Starting phenix.real_space_refine on Sat Aug 3 08:55:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6irs_9721/08_2024/6irs_9721.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6irs_9721/08_2024/6irs_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6irs_9721/08_2024/6irs_9721.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6irs_9721/08_2024/6irs_9721.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6irs_9721/08_2024/6irs_9721.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6irs_9721/08_2024/6irs_9721.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Residue "A ARG 181": "NH1" <-> "NH2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "B PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 421": "NH1" <-> "NH2" Residue "B ARG 427": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/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: {'PHE:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3} 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: 4.84, per 1000 atoms: 0.66 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 - 3.50 Amino acid : False - 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: 2.96 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 0.70 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: 1.84 Time building geometry restraints manager: 3.24 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: 95.75 - 103.53: 108 103.53 - 111.31: 3194 111.31 - 119.09: 3000 119.09 - 126.86: 3780 126.86 - 134.64: 128 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: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.270 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 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 7512 Z= 0.726 Angle : 1.357 12.491 10210 Z= 0.743 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 : 13.11 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.035 0.005 TRP A 558 HIS 0.012 0.003 HIS A 221 PHE 0.034 0.004 PHE A 552 TYR 0.050 0.004 TYR A 454 ARG 0.015 0.002 ARG A 227 *********************** 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 fitting. rotamer outliers: 28 poor density : 221 time to evaluate : 0.810 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: symmetry clash revert: symmetry clash REVERT: A 191 TRP cc_start: 0.7934 (m100) cc_final: 0.7555 (m-10) REVERT: A 290 ASP cc_start: 0.8431 (m-30) cc_final: 0.8038 (t0) REVERT: A 332 LYS cc_start: 0.8937 (tttt) cc_final: 0.8619 (tttm) REVERT: A 458 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8452 (mp) REVERT: A 480 LEU cc_start: 0.8759 (tp) cc_final: 0.8544 (tt) REVERT: A 554 TYR cc_start: 0.8030 (p90) cc_final: 0.7266 (p90) REVERT: B 137 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8171 (mt) REVERT: B 145 GLN cc_start: 0.8348 (mt0) cc_final: 0.8015 (mt0) REVERT: B 210 LEU cc_start: 0.8944 (tt) cc_final: 0.8678 (tt) REVERT: B 305 MET cc_start: 0.7393 (mtp) cc_final: 0.6996 (mtp) REVERT: B 452 TRP cc_start: 0.6384 (t60) cc_final: 0.6011 (t60) outliers start: 28 outliers final: 7 residues processed: 238 average time/residue: 0.2125 time to fit residues: 65.3854 Evaluate side-chains 144 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 135 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 76 optimal weight: 0.0000 chunk 68 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 0.0070 chunk 36 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 0.0970 chunk 82 optimal weight: 3.9990 overall best weight: 0.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 323 GLN A 620 HIS ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7512 Z= 0.208 Angle : 0.822 10.465 10210 Z= 0.400 Chirality : 0.047 0.217 1200 Planarity : 0.006 0.059 1254 Dihedral : 12.518 91.106 1254 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.70 % Favored : 92.08 % Rotamer: Outliers : 3.14 % Allowed : 15.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.23), residues: 922 helix: -2.29 (0.18), residues: 502 sheet: -1.11 (0.73), residues: 51 loop : -3.20 (0.28), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 558 HIS 0.009 0.002 HIS B 367 PHE 0.023 0.002 PHE B 474 TYR 0.014 0.002 TYR B 259 ARG 0.005 0.001 ARG A 314 *********************** 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 181 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 157 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 TRP cc_start: 0.7941 (m100) cc_final: 0.7479 (m-10) REVERT: A 192 LEU cc_start: 0.8730 (mm) cc_final: 0.8480 (mm) REVERT: A 278 LEU cc_start: 0.8266 (mt) cc_final: 0.8029 (mt) REVERT: A 290 ASP cc_start: 0.8313 (m-30) cc_final: 