Starting phenix.real_space_refine on Thu Jul 2 07:48:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6irs_9721/07_2026/6irs_9721.cif Found real_map, /net/cci-nas-00/data/ceres_data/6irs_9721/07_2026/6irs_9721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6irs_9721/07_2026/6irs_9721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6irs_9721/07_2026/6irs_9721.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6irs_9721/07_2026/6irs_9721.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6irs_9721/07_2026/6irs_9721.cif" model { file = "/net/cci-nas-00/data/ceres_data/6irs_9721/07_2026/6irs_9721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6irs_9721/07_2026/6irs_9721.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 27 5.16 5 C 4807 2.51 5 N 1172 2.21 5 O 1329 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 7337 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3650 Classifications: {'peptide': 469} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 446} Chain: "B" Number of atoms: 3479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3479 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 24, 'TRANS': 432} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'3PH': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.31, per 1000 atoms: 0.18 Number of scatterers: 7337 At special positions: 0 Unit cell: (82.916, 84.007, 124.374, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 2 15.00 O 1329 8.00 N 1172 7.00 C 4807 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS B 164 " distance=2.04 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 507 " " NAG D 1 " - " ASN A 366 " " NAG E 1 " - " ASN A 382 " " NAG F 1 " - " ASN A 425 " Time building additional restraints: 0.39 Conformation dependent library (CDL) restraints added in 263.0 milliseconds 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1704 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 3 sheets defined 57.8% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 167 through 175 Processing helix chain 'A' and resid 180 through 207 removed outlier: 3.677A pdb=" N LEU A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TRP A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET A 197 " --> pdb=" O GLY A 193 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 3.863A pdb=" N THR A 222 " --> pdb=" O TRP A 219 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY A 223 " --> pdb=" O TRP A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 236 Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'A' and resid 248 through 253 Processing helix chain 'A' and resid 287 through 301 removed outlier: 3.631A pdb=" N LYS A 300 " --> pdb=" O GLN A 296 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 342 removed outlier: 4.212A pdb=" N GLU A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 356 through 372 removed outlier: 3.676A pdb=" N PHE A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE A 371 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER A 372 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 393 removed outlier: 3.837A pdb=" N LEU A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 392 " --> pdb=" O GLN A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 428 removed outlier: 3.530A pdb=" N THR A 427 " --> pdb=" O TYR A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 461 removed outlier: 3.921A pdb=" N GLN A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LEU A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET A 457 " --> pdb=" O LEU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 519 through 534 removed outlier: 3.619A pdb=" N ARG A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 540 Processing helix chain 'B' and resid 53 through 64 removed outlier: 3.908A pdb=" N ILE B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 63 " --> pdb=" O ILE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.963A pdb=" N ILE B 68 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 69 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 70 " --> pdb=" O GLY B 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 65 through 70' Processing helix chain 'B' and resid 71 through 80 removed outlier: 3.760A pdb=" N GLU B 78 " --> pdb=" O GLY B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 110 removed outlier: 3.553A pdb=" N PHE B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER B 96 " --> pdb=" O CYS B 92 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE B 97 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.823A pdb=" N VAL B 123 " --> pdb=" O TYR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 137 removed outlier: 3.542A pdb=" N GLU B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 155 removed outlier: 3.860A pdb=" N GLN B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 