residues: 193 loop : -1.09 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 71 TYR 0.018 0.001 TYR B 236 PHE 0.026 0.002 PHE C 67 TRP 0.015 0.001 TRP F 335 HIS 0.007 0.001 HIS F 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (15018) covalent geometry : angle 0.66420 / 0.33 (20379) hydrogen bonds : bond 0.04304 / 2.91 ( 669) hydrogen bonds : angle 4.68890 / 3.26 ( 1878) metal coordination : bond 0.02246 / 1.09 ( 8) metal coordination : angle 9.29754 / 4.50 ( 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 320 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 213 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7885 (mp) REVERT: A 374 MET cc_start: 0.8944 (ppp) cc_final: 0.7894 (ptt) REVERT: B 42 LYS cc_start: 0.8389 (mmmm) cc_final: 0.8134 (mmmm) REVERT: B 115 ASP cc_start: 0.7396 (t0) cc_final: 0.6613 (p0) REVERT: B 151 ARG cc_start: 0.8118 (ptp-110) cc_final: 0.7367 (mmm160) REVERT: B 221 SER cc_start: 0.9076 (OUTLIER) cc_final: 0.8246 (p) REVERT: B 330 HIS cc_start: 0.7375 (OUTLIER) cc_final: 0.6479 (t-90) REVERT: B 390 ASN cc_start: 0.7745 (m-40) cc_final: 0.7264 (m-40) REVERT: C 62 GLN cc_start: 0.8237 (mp10) cc_final: 0.7990 (tt0) REVERT: D 175 TYR cc_start: 0.8958 (t80) cc_final: 0.8652 (t80) REVERT: E 56 ASN cc_start: 0.7964 (t0) cc_final: 0.7602 (t0) REVERT: E 75 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8364 (mm) REVERT: E 190 PHE cc_start: 0.9107 (OUTLIER) cc_final: 0.8365 (t80) REVERT: F 214 MET cc_start: 0.7613 (ptp) cc_final: 0.7229 (ptp) REVERT: F 288 MET cc_start: 0.8567 (mmm) cc_final: 0.7633 (mmt) REVERT: F 307 TYR cc_start: 0.7720 (t80) cc_final: 0.7282 (t80) REVERT: F 308 TRP cc_start: 0.8287 (m100) cc_final: 0.7913 (m100) REVERT: F 383 MET cc_start: 0.7142 (mmm) cc_final: 0.6636 (ttp) REVERT: F 389 ASN cc_start: 0.9280 (t0) cc_final: 0.9063 (t0) outliers start: 107 outliers final: 84 residues processed: 294 average time/residue: 0.1009 time to fit residues: 47.6329 Evaluate side-chains 294 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 205 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 31 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 69 THR 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 252 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 287 VAL 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 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 60 VAL 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 135 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 148 CYS 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 221 SER 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 312 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 330 HIS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 348 VAL 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 C residue 169 GLU Chi-restraints excluded: chain C residue 231 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 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 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 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 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 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 322 ASP 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: 0.9990 chunk 144 optimal weight: 0.0980 chunk 97 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 165 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 GLN B 74 ASN C 51 GLN ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.175037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.133484 restraints weight = 24630.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.134232 restraints weight = 16362.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.136118 restraints weight = 10927.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.138062 restraints weight = 8137.