Starting phenix.real_space_refine on Tue Mar 3 17:41:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6irs_9721/03_2026/6irs_9721.cif Found real_map, /net/cci-nas-00/data/ceres_data/6irs_9721/03_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_9721/03_2026/6irs_9721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6irs_9721/03_2026/6irs_9721.map" model { file = "/net/cci-nas-00/data/ceres_data/6irs_9721/03_2026/6irs_9721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6irs_9721/03_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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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: 1.75, per 1000 atoms: 0.24 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: 0.85 Conformation dependent library (CDL) restraints added in 308.8 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: 0.22 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: 1.16 Time building geometry restraints manager: 1.08 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 - 21.15: 4267 21.15 - 42.29: 213 42.29 - 63.44: 36 63.44 - 84.59: 13 84.59 - 105.74: 7 Dihedral angle restraints: 4536 sinusoidal: 1883 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 4533 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: 1.720 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.920 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: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 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 : 14.191 105.736 2829 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 covalent geometry : bond 0.01116 ( 7512) covalent geometry : angle 1.35716 (10210) SS BOND : bond 0.00722 ( 1) SS BOND : angle 1.63140 ( 2) hydrogen bonds : bond 0.30586 ( 311) hydrogen bonds : angle 10.45425 ( 915) link_BETA1-4 : bond 0.00209 ( 4) link_BETA1-4 : angle 2.39261 ( 12) link_NAG-ASN : bond 0.06460 ( 4) link_NAG-ASN : angle 10.93273 ( 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 : 0.319 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: 0.0846 time to fit residues: 26.5579 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 : 0.171 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 217 GLN ** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 HIS B 432 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.134541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.103514 restraints weight = 12008.608| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 3.07 r_work: 0.3285 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7521 Z= 0.156 Angle : 0.874 16.272 10236 Z= 0.411 Chirality : 0.047 0.221 1200 Planarity : 0.006 0.059 1254 Dihedral : 12.382 89.232 1254 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.27 % Favored : 92.62 % Rotamer: Outliers : 3.27 % Allowed : 14.79 % Favored : 81.94 % 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: -3.92 (0.23), residues: 922 helix: -2.27 (0.18), residues: 505 sheet: -1.09 (0.74), residues: 51 loop : -3.18 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 227 TYR 0.029 0.002 TYR B 271 PHE 0.024 0.002 PHE B 474 TRP 0.016 0.001 TRP A 558 HIS 0.010 0.002 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 7512) covalent geometry : angle 0.81793 (10210) SS BOND : bond 0.00319 ( 1) SS BOND : angle 0.44067 ( 2) hydrogen bonds : bond 0.05488 ( 311) hydrogen bonds : angle 5.46027 ( 915) link_BETA1-4 : bond 0.00822 ( 4) link_BETA1-4 : angle 2.46249 ( 12) link_NAG-ASN : bond 0.01040 ( 4) link_NAG-ASN : angle 8.75769 ( 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 184 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 TRP cc_start: 0.7879 (m100) cc_final: 0.7507 (m-10) REVERT: A 192 LEU cc_start: 0.8763 (mm) cc_final: 0.8516 (mm) REVERT: A 278 LEU cc_start: 0.8251 (mt) cc_final: 0.7992 (mt) REVERT: A 290 ASP cc_start: 0.8337 (m-30) cc_final: 0.7866 (t0) REVERT: A 300 LYS cc_start: 0.8519 (mmtt) cc_final: 0.8252 (mmtt) REVERT: A 332 LYS cc_start: 0.8938 (tttt) cc_final: 0.8635 (tttm) REVERT: A 454 TYR cc_start: 0.8525 (m-80) cc_final: 0.8170 (m-80) REVERT: A 458 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8508 (mp) REVERT: A 511 LYS cc_start: 0.8393 (mmtt) cc_final: 0.8109 (mmtt) REVERT: B 191 LYS cc_start: 0.7603 (tmtt) cc_final: 0.7348 (tmtt) REVERT: B 210 LEU cc_start: 0.8804 (tt) cc_final: 0.8467 (tt) REVERT: B 320 LEU cc_start: 0.7165 (tp) cc_final: 0.6695 (tp) outliers start: 25 outliers final: 10 residues processed: 175 average time/residue: 0.0860 time to fit residues: 20.0797 Evaluate side-chains 131 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 39 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3758 r_free = 0.3758 target = 0.128390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.097809 restraints weight = 12285.829| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.03 r_work: 0.3187 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 7521 Z= 0.251 Angle : 0.884 15.666 10236 Z= 0.420 Chirality : 0.049 0.200 1200 Planarity : 0.006 0.045 1254 Dihedral : 11.706 84.859 1239 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.68 % Favored : 91.21 % Rotamer: Outliers : 4.19 % Allowed : 17.93 % Favored : 77.88 % 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: -3.16 (0.24), residues: 922 helix: -1.57 (0.20), residues: 507 sheet: -1.00 (0.75), residues: 51 loop : -2.94 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 375 TYR 0.022 0.002 TYR B 103 PHE 0.022 0.003 PHE A 524 TRP 0.018 0.002 TRP B 405 HIS 0.014 0.003 HIS B 319 Details of bonding type rmsd covalent geometry : bond 0.00575 ( 7512) covalent geometry : angle 0.83701 (10210) SS BOND : bond 0.00269 ( 1) SS BOND : angle 0.32753 ( 2) hydrogen bonds : bond 0.05241 ( 311) hydrogen bonds : angle 5.07965 ( 915) link_BETA1-4 : bond 0.00380 ( 4) link_BETA1-4 : angle 2.54725 ( 12) link_NAG-ASN : bond 0.00428 ( 4) link_NAG-ASN : angle 7.95784 ( 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 : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 TRP cc_start: 0.7810 (m100) cc_final: 0.7458 (m-10) REVERT: A 192 LEU cc_start: 0.8727 (mm) cc_final: 0.8466 (mm) REVERT: A 290 ASP cc_start: 0.8453 (m-30) cc_final: 0.7969 (t0) REVERT: A 332 LYS cc_start: 0.8903 (tttt) cc_final: 0.8655 (tttm) REVERT: A 381 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8763 (m) REVERT: A 397 LYS cc_start: 0.7797 (mttt) cc_final: 0.7455 (ptmt) REVERT: A 458 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8625 (mp) REVERT: A 511 LYS cc_start: 0.8297 (mmtt) cc_final: 0.7977 (mmtt) REVERT: A 629 TYR cc_start: 0.8606 (t80) cc_final: 0.8333 (t80) REVERT: B 210 LEU cc_start: 0.8738 (tt) cc_final: 0.8501 (tt) REVERT: B 421 ARG cc_start: 0.7462 (mmp80) cc_final: 0.7140 (mmp80) REVERT: B 427 ARG cc_start: 0.7400 (mpt180) cc_final: 0.7171 (mtt90) REVERT: B 452 TRP cc_start: 0.6101 (t60) cc_final: 0.5829 (m-10) outliers start: 32 outliers final: 22 residues processed: 147 average time/residue: 0.0750 time to fit residues: 15.0342 Evaluate side-chains 131 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 317 ASN 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 539 HIS Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 621 GLU 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 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: 0.8980 chunk 30 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 367 HIS ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.131427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.100818 restraints weight = 12324.696| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.07 r_work: 0.3245 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7521 Z= 0.139 Angle : 0.753 15.036 10236 Z= 0.352 Chirality : 0.045 0.216 1200 Planarity : 0.005 0.046 1254 Dihedral : 10.904 78.891 1239 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.48 % Favored : 92.41 % Rotamer: Outliers : 2.88 % Allowed : 21.34 % Favored : 75.79 % 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: -2.39 (0.26), residues: 