0.7865 (t0) REVERT: A 332 LYS cc_start: 0.8897 (tttt) cc_final: 0.8580 (tttm) REVERT: A 454 TYR cc_start: 0.8386 (m-80) cc_final: 0.8113 (m-80) REVERT: A 458 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8365 (mp) REVERT: A 511 LYS cc_start: 0.8416 (mmtt) cc_final: 0.8193 (mmtt) REVERT: A 593 LYS cc_start: 0.7974 (mttp) cc_final: 0.7714 (ttpt) REVERT: A 614 ARG cc_start: 0.7765 (tpp80) cc_final: 0.7564 (mtp85) REVERT: B 58 ILE cc_start: 0.9000 (mt) cc_final: 0.8792 (mp) REVERT: B 137 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7777 (mt) REVERT: B 191 LYS cc_start: 0.7501 (tmtt) cc_final: 0.7229 (tmtt) REVERT: B 210 LEU cc_start: 0.8722 (tt) cc_final: 0.8358 (tt) REVERT: B 320 LEU cc_start: 0.7083 (tp) cc_final: 0.6617 (tp) outliers start: 24 outliers final: 8 residues processed: 174 average time/residue: 0.1983 time to fit residues: 45.6501 Evaluate side-chains 133 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 123 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 458 LEU 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 137 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 376 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7512 Z= 0.244 Angle : 0.754 9.510 10210 Z= 0.367 Chirality : 0.046 0.206 1200 Planarity : 0.005 0.044 1254 Dihedral : 11.573 84.543 1241 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.81 % Favored : 92.08 % Rotamer: Outliers : 4.06 % Allowed : 18.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.25), residues: 922 helix: -1.44 (0.20), residues: 506 sheet: -0.79 (0.76), residues: 51 loop : -2.96 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 405 HIS 0.009 0.002 HIS B 319 PHE 0.019 0.002 PHE B 474 TYR 0.019 0.002 TYR A 629 ARG 0.004 0.000 ARG A 314 *********************** 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 168 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 137 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 TRP cc_start: 0.7904 (m100) cc_final: 0.7427 (m-10) REVERT: A 192 LEU cc_start: 0.8694 (mm) cc_final: 0.8448 (mm) REVERT: A 290 ASP cc_start: 0.8326 (m-30) cc_final: 0.7913 (t0) REVERT: A 458 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8459 (mp) REVERT: A 511 LYS cc_start: 0.8295 (mmtt) cc_final: 0.7952 (mmtt) REVERT: B 124 TYR cc_start: 0.7029 (m-80) cc_final: 0.6741 (m-80) REVERT: B 191 LYS cc_start: 0.7514 (tmtt) cc_final: 0.7310 (tmtt) REVERT: B 210 LEU cc_start: 0.8705 (tt) cc_final: 0.8411 (tt) REVERT: B 320 LEU cc_start: 0.7145 (tp) cc_final: 0.6731 (tp) REVERT: B 421 ARG cc_start: 0.7256 (mmp80) cc_final: 0.6934 (mmp80) REVERT: B 444 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9009 (tp) outliers start: 31 outliers final: 17 residues processed: 155 average time/residue: 0.1929 time to fit residues: 40.2005 Evaluate side-chains 135 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 317 ASN 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 63 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 106 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 367 HIS Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 444 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7512 Z= 0.331 Angle : 0.779 9.603 10210 Z= 0.378 Chirality : 0.047 0.204 1200 Planarity : 0.005 0.047 1254 Dihedral : 11.196 83.194 1238 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.79 % Favored : 91.11 % Rotamer: Outliers : 4.45 % Allowed : 20.03 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.25), residues: 922 helix: -1.13 (0.21), residues: 506 sheet: -0.63 (0.76), residues: 52 loop : -2.82 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 405 HIS 0.011 0.002 HIS B 319 PHE 0.022 0.002 PHE B 451 TYR 0.019 0.002 TYR B 103 ARG 0.004 0.001 ARG A 227 *********************** 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 151 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 117 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 TRP cc_start: 0.7979 (m100) cc_final: 0.7459 (m-10) REVERT: A 192 LEU cc_start: 0.8727 (mm) cc_final: 0.8459 (mm) REVERT: A 290 ASP cc_start: 0.8460 (m-30) cc_final: 0.7967 (t0) REVERT: A 458 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8595 (mp) REVERT: A 511 LYS cc_start: 0.8299 (mmtt) cc_final: 0.8018 (mmtt) REVERT: B 210 LEU cc_start: 0.8702 (tt) cc_final: 0.8343 (tt) REVERT: B 213 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8672 (pp) REVERT: B 421 ARG cc_start: 0.7498 (mmp80) cc_final: 0.7258 (mmp80) REVERT: B 444 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8985 (tp) outliers start: 34 outliers final: 20 residues processed: 