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.138664 restraints weight = 6572.267| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15026 Z= 0.136 Angle : 0.672 18.668 20393 Z= 0.312 Chirality : 0.043 0.170 2306 Planarity : 0.004 0.066 2566 Dihedral : 7.458 76.803 2177 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 5.83 % Allowed : 24.66 % 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: -0.57 (0.19), residues: 1882 helix: 0.32 (0.19), residues: 807 sheet: -0.34 (0.37), residues: 193 loop : -0.98 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 71 TYR 0.013 0.001 TYR B 236 PHE 0.026 0.001 PHE C 67 TRP 0.025 0.001 TRP B 100 HIS 0.007 0.001 HIS F 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (15018) covalent geometry : angle 0.62986 / 0.31 (20379) hydrogen bonds : bond 0.03897 / 2.64 ( 669) hydrogen bonds : angle 4.55978 / 3.17 ( 1878) metal coordination : bond 0.01653 / 0.79 ( 8) metal coordination : angle 8.95423 / 4.48 ( 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 308 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 218 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7876 (mp) REVERT: B 42 LYS cc_start: 0.8399 (mmmm) cc_final: 0.8155 (mmmm) REVERT: B 115 ASP cc_start: 0.7340 (t0) cc_final: 0.6581 (p0) REVERT: B 151 ARG cc_start: 0.8035 (ptp-110) cc_final: 0.7295 (mmm160) REVERT: B 221 SER cc_start: 0.9033 (t) cc_final: 0.8172 (p) REVERT: B 330 HIS cc_start: 0.7286 (OUTLIER) cc_final: 0.6378 (t-90) REVERT: B 390 ASN cc_start: 0.7751 (m-40) cc_final: 0.7240 (m-40) REVERT: D 115 MET cc_start: 0.8282 (mmm) cc_final: 0.7986 (mmm) REVERT: D 175 TYR cc_start: 0.8912 (t80) cc_final: 0.8585 (t80) REVERT: E 75 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8343 (mm) REVERT: E 190 PHE cc_start: 0.9051 (OUTLIER) cc_final: 0.8363 (t80) REVERT: F 1 MET cc_start: 0.7188 (tpt) cc_final: 0.6891 (mpp) REVERT: F 154 ILE cc_start: 0.5425 (OUTLIER) cc_final: 0.5154 (mp) REVERT: F 214 MET cc_start: 0.7712 (ptp) cc_final: 0.7336 (ptp) REVERT: F 288 MET cc_start: 0.8458 (mmm) cc_final: 0.7563 (mmt) REVERT: F 307 TYR cc_start: 0.7657 (t80) cc_final: 0.7223 (t80) REVERT: F 308 TRP cc_start: 0.8279 (m100) cc_final: 0.7921 (m100) REVERT: F 383 MET cc_start: 0.7155 (mmm) cc_final: 0.6715 (ttp) outliers start: 90 outliers final: 66 residues processed: 285 average time/residue: 0.1008 time to fit residues: 45.7731 Evaluate side-chains 276 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 205 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 287 VAL 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 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 123 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 148 CYS 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 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 312 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 330 HIS Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 412 TYR Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain D residue 43 VAL 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 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 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 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 257 LYS Chi-restraints excluded: chain F residue 394 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 27 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 184 optimal weight: 8.9990 chunk 168 optimal weight: 20.0000 chunk 157 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.174597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.132916 restraints weight = 24599.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.132726 restraints weight = 15986.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.135148 restraints weight = 11921.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.136496 restraints weight = 8183.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.136642 restraints weight = 7102.629| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1969 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= 0.153 Angle : 0.696 17.230 20393 Z= 0.323 Chirality : 0.044 0.188 2306 Planarity : 0.004 0.068 2566 Dihedral : 7.441 76.830 2174 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 5.57 % Allowed : 25.05 % Favored : 69.39 % 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: -0.58 (0.19), residues: 1882 helix: 0.31 (0.19), residues: 807 sheet: -0.30 (0.37), residues: 193 loop : -1.00 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 71 TYR 0.024 0.001 TYR F 200 PHE 0.028 0.001 PHE C 67 TRP 0.019 0.002 TRP B 100 HIS 0.006 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (15018) covalent geometry : angle 0.65763 / 0.32 (20379) hydrogen bonds : bond 0.03969 / 2.68 ( 669) hydrogen bonds : angle 4.55719 / 3.17 ( 1878) metal coordination : bond 0.01700 / 0.84 ( 8) metal coordination : angle 8.72077 / 4.36 ( 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 294 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 