922 helix: -0.82 (0.21), residues: 505 sheet: -0.73 (0.76), residues: 51 loop : -2.79 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 440 TYR 0.029 0.002 TYR B 271 PHE 0.014 0.002 PHE B 439 TRP 0.012 0.001 TRP A 434 HIS 0.007 0.001 HIS B 319 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 7512) covalent geometry : angle 0.70641 (10210) SS BOND : bond 0.00144 ( 1) SS BOND : angle 0.19261 ( 2) hydrogen bonds : bond 0.04033 ( 311) hydrogen bonds : angle 4.55324 ( 915) link_BETA1-4 : bond 0.00539 ( 4) link_BETA1-4 : angle 2.43183 ( 12) link_NAG-ASN : bond 0.00484 ( 4) link_NAG-ASN : angle 7.32242 ( 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 140 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 191 TRP cc_start: 0.7908 (m100) cc_final: 0.7466 (m-10) REVERT: A 192 LEU cc_start: 0.8818 (mm) cc_final: 0.8587 (mm) REVERT: A 290 ASP cc_start: 0.8347 (m-30) cc_final: 0.7884 (t0) REVERT: A 374 ASP cc_start: 0.7876 (t0) cc_final: 0.7650 (t0) REVERT: A 397 LYS cc_start: 0.7922 (mttt) cc_final: 0.7489 (ptmt) REVERT: A 458 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8785 (mp) REVERT: A 511 LYS cc_start: 0.8339 (mmtt) cc_final: 0.8039 (mmtt) REVERT: B 210 LEU cc_start: 0.8760 (tt) cc_final: 0.8405 (tt) REVERT: B 213 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8785 (pp) REVERT: B 421 ARG cc_start: 0.7455 (mmp80) cc_final: 0.7217 (mmp80) REVERT: B 427 ARG cc_start: 0.7309 (mpt180) cc_final: 0.6970 (mtt-85) REVERT: B 444 LEU cc_start: 0.9248 (tp) cc_final: 0.8992 (tp) outliers start: 22 outliers final: 12 residues processed: 131 average time/residue: 0.0851 time to fit residues: 15.0072 Evaluate side-chains 124 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 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 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 440 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 80 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 89 optimal weight: 0.0370 chunk 20 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 7 optimal weight: 0.4980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3809 r_free = 0.3809 target = 0.132106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.101911 restraints weight = 12205.360| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.04 r_work: 0.3253 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4218 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= 0.129 Angle : 0.741 13.995 10236 Z= 0.344 Chirality : 0.044 0.225 1200 Planarity : 0.005 0.044 1254 Dihedral : 10.233 75.894 1238 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.70 % Favored : 92.19 % 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: -1.94 (0.26), residues: 922 helix: -0.40 (0.22), residues: 507 sheet: -0.53 (0.77), residues: 52 loop : -2.68 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 272 TYR 0.015 0.001 TYR B 103 PHE 0.016 0.001 PHE B 439 TRP 0.011 0.001 TRP B 405 HIS 0.010 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 7512) covalent geometry : angle 0.69844 (10210) SS BOND : bond 0.00105 ( 1) SS BOND : angle 0.45397 ( 2) hydrogen bonds : bond 0.03747 ( 311) hydrogen bonds : angle 4.35535 ( 915) link_BETA1-4 : bond 0.00534 ( 4) link_BETA1-4 : angle 2.51729 ( 12) link_NAG-ASN : bond 0.00598 ( 4) link_NAG-ASN : angle 6.87138 ( 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 144 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 TRP cc_start: 0.7902 (m100) cc_final: 0.7474 (m-10) REVERT: A 192 LEU cc_start: 0.8798 (mm) cc_final: 0.8565 (mm) REVERT: A 290 ASP cc_start: 0.8331 (m-30) cc_final: 0.7886 (t0) REVERT: A 374 ASP cc_start: 0.7875 (t0) cc_final: 0.7617 (t0) REVERT: A 397 LYS cc_start: 0.7923 (mttt) cc_final: 0.7466 (ptmt) REVERT: A 454 TYR cc_start: 0.8484 (m-80) cc_final: 0.8276 (m-80) REVERT: A 511 LYS cc_start: 0.8347 (mmtt) cc_final: 0.8089 (mmtt) REVERT: B 54 ASN cc_start: 0.8530 (m-40) cc_final: 0.8242 (p0) REVERT: B 191 LYS cc_start: 0.7398 (tmtt) cc_final: 0.7142 (tptm) REVERT: B 195 