139 average time/residue: 0.1890 time to fit residues: 35.4172 Evaluate side-chains 134 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 392 LEU 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 B residue 63 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 163 THR 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 367 HIS 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 458 CYS Chi-restraints excluded: chain B residue 476 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 60 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 44 optimal weight: 0.3980 chunk 78 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 29 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 358 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7512 Z= 0.174 Angle : 0.689 9.666 10210 Z= 0.330 Chirality : 0.044 0.227 1200 Planarity : 0.005 0.043 1254 Dihedral : 10.397 77.503 1238 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.59 % Favored : 92.30 % Rotamer: Outliers : 3.01 % Allowed : 22.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.26), residues: 922 helix: -0.50 (0.22), residues: 505 sheet: -0.47 (0.77), residues: 52 loop : -2.72 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 434 HIS 0.005 0.001 HIS B 367 PHE 0.017 0.001 PHE B 439 TYR 0.023 0.002 TYR A 629 ARG 0.004 0.000 ARG A 440 *********************** 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 151 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 TRP cc_start: 0.7966 (m100) cc_final: 0.7448 (m-10) REVERT: A 192 LEU cc_start: 0.8763 (mm) cc_final: 0.8532 (mm) REVERT: A 290 ASP cc_start: 0.8347 (m-30) cc_final: 0.7885 (t0) REVERT: A 511 LYS cc_start: 0.8288 (mmtt) cc_final: 0.8073 (mmtt) REVERT: A 535 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.6459 (ttp-170) REVERT: B 210 LEU cc_start: 0.8717 (tt) cc_final: 0.8324 (tt) REVERT: B 213 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8653 (pp) REVERT: B 365 MET cc_start: 0.7649 (mmt) cc_final: 0.7278 (tpp) REVERT: B 444 LEU cc_start: 0.9196 (tp) cc_final: 0.8980 (tp) outliers start: 23 outliers final: 17 residues processed: 140 average time/residue: 0.1871 time to fit residues: 35.9607 Evaluate side-chains 137 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 278 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 535 ARG 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 324 SER Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 367 HIS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 73 optimal weight: 0.4980 chunk 40 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 0.0270 chunk 84 optimal weight: 1.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7512 Z= 0.175 Angle : 0.671 9.697 10210 Z= 0.321 Chirality : 0.044 0.249 1200 Planarity : 0.004 0.043 1254 Dihedral : 9.673 74.425 1236 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.70 % Favored : 92.19 % Rotamer: Outliers : 3.40 % Allowed : 21.34 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.27), residues: 922 helix: -0.08 (0.23), residues: 505 sheet: -0.47 (0.76), residues: 52 loop : -2.65 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 405 HIS 0.004 0.001 HIS B 367 PHE 0.023 0.001 PHE B 474 TYR 0.017 0.001 TYR B 103 ARG 0.005 0.000 ARG B 421 *********************** 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 154 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 128 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 TRP cc_start: 0.7922 (m100) cc_final: 0.7431 (m-10) REVERT: A 192 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8522 (mm) REVERT: A 214 LEU cc_start: 0.7693 (mt) cc_final: 0.7477 (mt) REVERT: A 289 GLU cc_start: 0.8709 (mp0) cc_final: 0.8345 (mp0) REVERT: A 290 ASP cc_start: 0.8347 (m-30) cc_final: 0.7897 (t0) REVERT: A 300 LYS cc_start: 0.8626 (mmtt) cc_final: 0.8342 (mmtt) REVERT: A 415 HIS cc_start: 0.7548 (OUTLIER) cc_final: 0.7325 (t-170) REVERT: A 511 LYS cc_start: 0.8464 (mmtt) cc_final: 0.8193 (mmtt) REVERT: A 535 ARG cc_start: 0.6729 (OUTLIER) cc_final: 0.6468 (ttp-170) REVERT: A 559 ASP cc_start: 0.7761 (t0) cc_final: 0.7426 (m-30) REVERT: B 54 ASN cc_start: 0.8314 (m-40) cc_final: 0.7911 (p0) REVERT: B 58 ILE cc_start: 0.9075 (mt) cc_final: 0.8869 (mp) REVERT: B 191 LYS cc_start: 0.7392 (tmtt) cc_final: 0.7064 (tptm) REVERT: B 210 LEU cc_start: 0.8769 (tt) cc_final: 0.8364 (tt) REVERT: B 213 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8576 (pp) REVERT: B 291 LEU cc_start: 0.8272 (mp) cc_final: 0.7984 (mp) REVERT: B 365 MET cc_start: 0.7581 (mmt) cc_final: 0.7274 (tpp) outliers start: 26 outliers