186 removed outlier: 4.036A pdb=" N LEU B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 221 removed outlier: 3.848A pdb=" N ARG B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE B 200 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 205 " --> pdb=" O ALA B 201 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU B 208 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE B 219 " --> pdb=" O GLY B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 254 removed outlier: 3.866A pdb=" N VAL B 244 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 267 removed outlier: 3.916A pdb=" N MET B 267 " --> pdb=" O VAL B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 300 removed outlier: 3.698A pdb=" N ILE B 279 " --> pdb=" O PRO B 275 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Proline residue: B 283 - end of helix removed outlier: 4.205A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 308 removed outlier: 3.817A pdb=" N LEU B 306 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER B 308 " --> pdb=" O GLN B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 320 removed outlier: 3.796A pdb=" N ASP B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 338 removed outlier: 3.855A pdb=" N SER B 338 " --> pdb=" O SER B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 345 removed outlier: 3.657A pdb=" N THR B 345 " --> pdb=" O GLY B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 356 removed outlier: 4.397A pdb=" N PHE B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B 352 " --> pdb=" O ARG B 348 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 386 removed outlier: 3.510A pdb=" N MET B 383 " --> pdb=" O PHE B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 390 removed outlier: 3.585A pdb=" N SER B 390 " --> pdb=" O TYR B 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 387 through 390' Processing helix chain 'B' and resid 392 through 421 removed outlier: 3.619A pdb=" N ASN B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 402 " --> pdb=" O ASN B 398 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE B 403 " --> pdb=" O PHE B 399 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA B 409 " --> pdb=" O TRP B 405 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 453 removed outlier: 3.841A pdb=" N VAL B 437 " --> pdb=" O LEU B 433 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE B 439 " --> pdb=" O LEU B 435 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU B 441 " --> pdb=" O VAL B 437 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B 442 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 447 " --> pdb=" O CYS B 443 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 449 " --> pdb=" O PHE B 445 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 451 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N TRP B 452 " --> pdb=" O ALA B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 462 Processing helix chain 'B' and resid 469 through 474 Processing helix chain 'B' and resid 483 through 501 removed outlier: 3.953A pdb=" N GLN B 487 " --> pdb=" O LYS B 483 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY B 488 " --> pdb=" O TRP B 484 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS B 496 " --> pdb=" O THR B 492 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 377 through 379 removed outlier: 6.389A pdb=" N PHE A 346 " --> pdb=" O ILE A 378 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU A 307 " --> pdb=" O GLN A 347 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TYR A 226 " --> pdb=" O VAL A 261 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 268 removed outlier: 6.986A pdb=" N GLN A 280 " --> pdb=" O LYS A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 545 removed outlier: 4.514A pdb=" N SER A 553 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU A 624 " --> pdb=" O LEU A 597 " (cutoff:3.500A) 311 hydrogen bonds defined for protein. 915 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: 1.03 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1456 1.33 - 1.45: 1777 1.45 - 1.57: 4235 1.57 - 1.69: 4 1.69 - 1.81: 40 Bond restraints: 7512 Sorted by residual: bond pdb=" C31 3PH B 601 " pdb=" O31 3PH B 601 " ideal model delta sigma weight residual 1.325 1.454 -0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" C31 3PH B 602 " pdb=" O31 3PH B 602 " ideal model delta sigma weight residual 1.325 1.452 -0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C21 3PH B 602 " pdb=" O21 3PH B 602 " ideal model delta sigma weight residual 1.328 1.455 -0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" C21 3PH B 601 " pdb=" O21 3PH B 601 " ideal model delta sigma weight residual 1.328 1.455 -0.127 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C1 NAG D 1 " pdb=" C2 NAG D 1 " ideal model delta