ARG cc_start: 0.7057 (mtp85) cc_final: 0.6844 (ttt90) REVERT: B 210 LEU cc_start: 0.8780 (tt) cc_final: 0.8414 (tt) REVERT: B 213 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8782 (pp) REVERT: B 427 ARG cc_start: 0.7211 (mpt180) cc_final: 0.6959 (mtt90) REVERT: B 444 LEU cc_start: 0.9213 (tp) cc_final: 0.9008 (tp) outliers start: 24 outliers final: 16 residues processed: 135 average time/residue: 0.0806 time to fit residues: 14.7061 Evaluate side-chains 126 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.151 ------------------------------------------------------------------------------- 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 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 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 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: 0.6980 chunk 58 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 77 optimal weight: 0.0030 chunk 8 optimal weight: 4.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.132215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.102062 restraints weight = 12137.490| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 3.03 r_work: 0.3262 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7521 Z= 0.124 Angle : 0.716 13.781 10236 Z= 0.331 Chirality : 0.044 0.246 1200 Planarity : 0.004 0.043 1254 Dihedral : 9.684 72.889 1236 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.70 % Favored : 92.19 % Rotamer: Outliers : 3.93 % Allowed : 21.47 % 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: -1.56 (0.27), residues: 922 helix: -0.03 (0.23), residues: 508 sheet: -0.50 (0.75), residues: 52 loop : -2.60 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 421 TYR 0.017 0.001 TYR A 629 PHE 0.024 0.001 PHE B 474 TRP 0.011 0.001 TRP B 405 HIS 0.011 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 7512) covalent geometry : angle 0.67501 (10210) SS BOND : bond 0.00096 ( 1) SS BOND : angle 0.35665 ( 2) hydrogen bonds : bond 0.03504 ( 311) hydrogen bonds : angle 4.19941 ( 915) link_BETA1-4 : bond 0.00523 ( 4) link_BETA1-4 : angle 2.57167 ( 12) link_NAG-ASN : bond 0.00617 ( 4) link_NAG-ASN : angle 6.51198 ( 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 147 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 191 TRP cc_start: 0.7903 (m100) cc_final: 0.7475 (m-10) REVERT: A 192 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8604 (mm) REVERT: A 214 LEU cc_start: 0.7873 (mt) cc_final: 0.7621 (mt) REVERT: A 289 GLU cc_start: 0.8838 (mp0) cc_final: 0.8522 (mp0) REVERT: A 290 ASP cc_start: 0.8340 (m-30) cc_final: 0.7910 (t0) REVERT: A 300 LYS cc_start: 0.8673 (mmtt) cc_final: 0.8408 (mmtt) REVERT: A 374 ASP cc_start: 0.7938 (t0) cc_final: 0.7674 (t0) REVERT: A 397 LYS cc_start: 0.7871 (mttt) cc_final: 0.7442 (ptmt) REVERT: A 511 LYS cc_start: 0.8365 (mmtt) cc_final: 0.8084 (mmtt) REVERT: B 54 ASN cc_start: 0.8567 (m-40) cc_final: 0.8240 (p0) REVERT: B 191 LYS cc_start: 0.7433 (tmtt) cc_final: 0.7126 (tptm) REVERT: B 210 LEU cc_start: 0.8813 (tt) cc_final: 0.8398 (tt) REVERT: B 212 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.8027 (mm) REVERT: B 213 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8658 (pp) REVERT: B 453 LYS cc_start: 0.7746 (mmmt) cc_final: 0.7438 (mmtt) outliers start: 30 outliers final: 19 residues processed: 138 average time/residue: 0.0781 time to fit residues: 14.5841 Evaluate side-chains 131 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 621 GLU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 212 ILE 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 324 SER 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 25 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 59 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 chunk 75 optimal weight: 0.0570 chunk 76 optimal weight: 0.8980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.133752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.103461 restraints weight = 12100.035| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 