Starting phenix.real_space_refine on Sat Aug 23 03:27:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x3e_22020/08_2025/6x3e_22020.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x3e_22020/08_2025/6x3e_22020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6x3e_22020/08_2025/6x3e_22020.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x3e_22020/08_2025/6x3e_22020.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x3e_22020/08_2025/6x3e_22020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x3e_22020/08_2025/6x3e_22020.map" } resolution = 3.42 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= 0.003 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 S 69 5.16 5 Na 3 4.78 5 C 6200 2.51 5 N 1505 2.21 5 O 1692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9469 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3193 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 11, 'TRANS': 407} Chain breaks: 2 Chain: "B" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3132 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 11, 'TRANS': 399} Chain breaks: 2 Chain: "C" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3132 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 11, 'TRANS': 399} Chain breaks: 2 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' NA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.71, per 1000 atoms: 0.18 Number of scatterers: 9469 At special positions: 0 Unit cell: (112.32, 108.16, 86.528, 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 69 16.00 Na 3 11.00 O 1692 8.00 N 1505 7.00 C 6200 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 224.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2296 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 5 sheets defined 80.8% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 18 through 42 removed outlier: 3.767A pdb=" N LEU A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR A 24 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 37 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ARG A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 53 through 81 removed outlier: 3.541A pdb=" N LEU A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix removed outlier: 3.845A pdb=" N VAL A 79 " --> pdb=" O MET A 75 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 117 removed outlier: 3.611A pdb=" N TYR A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE A 104 " --> pdb=" O CYS A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.546A pdb=" N ASP A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 211 through 228 Processing helix chain 'A' and resid 229 through 232 removed outlier: 3.580A pdb=" N LYS A 232 " --> pdb=" O MET A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 233 through 250 removed outlier: 3.529A pdb=" N VAL A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 266 removed outlier: 4.068A pdb=" N CYS A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.554A pdb=" N LEU A 263 " --> pdb=" O PRO A 259 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.705A pdb=" N PHE A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 299 removed outlier: 4.375A pdb=" N THR A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY A 292 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 309 removed outlier: 3.520A pdb=" N PHE A 306 " --> pdb=" O PRO A 302 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.682A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 removed outlier: 3.540A pdb=" N MET A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 351 through 365 removed outlier: 3.543A pdb=" N ARG A 356 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix removed outlier: 3.878A pdb=" N THR A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 384 removed outlier: 3.983A pdb=" N VAL A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 408 removed outlier: 3.823A pdb=" N ILE A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.595A pdb=" N VAL A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 436 removed outlier: 3.556A pdb=" N ASP A 432 " --> pdb=" O PRO A 429 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 433 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR A 434 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 435 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 466 removed outlier: 3.659A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 450 " --> pdb=" O PHE A 446 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'B' and resid 21 through 40 removed outlier: 3.502A pdb=" N ALA B 27 " --> pdb=" O SER B 23 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 53 removed outlier: 3.816A pdb=" N ALA B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 86 removed outlier: 3.723A pdb=" N LEU B 59 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS B 64 " --> pdb=" O MET B 60 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE B 66 " --> pdb=" O MET B 62 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU B 68 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Proline residue: B 69 - end of helix removed outlier: 3.706A pdb=" N SER B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 117 removed outlier: 3.641A pdb=" N VAL