sigma weight residual 1.532 1.632 -0.100 2.00e-02 2.50e+03 2.50e+01 ... (remaining 7507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 9580 2.50 - 5.00: 514 5.00 - 7.49: 87 7.49 - 9.99: 21 9.99 - 12.49: 8 Bond angle restraints: 10210 Sorted by residual: angle pdb=" C SER A 176 " pdb=" N PRO A 177 " pdb=" CA PRO A 177 " ideal model delta sigma weight residual 119.84 129.79 -9.95 1.25e+00 6.40e-01 6.34e+01 angle pdb=" N MET A 490 " pdb=" CA MET A 490 " pdb=" C MET A 490 " ideal model delta sigma weight residual 109.15 97.87 11.28 1.44e+00 4.82e-01 6.14e+01 angle pdb=" N MET A 508 " pdb=" CA MET A 508 " pdb=" C MET A 508 " ideal model delta sigma weight residual 111.28 118.86 -7.58 1.09e+00 8.42e-01 4.84e+01 angle pdb=" N HIS B 319 " pdb=" CA HIS B 319 " pdb=" C HIS B 319 " ideal model delta sigma weight residual 111.28 117.70 -6.42 1.09e+00 8.42e-01 3.47e+01 angle pdb=" C PHE B 161 " pdb=" N PRO B 162 " pdb=" CA PRO B 162 " ideal model delta sigma weight residual 119.84 127.10 -7.26 1.25e+00 6.40e-01 3.38e+01 ... (remaining 10205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4057 17.73 - 35.46: 217 35.46 - 53.19: 62 53.19 - 70.92: 11 70.92 - 88.65: 3 Dihedral angle restraints: 4350 sinusoidal: 1697 harmonic: 2653 Sorted by residual: dihedral pdb=" CB CYS A 211 " pdb=" SG CYS A 211 " pdb=" SG CYS B 164 " pdb=" CB CYS B 164 " ideal model delta sinusoidal sigma weight residual 93.00 -178.35 -88.65 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CA PRO B 360 " pdb=" C PRO B 360 " pdb=" N SER B 361 " pdb=" CA SER B 361 " ideal model delta harmonic sigma weight residual -180.00 -155.14 -24.86 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA HIS A 221 " pdb=" C HIS A 221 " pdb=" N THR A 222 " pdb=" CA THR A 222 " ideal model delta harmonic sigma weight residual 180.00 -155.73 -24.27 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 4347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 983 0.081 - 0.162: 184 0.162 - 0.242: 23 0.242 - 0.323: 6 0.323 - 0.404: 4 Chirality restraints: 1200 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.17e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.58e+01 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 507 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.07e+00 ... (remaining 1197 not shown) Planarity restraints: 1258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.337 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG D 2 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.177 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.503 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.321 2.00e-02 2.50e+03 2.77e-01 9.60e+02 pdb=" C7 NAG D 1 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.021 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.481 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.210 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 507 " -0.090 2.00e-02 2.50e+03 1.14e-01 1.62e+02 pdb=" CG ASN A 507 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN A 507 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 507 " 0.196 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.133 2.00e-02 2.50e+03 ... (remaining 1255 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 399 2.70 - 3.25: 7072 3.25 - 3.80: 11547 3.80 - 4.35: 14537 4.35 - 4.90: 23858 Nonbonded interactions: 57413 Sorted by model distance: nonbonded pdb=" ND1 HIS B 367 " pdb=" CD PRO B 368 " model vdw 2.150 3.520 nonbonded pdb=" O GLY B 107 " pdb=" OG SER B 111 " model vdw 2.199 3.040 nonbonded pdb=" C TRP A 492 " pdb=" CG2 THR A 509 " model vdw 2.221 3.690 nonbonded pdb=" CD1 ILE A 228 " pdb=" CZ PHE A 234 " model vdw 2.250 3.760 nonbonded pdb=" O CYS B 92 " pdb=" OH TYR B 254 " model vdw 2.277 3.040 ... (remaining 57408 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 6.360 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 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 : 0.011 0.129 7521 Z= 0.514 Angle : 1.409 17.746 10236 Z= 0.753 Chirality : 0.069 0.404 1200 Planarity : 0.014 0.287 1254 Dihedral : 12.692 77.395 2643 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.87 % Allowed : 8.79 % Favored : 90.35 % Rotamer: Outliers : 3.66 % Allowed : 6.81 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -5.69 (0.19), residues: 922 helix: -4.10 (0.12), residues: 475 sheet: -1.86 (0.67), residues: 51 loop : -3.48 (0.25), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG A 227 TYR 0.050 0.004 TYR A 454 PHE 0.034 0.004 PHE A 552 TRP 0.035 0.005 TRP A 558 HIS 0.012 0.003 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.01116 / 0.51 ( 7512) covalent geometry : angle 1.35716 / 0.74 (10210) SS BOND : bond 0.00722 / 0.38 ( 1) SS BOND : angle 1.63140 / 0.79 ( 2) hydrogen bonds : bond 0.30586 / 19.67 ( 311) hydrogen bonds : angle 10.45425 / 7.38 ( 