3.05 r_work: 0.3285 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7521 Z= 0.118 Angle : 0.716 13.759 10236 Z= 0.331 Chirality : 0.043 0.274 1200 Planarity : 0.004 0.044 1254 Dihedral : 9.199 68.962 1236 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.59 % Favored : 92.30 % Rotamer: Outliers : 3.14 % Allowed : 22.91 % Favored : 73.95 % 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: 0.23 (0.23), residues: 509 sheet: -0.50 (0.74), residues: 52 loop : -2.49 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 272 TYR 0.016 0.001 TYR B 103 PHE 0.015 0.001 PHE B 439 TRP 0.011 0.001 TRP B 405 HIS 0.008 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 7512) covalent geometry : angle 0.67741 (10210) SS BOND : bond 0.00055 ( 1) SS BOND : angle 0.39356 ( 2) hydrogen bonds : bond 0.03339 ( 311) hydrogen bonds : angle 4.06987 ( 915) link_BETA1-4 : bond 0.00528 ( 4) link_BETA1-4 : angle 2.59160 ( 12) link_NAG-ASN : bond 0.00619 ( 4) link_NAG-ASN : angle 6.31304 ( 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 154 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 191 TRP cc_start: 0.7766 (m100) cc_final: 0.7392 (m-10) REVERT: A 192 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8578 (mm) REVERT: A 290 ASP cc_start: 0.8166 (m-30) cc_final: 0.7660 (t0) REVERT: A 300 LYS cc_start: 0.8644 (mmtt) cc_final: 0.8411 (mmtt) REVERT: A 415 HIS cc_start: 0.7529 (OUTLIER) cc_final: 0.7298 (t-170) REVERT: A 511 LYS cc_start: 0.8510 (mmtt) cc_final: 0.8206 (mmtt) REVERT: A 559 ASP cc_start: 0.7894 (t0) cc_final: 0.7563 (m-30) REVERT: B 54 ASN cc_start: 0.8544 (m-40) cc_final: 0.8242 (p0) REVERT: B 191 LYS cc_start: 0.7401 (tmtt) cc_final: 0.7108 (tptm) REVERT: B 210 LEU cc_start: 0.8843 (tt) cc_final: 0.8450 (tt) REVERT: B 213 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8648 (pp) REVERT: B 453 LYS cc_start: 0.7772 (mmmt) cc_final: 0.7536 (mmmt) outliers start: 24 outliers final: 19 residues processed: 143 average time/residue: 0.0874 time to fit residues: 16.6151 Evaluate side-chains 134 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 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 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 290 VAL Chi-restraints excluded: chain B residue 324 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 1 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 42 optimal weight: 0.1980 chunk 77 optimal weight: 1.9990 chunk 73 optimal weight: 0.0970 chunk 74 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN ** B 319 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 = 0.3824 r_free = 0.3824 target = 0.133264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.103312 restraints weight = 12170.186| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 3.04 r_work: 0.3278 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7521 Z= 0.124 Angle : 0.730 13.369 10236 Z= 0.338 Chirality : 0.044 0.285 1200 Planarity : 0.004 0.043 1254 Dihedral : 8.967 66.763 1236 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.59 % Favored : 92.30 % Rotamer: Outliers : 3.14 % Allowed : 23.82 % Favored : 73.04 % 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: -1.11 (0.27), residues: 922 helix: 0.39 (0.23), residues: 510 sheet: -0.48 (0.79), residues: 47 loop : -2.46 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 349 TYR 0.020 0.001 TYR B 103 PHE 0.026 0.001 PHE B 474 TRP 0.011 0.001 TRP B 405 HIS 0.009 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 7512) covalent geometry : angle 0.69395 (10210) SS BOND : bond 0.00002 ( 1) SS BOND : angle 0.62532 ( 2) hydrogen bonds : bond 0.03366 ( 311) hydrogen bonds : angle 4.06824 ( 915) link_BETA1-4 : bond 0.00540 ( 4) link_BETA1-4 : angle 2.55972 ( 12) link_NAG-ASN : bond 0.00647 ( 4) link_NAG-ASN : angle 6.15762 ( 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 141 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 TRP cc_start: 0.7772 (m100) cc_final: 0.7379 (m-10) REVERT: A 192 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8550 (mm) REVERT: A 290 ASP cc_start: 0.8185 (m-30) cc_final: 0.7671 (t0) REVERT: A 300 LYS cc_start: 0.8630 (mmtt) cc_final: 0.8421 (mmtt) REVERT: A 415 HIS cc_start: 0.7533 (OUTLIER) cc_final: 0.7132 (t-170) REVERT: A 511 LYS cc_start: 0.8522 (mmtt) cc_final: 0.8222 (mmtt) REVERT: B 54 ASN cc_start: 0.8519 (m-40) cc_final: 0.8202 (p0) REVERT: B 191 LYS cc_start: 0.7391 (tmtt) cc_final: 0.7102 (tptm) REVERT: B 210 LEU cc_start: 0.8777 (tt) cc_final: 0.8353 (tt) REVERT: B 213 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8621 (pp) REVERT: B 291 LEU cc_start: 0.8357 (mp) cc_final: 0.8067 (mp) outliers start: 24 outliers final: 18 residues processed: 130 average time/residue: 0.0847 time to fit residues: 14.7584 Evaluate side-chains 130 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 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 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 444 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 31 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 0.0020 chunk 70 optimal weight: 0.6980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 319 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 = 0.3825 r_free = 0.3825 target = 0.133321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.103116 restraints weight = 12015.467| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 3.02 r_work: 0.3281 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7521 Z= 0.124 Angle : 0.739 13.078 10236 Z= 0.340 Chirality : 0.044 0.289 1200 Planarity : 0.004 0.042 1254 Dihedral : 8.831 64.132 1236 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.13 % Favored : 91.76 % Rotamer: Outliers : 3.01 % Allowed : 24.35 % Favored : 72.64 % 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: -1.00 (0.27), residues: 922 helix: 0.53 (0.23), residues: 510 sheet: -0.50 (0.79), residues: 47 loop : -2.47 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 440 TYR 0.020 0.001 TYR B 103 PHE 0.024 0.001 PHE B 474 TRP 0.011 0.001 TRP B 405 HIS 0.010 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 7512) covalent geometry : angle 0.70569 (10210) SS BOND : bond 0.00068 ( 1) SS BOND : angle 0.72532 ( 2) hydrogen bonds : bond 0.03328 ( 311) hydrogen bonds : angle 4.08381 ( 915) link_BETA1-4 : bond 0.00522 ( 4) link_BETA1-4 : angle 2.47463 ( 12) link_NAG-ASN : bond 0.00569 ( 4) link_NAG-ASN : angle 6.01782 ( 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: 23 poor density : 118 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 TRP cc_start: 0.7754 (m100) cc_final: 0.7412 (m-10) REVERT: A 192 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8529 (mm) REVERT: A 290 ASP cc_start: 0.8154 (m-30) cc_final: 0.7643 (t0) REVERT: A 300 LYS cc_start: 0.8626 (mmtt) cc_final: 0.8418 (mmtt) REVERT: A 559 ASP cc_start: 0.7965 (t0) cc_final: 0.7629 (m-30) REVERT: B 54 ASN cc_start: 0.8488 (m-40) cc_final: 0.8180 (p0) REVERT: B 191 LYS cc_start: 0.7426 (tmtt) cc_final: 0.7125 (tptm) REVERT: B 210 LEU cc_start: 0.8777 (tt) cc_final: 0.8347 (tt) REVERT: B 213 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8620 (pp) outliers start: 23 outliers final: 17 residues processed: 130 average time/residue: 0.0825 time to fit residues: 14.3824 Evaluate side-chains 131 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.157 ------------------------------------------------------------------------------- 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 489 VAL Chi-restraints excluded: chain A residue 522 SER 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 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 444 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 66 optimal weight: 0.0670 chunk 87 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN ** B 319 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 = 0.3779 r_free = 0.3779 target = 0.130014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.099779 restraints