208 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7863 (mp) REVERT: A 292 MET cc_start: 0.6889 (ppp) cc_final: 0.6550 (ptt) REVERT: B 42 LYS cc_start: 0.8467 (mmmm) cc_final: 0.8177 (mmmm) REVERT: B 115 ASP cc_start: 0.7410 (t0) cc_final: 0.6603 (p0) REVERT: B 151 ARG cc_start: 0.8097 (ptp-110) cc_final: 0.7262 (mmm160) REVERT: B 221 SER cc_start: 0.9034 (t) cc_final: 0.8181 (p) REVERT: B 308 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8260 (tm) REVERT: B 330 HIS cc_start: 0.7359 (OUTLIER) cc_final: 0.6452 (t-90) REVERT: B 390 ASN cc_start: 0.7741 (m-40) cc_final: 0.7271 (m-40) REVERT: D 115 MET cc_start: 0.8411 (mmm) cc_final: 0.8129 (mmm) REVERT: D 175 TYR cc_start: 0.8974 (t80) cc_final: 0.8627 (t80) REVERT: E 75 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8361 (mm) REVERT: E 186 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7241 (mtp) REVERT: E 190 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8338 (t80) REVERT: F 1 MET cc_start: 0.7263 (tpt) cc_final: 0.6707 (mpp) REVERT: F 154 ILE cc_start: 0.5492 (OUTLIER) cc_final: 0.5225 (mp) REVERT: F 214 MET cc_start: 0.7895 (ptp) cc_final: 0.7490 (ptp) REVERT: F 276 MET cc_start: 0.8442 (pmm) cc_final: 0.8176 (pmm) REVERT: F 288 MET cc_start: 0.8539 (mmm) cc_final: 0.7585 (mmt) REVERT: F 307 TYR cc_start: 0.7661 (t80) cc_final: 0.7176 (t80) REVERT: F 308 TRP cc_start: 0.8207 (m100) cc_final: 0.7870 (m100) REVERT: F 382 MET cc_start: 0.8436 (mpp) cc_final: 0.8133 (mtm) REVERT: F 383 MET cc_start: 0.7080 (mmm) cc_final: 0.6520 (ttp) outliers start: 86 outliers final: 70 residues processed: 276 average time/residue: 0.1002 time to fit residues: 44.2193 Evaluate side-chains 277 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 200 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 244 VAL Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 287 VAL 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 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 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 148 CYS 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 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 310 THR 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 348 VAL Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 412 TYR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 106 LEU 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 169 GLU Chi-restraints excluded: chain D residue 43 VAL 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 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 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 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 257 LYS 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: 1.9990 chunk 59 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 106 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 chunk 183 optimal weight: 4.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.172675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.130371 restraints weight = 24534.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.131312 restraints weight = 16607.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.132568 restraints weight = 11761.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.133724 restraints weight = 9269.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.134015 restraints weight = 7791.396| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15026 Z= 0.199 Angle : 0.743 16.448 20393 Z= 0.347 Chirality : 0.045 0.185 2306 Planarity : 0.005 0.069 2566 Dihedral : 7.562 77.011 2174 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 5.44 % Allowed : 25.44 % Favored : 69.13 % 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: -0.68 (0.19), residues: 1882 helix: 0.24 (0.19), residues: 807 sheet: -0.35 (0.37), residues: 193 loop : -1.06 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 315 TYR 0.019 0.002 TYR B 236 PHE 0.029 0.002 PHE C 67 TRP 0.020 0.002 TRP F 335 HIS 0.006 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 (15018) covalent geometry : angle 0.70348 / 0.35 (20379) hydrogen bonds : bond 0.04305 / 2.91 ( 669) hydrogen bonds : angle 4.66689 / 3.24 ( 1878) metal coordination : bond 0.02090 / 1.06 ( 8) metal coordination : angle 9.11592 / 4.44 ( 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 285 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 201 