915) link_BETA1-4 : bond 0.00209 / 0.09 ( 4) link_BETA1-4 : angle 2.39261 / 1.21 ( 12) link_NAG-ASN : bond 0.06460 / 3.25 ( 4) link_NAG-ASN : angle 10.93273 / 5.80 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 221 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 TRP cc_start: 0.7934 (m100) cc_final: 0.7554 (m-10) REVERT: A 290 ASP cc_start: 0.8431 (m-30) cc_final: 0.8038 (t0) REVERT: A 330 LYS cc_start: 0.8819 (mttm) cc_final: 0.8439 (tppt) REVERT: A 332 LYS cc_start: 0.8937 (tttt) cc_final: 0.8620 (tttm) REVERT: A 458 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8454 (mp) REVERT: A 480 LEU cc_start: 0.8759 (tp) cc_final: 0.8540 (tt) REVERT: A 554 TYR cc_start: 0.8031 (p90) cc_final: 0.7265 (p90) REVERT: B 137 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8147 (mt) REVERT: B 145 GLN cc_start: 0.8348 (mt0) cc_final: 0.8017 (mt0) REVERT: B 210 LEU cc_start: 0.8944 (tt) cc_final: 0.8679 (tt) REVERT: B 305 MET cc_start: 0.7393 (mtp) cc_final: 0.6994 (mtp) REVERT: B 452 TRP cc_start: 0.6384 (t60) cc_final: 0.6010 (t60) outliers start: 28 outliers final: 7 residues processed: 238 average time/residue: 0.0781 time to fit residues: 24.4021 Evaluate side-chains 143 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 370 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.0770 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.0050 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.4552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 HIS B 432 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.134560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.103633 restraints weight = 12021.068| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 3.06 r_work: 0.3286 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7521 Z= 0.152 Angle : 0.867 15.749 10236 Z= 0.407 Chirality : 0.047 0.226 1200 Planarity : 0.006 0.059 1254 Dihedral : 8.829 58.655 1068 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.16 % Favored : 92.73 % Rotamer: Outliers : 3.40 % Allowed : 14.92 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.91 (0.23), residues: 922 helix: -2.27 (0.18), residues: 505 sheet: -1.09 (0.73), residues: 51 loop : -3.17 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 314 TYR 0.030 0.002 TYR B 271 PHE 0.023 0.002 PHE B 451 TRP 0.015 0.001 TRP A 558 HIS 0.011 0.002 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 ( 7512) covalent geometry : angle 0.81092 / 0.39 (10210) SS BOND : bond 0.00274 / 0.14 ( 1) SS BOND : angle 0.29961 / 0.14 ( 2) hydrogen bonds : bond 0.05308 / 3.42 ( 311) hydrogen bonds : angle 5.45382 / 3.72 ( 915) link_BETA1-4 : bond 0.00472 / 0.24 ( 4) link_BETA1-4 : angle 2.08952 / 1.19 ( 12) link_NAG-ASN : bond 0.01076 / 0.55 ( 4) link_NAG-ASN : angle 8.76195 / 4.56 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 TRP cc_start: 0.7843 (m100) cc_final: 0.7493 (m-10) REVERT: A 192 LEU cc_start: 0.8766 (mm) cc_final: 0.8519 (mm) REVERT: A 278 LEU cc_start: 0.8278 (mt) cc_final: 0.8023 (mt) REVERT: A 290 ASP cc_start: 0.8343 (m-30) cc_final: 0.7867 (t0) REVERT: A 300 LYS cc_start: 0.8498 (mmtt) cc_final: 0.8222 (mmtt) REVERT: A 332 LYS cc_start: 0.8931 (tttt) cc_final: 0.8628 (tttm) REVERT: A 454 TYR cc_start: 0.8536 (m-80) cc_final: 0.8184 (m-80) REVERT: A 458 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8497 (mp) REVERT: A 469 TYR cc_start: 0.8571 (p90) cc_final: 0.8341 (p90) REVERT: A 511 LYS cc_start: 0.8303 (mmtt) cc_final: 0.8011 (mmtt) REVERT: B 191 LYS cc_start: 0.7607 (tmtt) cc_final: 0.7367 (tmtt) REVERT: B 195 ARG cc_start: 0.7731 (mtp85) cc_final: 0.6889 (ttt90) REVERT: B 210 LEU cc_start: 0.8796 (tt) cc_final: 0.8466 (tt) REVERT: B 320 LEU cc_start: 0.7208 (tp) cc_final: 0.6724 (tp) outliers start: 26 outliers final: 11 residues processed: 176 average time/residue: 0.0767 time to fit residues: 18.0168 Evaluate side-chains 128 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 444 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 25 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 GLN ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN ** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.128159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.097923 restraints weight = 12301.745| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.99 r_work: 0.3182 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 7521 Z= 0.254 Angle : 0.876 15.679 10236 Z= 0.420 Chirality : 0.049 0.228 1200 Planarity : 0.006 0.047 1254 Dihedral : 8.519 58.922 1053 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.68 % Favored : 91.21 % Rotamer: Outliers : 4.19 % Allowed : 18.32 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.24), residues: 922 helix: -1.57 (0.20), residues: 505 sheet: -0.95 (0.75), residues: 51 loop : -2.91 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 227 TYR 0.022 0.003 TYR A 469 PHE 0.022 0.002 PHE A 524 TRP 0.018 0.002 TRP B 405 HIS 0.013 0.003 HIS B 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.25 ( 7512) covalent geometry : angle 0.83100 / 0.41 (10210) SS BOND : bond 0.00275 / 0.14 ( 1) SS BOND : angle 0.42351 / 0.25 ( 2) hydrogen bonds : bond 0.05274 / 3.43 ( 311) hydrogen bonds : angle 5.07481 / 3.48 ( 915) link_BETA1-4 : bond 0.00474 / 0.22 ( 4) link_BETA1-4 : angle 2.21682 / 1.30 ( 12) link_NAG-ASN : bond 0.00474 / 0.23 ( 4) link_NAG-ASN : angle 7.86992 / 4.