final: 17 residues processed: 141 average time/residue: 0.1880 time to fit residues: 35.7876 Evaluate side-chains 138 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 535 ARG 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 367 HIS Chi-restraints excluded: chain B residue 376 SER 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 500 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 64 optimal weight: 0.0980 chunk 49 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 87 optimal weight: 0.4980 chunk 54 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7512 Z= 0.178 Angle : 0.669 9.693 10210 Z= 0.320 Chirality : 0.043 0.269 1200 Planarity : 0.004 0.042 1254 Dihedral : 9.310 71.889 1236 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.92 % Favored : 91.97 % Rotamer: Outliers : 4.32 % Allowed : 20.94 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.27), residues: 922 helix: 0.11 (0.23), residues: 513 sheet: -0.44 (0.75), residues: 52 loop : -2.56 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 405 HIS 0.003 0.001 HIS B 367 PHE 0.021 0.001 PHE B 474 TYR 0.017 0.001 TYR B 103 ARG 0.005 0.000 ARG A 212 *********************** 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 156 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 123 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 TRP cc_start: 0.7830 (m100) cc_final: 0.7386 (m-10) REVERT: A 192 LEU cc_start: 0.8722 (mm) cc_final: 0.8470 (mm) REVERT: A 290 ASP cc_start: 0.8355 (m-30) cc_final: 0.7735 (t0) REVERT: A 300 LYS cc_start: 0.8613 (mmtt) cc_final: 0.8347 (mmtt) REVERT: A 511 LYS cc_start: 0.8464 (mmtt) cc_final: 0.8187 (mmtt) REVERT: A 535 ARG cc_start: 0.6738 (OUTLIER) cc_final: 0.6421 (ttp-170) REVERT: A 559 ASP cc_start: 0.7714 (t0) cc_final: 0.7477 (m-30) REVERT: B 54 ASN cc_start: 0.8325 (m-40) cc_final: 0.8124 (p0) REVERT: B 191 LYS cc_start: 0.7377 (tmtt) cc_final: 0.7057 (tptm) REVERT: B 210 LEU cc_start: 0.8701 (tt) cc_final: 0.8229 (tt) REVERT: B 213 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8568 (pp) REVERT: B 365 MET cc_start: 0.7582 (mmt) cc_final: 0.7281 (tpp) outliers start: 33 outliers final: 21 residues processed: 142 average time/residue: 0.1973 time to fit residues: 37.8984 Evaluate side-chains 138 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 278 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 535 ARG 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 366 ILE Chi-restraints excluded: chain B residue 367 HIS 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.3531 > 50: distance: 35 - 40: 23.088 distance: 40 - 41: 32.167 distance: 41 - 42: 59.390 distance: 41 - 44: 9.857 distance: 42 - 43: 39.254 distance: 42 - 45: 48.336 distance: 45 - 46: 16.299 distance: 46 - 47: 19.897 distance: 46 - 49: 24.184 distance: 47 - 48: 44.102 distance: 47 - 54: 24.892 distance: 49 - 50: 38.762 distance: 50 - 51: 55.531 distance: 51 - 52: 58.795 distance: 52 - 53: 43.643 distance: 54 - 55: 46.468 distance: 54 - 158: 37.635 distance: 55 - 56: 42.704 distance: 55 - 58: 47.610 distance: 56 - 57: 40.237 distance: 56 - 59: 41.505 distance: 57 - 155: 32.717 distance: 59 - 60: 39.788 distance: 59 - 216: 29.282 distance: 60 - 61: 26.480 distance: 60 - 63: 53.509 distance: 61 - 62: 17.690 distance: 61 - 67: 60.633 distance: 62 - 213: 33.001 distance: 63 - 64: 11.519 distance: 64 - 65: 55.760 distance: 64 - 66: 17.636 distance: 67 - 68: 40.030 distance: 68 - 69: 5.856 distance: 68 - 71: 14.552 distance: 69 - 70: 13.424 distance: 69 - 75: 32.713 distance: 71 - 72: 33.357 distance: 72 - 73: 48.942 distance: 72 - 74: 57.869 distance: 75 - 201: 35.966 distance: 76 - 77: 18.517 distance: 77 - 78: 41.615 distance: 77 - 83: 42.074 distance: 79 - 80: 41.956 distance: 80 - 81: 52.238 distance: 80 - 82: 53.432 distance: 83 - 84: 49.041 distance: 84 - 85: 33.297 distance: 84 - 87: 56.393 distance: 85 - 86: 48.057 distance: 85 - 91: 49.919 distance: 87 - 88: 32.633 distance: 88 - 89: 39.689 distance: 88 - 90: 27.598 distance: 91 - 92: 34.079 distance: 92 - 93: 43.644 distance: 92 - 95: 19.398 distance: 93 - 94: 43.969 distance: 93 - 97: 43.144 distance: 95 - 96: 31.394 distance: 97 - 98: 8.702 distance: 98 - 99: 49.546 distance: 98 - 101: 7.396 distance: 99 - 100: 43.066 distance: 99 - 104: 18.039 distance: 101 - 102: 48.839 distance: 101 - 103: 46.887 distance: 104 - 105: 9.713 distance: 105 - 106: 58.910 distance: 105 - 108: 59.453 distance: 106 - 107: 26.291 distance: 106 - 113: 24.951 distance: 108 - 109: 21.156 distance: 109 - 110: 16.493 distance: 110 - 111: 41.864 distance: 110 - 112: 43.776