weight = 12208.733| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.04 r_work: 0.3231 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7521 Z= 0.173 Angle : 0.782 13.387 10236 Z= 0.364 Chirality : 0.046 0.282 1200 Planarity : 0.005 0.044 1254 Dihedral : 8.972 62.660 1236 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.92 % Favored : 91.97 % Rotamer: Outliers : 2.49 % Allowed : 24.74 % Favored : 72.77 % 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: -1.17 (0.27), residues: 922 helix: 0.31 (0.23), residues: 513 sheet: -0.62 (0.73), residues: 52 loop : -2.44 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 440 TYR 0.028 0.002 TYR B 271 PHE 0.029 0.002 PHE B 474 TRP 0.015 0.001 TRP B 405 HIS 0.010 0.002 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 7512) covalent geometry : angle 0.75029 (10210) SS BOND : bond 0.00189 ( 1) SS BOND : angle 0.72910 ( 2) hydrogen bonds : bond 0.03795 ( 311) hydrogen bonds : angle 4.27717 ( 915) link_BETA1-4 : bond 0.00471 ( 4) link_BETA1-4 : angle 2.37457 ( 12) link_NAG-ASN : bond 0.00415 ( 4) link_NAG-ASN : angle 6.02788 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 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 133 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 191 TRP cc_start: 0.7769 (m100) cc_final: 0.7373 (m-10) REVERT: A 192 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8528 (mm) REVERT: A 290 ASP cc_start: 0.8198 (m-30) cc_final: 0.7849 (t0) REVERT: A 300 LYS cc_start: 0.8670 (mmtt) cc_final: 0.8450 (mmtt) REVERT: A 397 LYS cc_start: 0.8139 (mttt) cc_final: 0.7710 (ptmt) REVERT: A 415 HIS cc_start: 0.7407 (OUTLIER) cc_final: 0.7002 (t-170) REVERT: B 54 ASN cc_start: 0.8581 (m-40) cc_final: 0.8241 (p0) REVERT: B 191 LYS cc_start: 0.7436 (tmtt) cc_final: 0.7188 (tptm) REVERT: B 210 LEU cc_start: 0.8799 (tt) cc_final: 0.8350 (tt) REVERT: B 213 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8557 (pp) REVERT: B 452 TRP cc_start: 0.6093 (t60) cc_final: 0.5862 (t60) outliers start: 19 outliers final: 16 residues processed: 123 average time/residue: 0.0884 time to fit residues: 14.3927 Evaluate side-chains 129 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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 489 VAL Chi-restraints excluded: chain A residue 522 SER 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 376 SER 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 444 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 85 optimal weight: 0.0670 chunk 69 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 0.0070 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN B 145 GLN ** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.132943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.102705 restraints weight = 12037.024| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.02 r_work: 0.3270 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7521 Z= 0.126 Angle : 0.764 14.107 10236 Z= 0.352 Chirality : 0.044 0.291 1200 Planarity : 0.004 0.041 1254 Dihedral : 8.882 58.073 1236 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.13 % Favored : 91.76 % Rotamer: Outliers : 2.62 % Allowed : 25.13 % Favored : 72.25 % 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: -0.96 (0.28), residues: 922 helix: 0.52 (0.23), residues: 514 sheet: -0.43 (0.80), residues: 47 loop : -2.42 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 272 TYR 0.019 0.001 TYR B 103 PHE 0.027 0.001 PHE B 474 TRP 0.047 0.001 TRP B 452 HIS 0.009 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 7512) covalent geometry : angle 0.73133 (10210) SS BOND : bond 0.00054 ( 1) SS BOND : angle 0.75462 ( 2) hydrogen bonds : bond 0.03404 ( 311) hydrogen bonds : angle 4.16440 ( 915) link_BETA1-4 : bond 0.00530 ( 4) link_BETA1-4 : angle 2.38655 ( 12) link_NAG-ASN : bond 0.00360 ( 4) link_NAG-ASN : angle 6.12005 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1813.52 seconds wall clock time: 31 minutes 41.07 seconds (1901.07 seconds total)