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 TRP cc_start: 0.7784 (m100) cc_final: 0.7448 (m-10) REVERT: A 192 LEU cc_start: 0.8759 (mm) cc_final: 0.8502 (mm) REVERT: A 290 ASP cc_start: 0.8426 (m-30) cc_final: 0.7961 (t0) REVERT: A 381 THR cc_start: 0.8997 (OUTLIER) cc_final: 0.8774 (m) REVERT: A 397 LYS cc_start: 0.7970 (mttt) cc_final: 0.7535 (ptmt) REVERT: A 458 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8618 (mp) REVERT: A 511 LYS cc_start: 0.8301 (mmtt) cc_final: 0.7984 (mmtt) REVERT: A 629 TYR cc_start: 0.8606 (t80) cc_final: 0.8338 (t80) REVERT: B 195 ARG cc_start: 0.7287 (mtp85) cc_final: 0.6954 (ttt90) REVERT: B 210 LEU cc_start: 0.8730 (tt) cc_final: 0.8463 (tt) REVERT: B 421 ARG cc_start: 0.7480 (mmp80) cc_final: 0.7162 (mmp80) REVERT: B 427 ARG cc_start: 0.7404 (mpt180) cc_final: 0.7176 (mtt90) REVERT: B 444 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9046 (tp) REVERT: B 452 TRP cc_start: 0.6144 (t60) cc_final: 0.5850 (m-10) outliers start: 32 outliers final: 19 residues processed: 147 average time/residue: 0.0776 time to fit residues: 15.4772 Evaluate side-chains 130 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 476 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.131511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.101096 restraints weight = 12336.903| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.05 r_work: 0.3236 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7521 Z= 0.138 Angle : 0.743 14.340 10236 Z= 0.349 Chirality : 0.044 0.224 1200 Planarity : 0.005 0.042 1254 Dihedral : 8.147 57.524 1053 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.81 % Favored : 92.08 % Rotamer: Outliers : 2.75 % Allowed : 21.86 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.26), residues: 922 helix: -0.83 (0.22), residues: 500 sheet: -0.70 (0.76), residues: 51 loop : -2.77 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 440 TYR 0.028 0.002 TYR B 271 PHE 0.015 0.001 PHE B 451 TRP 0.012 0.001 TRP A 434 HIS 0.011 0.002 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 7512) covalent geometry : angle 0.69796 / 0.34 (10210) SS BOND : bond 0.00129 / 0.07 ( 1) SS BOND : angle 0.19402 / 0.11 ( 2) hydrogen bonds : bond 0.04082 / 2.68 ( 311) hydrogen bonds : angle 4.58021 / 3.13 ( 915) link_BETA1-4 : bond 0.00495 / 0.23 ( 4) link_BETA1-4 : angle 2.06562 / 1.19 ( 12) link_NAG-ASN : bond 0.00533 / 0.26 ( 4) link_NAG-ASN : angle 7.21414 / 3.73 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 TRP cc_start: 0.7904 (m100) cc_final: 0.7459 (m-10) REVERT: A 192 LEU cc_start: 0.8827 (mm) cc_final: 0.8581 (mm) REVERT: A 290 ASP cc_start: 0.8341 (m-30) cc_final: 0.7883 (t0) REVERT: A 397 LYS cc_start: 0.7926 (mttt) cc_final: 0.7487 (ptmt) REVERT: A 458 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8786 (mp) REVERT: A 511 LYS cc_start: 0.8344 (mmtt) cc_final: 0.8094 (mmtt) REVERT: B 210 LEU cc_start: 0.8723 (tt) cc_final: 0.8426 (tt) REVERT: B 213 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8831 (pp) REVERT: B 421 ARG cc_start: 0.7452 (mmp80) cc_final: 0.7211 (mmp80) REVERT: B 427 ARG cc_start: 0.7275 (mpt180) cc_final: 0.6930 (mtt90) REVERT: B 444 LEU cc_start: 0.9252 (tp) cc_final: 0.8995 (tp) outliers start: 21 outliers final: 10 residues processed: 128 average time/residue: 0.0705 time to fit residues: 12.4943 Evaluate side-chains 121 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 440 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 80 optimal weight: 0.8980 chunk 53 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 89 optimal weight: 0.0770 chunk 20 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 GLN A 323 GLN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.132529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.102118 restraints weight = 12217.812| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 3.06 r_work: 0.3257 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7521 Z= 0.129 Angle : 0.728 14.167 10236 Z= 0.342 Chirality : 0.043 0.220 1200 Planarity : 0.004 0.041 1254 Dihedral : 7.793 56.311 1052 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.92 % Favored : 91.97 % Rotamer: Outliers : 3.14 % Allowed : 22.25 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.26), residues: 922 helix: -0.42 (0.22), residues: 502 sheet: -0.45 (0.77), residues: 52 loop : -2.71 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 314 TYR 0.015 0.001 TYR B 103 PHE 0.022 0.002 PHE B 474 TRP 0.011 0.001 TRP B 405 HIS 0.008 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 7512) covalent geometry : angle 0.68774 / 0.33 (10210) SS BOND : bond 0.00096 / 0.05 ( 1) SS BOND : angle 0.52590 / 0.26 ( 2) hydrogen bonds : bond 0.03785 / 2.50 ( 311) hydrogen bonds : angle 4.35660 / 2.98 ( 915) link_BETA1-4 : bond 0.00505 / 0.23 ( 4) link_BETA1-4 : angle 2.02778 / 1.17 ( 12) link_NAG-ASN : bond 0.00520 / 0.25 ( 4) link_NAG-ASN : angle 6.76491 / 3.48 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 191 TRP cc_start: 0.7881 (m100) cc_final: 0.7466 (m-10) REVERT: A 192 LEU cc_start: 0.8805 (mm) cc_final: 0.8572 (mm) REVERT: A 290 ASP cc_start: 0.8314 (m-30) cc_final: 0.7881 (t0) REVERT: A 374 ASP cc_start: 0.7828 (t0) cc_final: 0.7618 (t0) REVERT: A 397 LYS cc_start: 0.7916 (mttt) cc_final: 0.7459 (ptmt) REVERT: A 454 TYR cc_start: 0.8478 (m-80) cc_final: 0.8269 (m-80) REVERT: A 511 LYS cc_start: 0.8355 (mmtt) cc_final: 0.8098 (mmtt) REVERT: B 191 LYS cc_start: 0.7389 (tmtt) cc_final: 0.7078 (tptm) REVERT: B 210 LEU cc_start: 0.8793 (tt) cc_final: 0.8446 (tt) REVERT: B 213 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8775 (pp) REVERT: B 427 ARG cc_start: 0.7175 (mpt180) cc_final: 0.6966 (mtt90) REVERT: B 444 LEU cc_start: 0.9217 (tp) cc_final: 0.9013 (tp) outliers start: 24 outliers final: 16 residues processed: 133 average time/residue: 0.0682 time to fit residues: 12.4408 Evaluate side-chains 125 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 469 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN B 358 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.130481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.100474 restraints weight = 12235.917| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 3.06 r_work: 0.3235 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7521 Z= 0.144 Angle : 0.722 13.080 10236 Z= 0.339 Chirality : 0.043 0.227 1200 Planarity : 0.004 0.042 1254 Dihedral : 7.476 56.747 1050 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.46 % Favored : 91.43 % Rotamer: Outliers : 4.19 % Allowed : 21.73 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.27), residues: 922 helix: -0.14 (0.23), residues: 506 sheet: -0.48 (0.76), residues: 52 loop : -2.61 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 421 TYR 0.019 0.002 TYR A 629 PHE 0.018 0.002 PHE B 474 TRP 0.013 0.001 TRP B 405 HIS 0.008 0.002 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 7512) covalent geometry : angle 0.68615 / 0.33 (10210) SS BOND : bond 0.00126 / 0.07 ( 1) SS BOND : angle 0.40327 / 0.21 ( 2) hydrogen bonds : bond 0.03729 / 2.45 ( 311) hydrogen bonds : angle 4.26083 / 2.93 ( 915) link_BETA1-4 : bond 0.00517 / 0.23 ( 4) link_BETA1-4 : angle 2.01670 / 1.15 ( 12) link_NAG-ASN : bond 0.00561 / 0.27 ( 4) link_NAG-ASN : angle 6.30350 / 3.24 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 TRP cc_start: 0.7888 (m100) cc_final: 0.7448 (m-10) REVERT: A 192 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8576 (mm) REVERT: A 290 ASP cc_start: 0.8375 (m-30) cc_final: 0.7923 (t0) REVERT: A 374 ASP cc_start: 0.7976 (t0) cc_final: 0.7751 (t0) REVERT: A 397 LYS cc_start: 0.7856 (mttt) cc_final: 0.7428 (ptmt) REVERT: A 404 SER cc_start: 0.8924 (m) cc_final: 0.8712 (p) REVERT: A 511 LYS cc_start: 0.8335 (mmtt) cc_final: 0.8059 (mmtt) REVERT: B 191 LYS cc_start: 0.7421 (tmtt) cc_final: 0.7122 (tptm) REVERT: B 210 LEU cc_start: 0.8820 (tt) cc_final: 0.8427 (tt) REVERT: B 213 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8660 (pp) REVERT: B 453 LYS cc_start: 0.7761 (mmmt) cc_final: 0.7442 (mmtt) outliers start: 32 outliers final: 21 residues processed: 139 average time/residue: 0.0710 time to fit residues: 13.6602 Evaluate side-chains 133 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 476 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 25 optimal weight: 0.6980 chunk 43 optimal weight: 0.0980 chunk 85 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 HIS ** 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 = 0.3807 r_free = 0.3807 target = 0.131809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.101876 restraints weight = 12169.910| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.03 r_work: 0.3258 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7521 Z= 0.122 Angle : 0.710 12.732 10236 Z= 0.330 Chirality : 0.043 0.225 1200 Planarity : 0.004 0.042 1254 Dihedral : 7.262 56.914 1050 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.70 % Favored : 92.19 % Rotamer: Outliers : 3.66 % Allowed : 22.25 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.27), residues: 922 helix: 0.13 (0.23), residues: 