B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 removed outlier: 3.584A pdb=" N MET B 142 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 146 " --> pdb=" O MET B 142 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 158 Processing helix chain 'B' and resid 211 through 230 removed outlier: 3.551A pdb=" N GLY B 227 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY B 230 " --> pdb=" O ILE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 273 Proline residue: B 259 - end of helix removed outlier: 3.549A pdb=" N LEU B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 299 removed outlier: 3.729A pdb=" N THR B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 309 removed outlier: 3.698A pdb=" N VAL B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 319 removed outlier: 3.524A pdb=" N PHE B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY B 319 " --> pdb=" O ARG B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 330 removed outlier: 3.692A pdb=" N LEU B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR B 326 " --> pdb=" O GLN B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 349 removed outlier: 4.141A pdb=" N ARG B 342 " --> pdb=" O PRO B 338 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN B 347 " --> pdb=" O CYS B 343 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 366 removed outlier: 4.172A pdb=" N PHE B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 359 " --> pdb=" O THR B 355 " (cutoff:3.500A) Proline residue: B 360 - end of helix removed outlier: 4.410A pdb=" N THR B 364 " --> pdb=" O PRO B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 385 removed outlier: 3.567A pdb=" N VAL B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 401 Processing helix chain 'B' and resid 412 through 415 removed outlier: 3.881A pdb=" N GLY B 415 " --> pdb=" O PRO B 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 412 through 415' Processing helix chain 'B' and resid 416 through 427 removed outlier: 3.780A pdb=" N VAL B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 432 removed outlier: 3.572A pdb=" N ASP B 432 " --> pdb=" O PRO B 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 429 through 432' Processing helix chain 'B' and resid 433 through 438 Processing helix chain 'B' and resid 439 through 466 removed outlier: 3.613A pdb=" N LEU B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ARG B 445 " --> pdb=" O TRP B 441 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N PHE B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR B 448 " --> pdb=" O ASP B 444 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET B 449 " --> pdb=" O ARG B 445 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP B 455 " --> pdb=" O ASN B 451 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR B 459 " --> pdb=" O ASP B 455 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU B 463 " --> pdb=" O THR B 459 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS B 464 " --> pdb=" O GLY B 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 40 removed outlier: 3.601A pdb=" N ALA C 27 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG C 39 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 53 removed outlier: 3.762A pdb=" N ALA C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 86 removed outlier: 3.657A pdb=" N LEU C 59 " --> pdb=" O PRO C 55 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS C 64 " --> pdb=" O MET C 60 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE C 66 " --> pdb=" O MET C 62 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU C 68 " --> pdb=" O LYS C 64 " (cutoff:3.500A) Proline residue: C 69 - end of helix removed outlier: 3.747A pdb=" N SER C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 117 removed outlier: 3.612A pdb=" N VAL C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.537A pdb=" N MET C 142 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE C 146 " --> pdb=" O MET C 142 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE C 150 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 158 Processing helix chain 'C' and resid 211 through 230 removed outlier: 3.558A pdb=" N GLY C 227 " --> pdb=" O GLY C 223 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY C 230 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 273 removed outlier: 3.503A pdb=" N GLN C 252 " --> pdb=" O MET C 248 " (cutoff:3.500A) Proline residue: C 259 - end of helix removed outlier: 3.676A pdb=" N PHE C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU C 272 " --> pdb=" O GLY C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 299 removed outlier: 3.716A pdb=" N THR C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 309 removed outlier: 3.725A pdb=" N VAL C 308 " --> pdb=" O ILE C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 319 Processing helix chain 'C' and resid 320 through 330 removed outlier: 3.621A pdb=" N THR C 326 " --> pdb=" O GLN C 322 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 349 removed outlier: 4.243A pdb=" N ARG C 342 " --> pdb=" O PRO C 338 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU C 345 " --> pdb=" O PHE C 341 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN C 347 " --> pdb=" O CYS C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 