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7885 (mp) REVERT: B 42 LYS cc_start: 0.8563 (mmmm) cc_final: 0.8288 (mmmm) REVERT: B 115 ASP cc_start: 0.7437 (t0) cc_final: 0.6640 (p0) REVERT: B 151 ARG cc_start: 0.8186 (ptp-110) cc_final: 0.7230 (mmm160) REVERT: B 221 SER cc_start: 0.9016 (OUTLIER) cc_final: 0.8226 (p) REVERT: B 308 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8334 (tm) REVERT: B 330 HIS cc_start: 0.7295 (OUTLIER) cc_final: 0.6445 (t-90) REVERT: B 390 ASN cc_start: 0.7787 (m-40) cc_final: 0.7328 (m-40) REVERT: D 115 MET cc_start: 0.8447 (mmm) cc_final: 0.8186 (mmm) REVERT: D 175 TYR cc_start: 0.8989 (t80) cc_final: 0.8665 (t80) REVERT: E 75 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8349 (mm) REVERT: E 186 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7444 (mtp) REVERT: E 190 PHE cc_start: 0.9116 (OUTLIER) cc_final: 0.8322 (t80) REVERT: F 104 ARG cc_start: 0.8262 (mtp180) cc_final: 0.7627 (mmm160) REVERT: F 154 ILE cc_start: 0.5528 (OUTLIER) cc_final: 0.5268 (mp) REVERT: F 214 MET cc_start: 0.7940 (ptp) cc_final: 0.7522 (ptp) REVERT: F 276 MET cc_start: 0.8491 (pmm) cc_final: 0.8212 (pmm) REVERT: F 288 MET cc_start: 0.8547 (mmm) cc_final: 0.7591 (mmt) REVERT: F 295 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7593 (pm20) REVERT: F 307 TYR cc_start: 0.7665 (t80) cc_final: 0.7288 (t80) REVERT: F 308 TRP cc_start: 0.8265 (m100) cc_final: 0.7894 (m100) REVERT: F 382 MET cc_start: 0.8464 (mpp) cc_final: 0.8166 (mtm) REVERT: F 383 MET cc_start: 0.7085 (mmm) cc_final: 0.6530 (ttp) outliers start: 84 outliers final: 73 residues processed: 271 average time/residue: 0.1003 time to fit residues: 43.0561 Evaluate side-chains 276 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 194 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 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 244 VAL Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 287 VAL 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 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 148 CYS 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 221 SER Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 250 ILE 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 310 THR 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 348 VAL Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 412 TYR Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 106 LEU 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 C residue 169 GLU Chi-restraints excluded: chain D residue 43 VAL 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 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 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 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 322 ASP 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: 3.9990 chunk 4 optimal weight: 0.0270 chunk 53 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 149 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.175729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.134086 restraints weight = 24296.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.134918 restraints weight = 16810.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.136159 restraints weight = 10997.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.136965 restraints weight = 9840.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.137232 restraints weight = 8389.996| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15026 Z= 0.131 Angle : 0.710 18.710 20393 Z= 0.327 Chirality : 0.043 0.176 2306 Planarity : 0.004 0.070 2566 Dihedral : 7.410 76.463 2174 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.85 % Allowed : 26.41 % Favored : 68.74 % 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: -0.50 (0.20), residues: 1882 helix: 0.39 (0.19), residues: 807 sheet: -0.27 (0.38), residues: 193 loop : -0.98 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 71 TYR 0.013 0.001 TYR B 236 PHE 0.027 0.001 PHE C 67 TRP 0.021 0.001 TRP F 335 HIS 0.006 0.001 HIS F 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (15018) covalent geometry : angle 0.66592 / 0.33 (20379) hydrogen bonds : bond 0.03843 / 2.60 ( 669) hydrogen bonds : angle 4.49255 / 3.12 ( 1878) metal coordination : bond 0.02610 / 1.19 ( 8) metal coordination : angle 9.45221 / 4.52 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2412.98 seconds wall clock time: 42 minutes 49.03 seconds (2569.03 seconds total)