507 sheet: -0.47 (0.75), residues: 52 loop : -2.53 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 272 TYR 0.016 0.001 TYR B 103 PHE 0.017 0.001 PHE B 439 TRP 0.011 0.001 TRP B 405 HIS 0.009 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 7512) covalent geometry : angle 0.67736 / 0.32 (10210) SS BOND : bond 0.00064 / 0.03 ( 1) SS BOND : angle 0.34567 / 0.17 ( 2) hydrogen bonds : bond 0.03487 / 2.28 ( 311) hydrogen bonds : angle 4.14668 / 2.86 ( 915) link_BETA1-4 : bond 0.00518 / 0.24 ( 4) link_BETA1-4 : angle 1.99886 / 1.14 ( 12) link_NAG-ASN : bond 0.00591 / 0.29 ( 4) link_NAG-ASN : angle 5.95265 / 3.05 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 191 TRP cc_start: 0.7854 (m100) cc_final: 0.7462 (m-10) REVERT: A 192 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8603 (mm) REVERT: A 290 ASP cc_start: 0.8325 (m-30) cc_final: 0.7726 (t0) REVERT: A 300 LYS cc_start: 0.8645 (mmtt) cc_final: 0.8413 (mmtt) REVERT: A 374 ASP cc_start: 0.7972 (t0) cc_final: 0.7749 (t0) REVERT: A 397 LYS cc_start: 0.7868 (mttt) cc_final: 0.7422 (ptmt) REVERT: A 415 HIS cc_start: 0.7568 (OUTLIER) cc_final: 0.7324 (t-170) REVERT: A 511 LYS cc_start: 0.8370 (mmtt) cc_final: 0.8090 (mmtt) REVERT: A 559 ASP cc_start: 0.8001 (t0) cc_final: 0.7785 (m-30) REVERT: B 191 LYS cc_start: 0.7395 (tmtt) cc_final: 0.7097 (tptm) REVERT: B 210 LEU cc_start: 0.8833 (tt) cc_final: 0.8417 (tt) REVERT: B 213 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8682 (pp) REVERT: B 271 TYR cc_start: 0.7647 (p90) cc_final: 0.7440 (p90) REVERT: B 453 LYS cc_start: 0.7780 (mmmt) cc_final: 0.7560 (mmmt) outliers start: 28 outliers final: 20 residues processed: 136 average time/residue: 0.0777 time to fit residues: 14.4676 Evaluate side-chains 133 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 469 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 1 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 34 optimal weight: 0.0870 chunk 62 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS ** B 367 HIS ** 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 = 0.3815 r_free = 0.3815 target = 0.132464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.102381 restraints weight = 12218.430| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 3.05 r_work: 0.3245 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7521 Z= 0.130 Angle : 0.730 11.875 10236 Z= 0.342 Chirality : 0.043 0.224 1200 Planarity : 0.004 0.042 1254 Dihedral : 7.146 58.687 1050 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.13 % Favored : 91.76 % Rotamer: Outliers : 3.40 % Allowed : 23.30 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.27), residues: 922 helix: 0.28 (0.23), residues: 507 sheet: -0.49 (0.74), residues: 52 loop : -2.56 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 421 TYR 0.017 0.001 TYR B 103 PHE 0.026 0.001 PHE B 474 TRP 0.011 0.001 TRP B 405 HIS 0.015 0.002 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 7512) covalent geometry : angle 0.70108 / 0.34 (10210) SS BOND : bond 0.00026 / 0.01 ( 1) SS BOND : angle 0.48630 / 0.23 ( 2) hydrogen bonds : bond 0.03436 / 2.25 ( 311) hydrogen bonds : angle 4.13831 / 2.86 ( 915) link_BETA1-4 : bond 0.00495 / 0.22 ( 4) link_BETA1-4 : angle 1.99326 / 1.14 ( 12) link_NAG-ASN : bond 0.00584 / 0.29 ( 4) link_NAG-ASN : angle 5.71554 / 2.94 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 TRP cc_start: 0.7832 (m100) cc_final: 0.7437 (m-10) REVERT: A 192 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8558 (mm) REVERT: A 290 ASP cc_start: 0.8297 (m-30) cc_final: 0.7696 (t0) REVERT: A 300 LYS cc_start: 0.8661 (mmtt) cc_final: 0.8425 (mmtt) REVERT: A 374 ASP cc_start: 0.7909 (t0) cc_final: 0.7703 (t0) REVERT: A 397 LYS cc_start: 0.7910 (mttt) cc_final: 0.7462 (ptmt) REVERT: A 415 HIS cc_start: 0.7565 (OUTLIER) cc_final: 0.7123 (t-170) REVERT: A 511 LYS cc_start: 0.8341 (mmtt) cc_final: 0.8063 (mmtt) REVERT: B 191 LYS cc_start: 0.7396 (tmtt) cc_final: 0.7103 (tptm) REVERT: B 210 LEU cc_start: 0.8843 (tt) cc_final: 0.8437 (tt) REVERT: B 213 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8596 (pp) REVERT: B 291 LEU cc_start: 0.8357 (mp) cc_final: 0.8069 (mp) REVERT: B 453 LYS cc_start: 0.7780 (mmmt) cc_final: 0.7483 (mmtt) outliers start: 26 outliers final: 18 residues processed: 132 average time/residue: 0.0787 time to fit residues: 14.0129 Evaluate side-chains 131 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 469 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 31 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 26 optimal weight: 0.0870 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 88 optimal weight: 0.2980 chunk 72 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 HIS ** 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 = 0.3819 r_free = 0.3819 target = 0.133060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.102864 restraints weight = 12060.189| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.03 r_work: 0.3274 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7521 Z= 0.123 Angle : 0.715 11.749 10236 Z= 0.335 Chirality : 0.043 0.225 1200 Planarity : 0.004 0.042 1254 Dihedral : 7.227 57.837 1050 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.70 % Favored : 92.19 % Rotamer: Outliers : 3.14 % Allowed : 23.43 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.27), residues: 922 helix: 0.45 (0.23), residues: 511 sheet: -0.49 (0.79), residues: 47 loop : -2.51 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 349 TYR 0.028 0.002 TYR B 271 PHE 0.017 0.001 PHE B 439 TRP 0.011 0.001 TRP B 405 HIS 0.015 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 7512) covalent geometry : angle 0.68857 / 0.33 (10210) SS BOND : bond 0.00055 / 0.03 ( 1) SS BOND : angle 0.50432 / 0.25 ( 2) hydrogen bonds : bond 0.03355 / 2.20 ( 311) hydrogen bonds : angle 4.10664 / 2.85 ( 915) link_BETA1-4 : bond 0.00579 / 0.26 ( 4) link_BETA1-4 : angle 1.88058 / 1.08 ( 12) link_NAG-ASN : bond 0.00533 / 0.26 ( 4) link_NAG-ASN : angle 5.42801 / 2.78 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 191 TRP cc_start: 0.7780 (m100) cc_final: 0.7396 (m-10) REVERT: A 192 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8563 (mm) REVERT: A 290 ASP cc_start: 0.8174 (m-30) cc_final: 0.7669 (t0) REVERT: A 300 LYS cc_start: 0.8629 (mmtt) cc_final: 0.8412 (mmtt) REVERT: A 397 LYS cc_start: 0.7876 (mttt) cc_final: 0.7555 (ptmt) REVERT: A 415 HIS cc_start: 0.7426 (OUTLIER) cc_final: 0.7017 (t-170) REVERT: A 454 TYR cc_start: 0.8511 (m-80) cc_final: 0.8063 (m-80) REVERT: A 511 LYS cc_start: 0.8372 (mmtt) cc_final: 0.8143 (mmtt) REVERT: B 191 LYS cc_start: 0.7419 (tmtt) cc_final: 0.7117 (tptm) REVERT: B 210 LEU cc_start: 0.8782 (tt) cc_final: 0.8366 (tt) REVERT: B 212 ILE cc_start: 0.8181 (mm) cc_final: 0.7976 (mm) REVERT: B 213 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8735 (pp) REVERT: B 453 LYS cc_start: 0.7784 (mmmt) cc_final: 0.7555 (mmmt) outliers start: 24 outliers final: 15 residues processed: 129 average time/residue: 0.0792 time to fit residues: 13.7434 Evaluate side-chains 127 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 440 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.7744 > 50: distance: 91 - 98: 18.302 distance: 98 - 99: 11.022 distance: 99 - 100: 10.214 distance: 99 - 102: 7.100 distance: 100 - 101: 10.294 distance: 100 - 106: 16.091 distance: 102 - 103: 10.375 distance: 103 - 104: 8.375 distance: 103 - 105: 5.733 distance: 106 - 107: 8.633 distance: 107 - 108: 6.173 distance: 107 - 110: 4.998 distance: 108 - 109: 5.113 distance: 108 - 115: 14.187 distance: 110 - 111: 14.543 distance: 111 - 112: 5.337 distance: 112 - 113: 11.526 distance: 112 - 114: 4.684 distance: 115 - 116: 16.625 distance: 116 - 117: 11.525 distance: 116 - 119: 11.148 distance: 117 - 118: 27.249 distance: 117 - 126: 27.145 distance: 119 - 120: 7.580 distance: 120 - 121: 19.769 distance: 121 - 122: 12.977 distance: 123 - 124: 4.142 distance: 123 - 125: 9.358 distance: 126 - 127: 13.473 distance: 127 - 128: 19.282 distance: 127 - 130: 8.887 distance: 128 - 129: 7.830 distance: 128 - 134: 19.125 distance: 130 - 131: 27.246 distance: 131 - 132: 35.865 distance: 131 - 133: 55.774 distance: 134 - 135: 8.765 distance: 135 - 136: 4.322 distance: 135 - 138: 12.355 distance: 136 - 137: 14.279 distance: 136 - 143: 12.306 distance: 138 - 139: 21.130 distance: 139 - 140: 17.089 distance: 140 - 141: 12.717 distance: 141 - 142: 20.540 distance: 143 - 144: 30.867 distance: 144 - 145: 27.852 distance: 144 - 147: 25.899 distance: 145 - 146: 13.421 distance: 145 - 151: 24.583 distance: 147 - 148: 16.065 distance: 148 - 149: 8.621 distance: 148 - 150: 17.474 distance: 151 - 152: 14.000 distance: 152 - 153: 27.493 distance: 152 - 155: 20.362 distance: 153 - 154: 27.850 distance: 153 - 160: 25.543 distance: 155 - 156: 13.221 distance: 156 - 157: 26.375 distance: 157 - 158: 18.608 distance: 157 - 159: 23.607 distance: 160 - 161: 20.277 distance: 160 - 166: 12.969 distance: 161 - 162: 16.331 distance: 161 - 164: 17.511 distance: 162 - 163: 16.948 distance: 162 - 167: 12.631 distance: 164 - 165: 20.030 distance: 165 - 166: 16.870 distance: 167 - 168: 7.051 distance: 168 - 169: 7.883 distance: 168 - 171: 18.952 distance: 169 - 170: 7.350 distance: 169 - 177: 8.926 distance: 171 - 172: 8.061 distance: 172 - 173: 14.002 distance: 172 - 174: 15.172 distance: 173 - 175: 12.124 distance: 174 - 176: 13.747 distance: 175 - 176: 12.222 distance: 177 - 178: 30.813 distance: 178 - 179: 13.184 distance: 178 - 181: 22.953 distance: 179 - 180: 24.413 distance: 179 - 186: 24.252 distance: 181 - 182: 25.997 distance: 182 - 183: 12.375 distance: 183 - 184: 16.923