366 removed outlier: 4.177A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C 359 " --> pdb=" O THR C 355 " (cutoff:3.500A) Proline residue: C 360 - end of helix removed outlier: 4.274A pdb=" N THR C 364 " --> pdb=" O PRO C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 385 removed outlier: 3.558A pdb=" N VAL C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 401 removed outlier: 3.622A pdb=" N THR C 396 " --> pdb=" O GLY C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 412 through 415 removed outlier: 3.911A pdb=" N GLY C 415 " --> pdb=" O PRO C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 416 through 427 removed outlier: 3.777A pdb=" N VAL C 426 " --> pdb=" O VAL C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 432 removed outlier: 3.591A pdb=" N ASP C 432 " --> pdb=" O PRO C 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 429 through 432' Processing helix chain 'C' and resid 433 through 438 Processing helix chain 'C' and resid 439 through 466 removed outlier: 3.598A pdb=" N LEU C 443 " --> pdb=" O VAL C 439 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ARG C 445 " --> pdb=" O TRP C 441 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N PHE C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR C 448 " --> pdb=" O ASP C 444 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET C 449 " --> pdb=" O ARG C 445 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP C 455 " --> pdb=" O ASN C 451 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR C 459 " --> pdb=" O ASP C 455 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU C 463 " --> pdb=" O THR C 459 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS C 464 " --> pdb=" O GLY C 460 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 Processing sheet with id=AA2, first strand: chain 'B' and resid 160 through 161 Processing sheet with id=AA3, first strand: chain 'B' and resid 164 through 167 Processing sheet with id=AA4, first strand: chain 'C' and resid 160 through 161 Processing sheet with id=AA5, first strand: chain 'C' and resid 164 through 167 595 hydrogen bonds defined for protein. 1761 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: 1.04 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1816 1.33 - 1.45: 1998 1.45 - 1.57: 5666 1.57 - 1.69: 0 1.69 - 1.81: 123 Bond restraints: 9603 Sorted by residual: bond pdb=" N LEU C 372 " pdb=" CA LEU C 372 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.17e+00 bond pdb=" N LEU B 30 " pdb=" CA LEU B 30 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.33e-02 5.65e+03 4.97e+00 bond pdb=" N CYS A 100 " pdb=" CA CYS A 100 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.31e-02 5.83e+03 4.78e+00 bond pdb=" N LYS A 269 " pdb=" CA LYS A 269 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.28e-02 6.10e+03 4.65e+00 bond pdb=" N LEU B 372 " pdb=" CA LEU B 372 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.52e+00 ... (remaining 9598 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 12305 1.74 - 3.47: 604 3.47 - 5.20: 71 5.20 - 6.94: 30 6.94 - 8.67: 17 Bond angle restraints: 13027 Sorted by residual: angle pdb=" N GLN A 122 " pdb=" CA GLN A 122 " pdb=" C GLN A 122 " ideal model delta sigma weight residual 110.44 102.53 7.91 1.20e+00 6.94e-01 4.35e+01 angle pdb=" CA LYS A 123 " pdb=" C LYS A 123 " pdb=" N VAL A 124 " ideal model delta sigma weight residual 117.17 122.37 -5.20 1.18e+00 7.18e-01 1.94e+01 angle pdb=" C VAL A 120 " pdb=" N THR A 121 " pdb=" CA THR A 121 " ideal model delta sigma weight residual 122.40 128.71 -6.31 1.45e+00 4.76e-01 1.89e+01 angle pdb=" CA GLN A 413 " pdb=" CB GLN A 413 " pdb=" CG GLN A 413 " ideal model delta sigma weight residual 114.10 122.73 -8.63 2.00e+00 2.50e-01 1.86e+01 angle pdb=" C ASP C 388 " pdb=" N LEU C 389 " pdb=" CA LEU C 389 " ideal model delta sigma weight residual 121.54 128.96 -7.42 1.91e+00 2.74e-01 1.51e+01 ... (remaining 13022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 5202 17.90 - 35.79: 437 35.79 - 53.68: 84 53.68 - 71.58: 17 71.58 - 89.47: 10 Dihedral angle restraints: 5750 sinusoidal: 2192 harmonic: 3558 Sorted by residual: dihedral pdb=" CA GLU A 272 " pdb=" C GLU A 272 " pdb=" N VAL A 273 " pdb=" CA VAL A 273 " ideal model delta harmonic sigma weight residual -180.00 -158.11 -21.89 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA LEU B 384 " pdb=" C LEU B 384 " pdb=" N ASN B 385 " pdb=" CA ASN B 385 " ideal model delta harmonic sigma weight residual 180.00 160.31 19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA LEU C 384 " pdb=" C LEU C 384 " pdb=" N ASN C 385 " pdb=" CA ASN C 385 " ideal model delta harmonic sigma weight residual 180.00 160.67 19.33 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 5747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1388 0.070 - 0.141: 237 0.141 - 0.211: 21 0.211 - 0.281: 7 0.281 - 0.352: 1 Chirality restraints: 1654 Sorted by residual: chirality pdb=" CB VAL A 411 " pdb=" CA VAL A 411 " pdb=" CG1 VAL A 411 " pdb=" CG2 VAL A 411 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CB ILE A 278 " pdb=" CA ILE A 278 " pdb=" CG1 ILE A 278 " pdb=" CG2 ILE A 278 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB VAL A 426 " pdb=" CA VAL A 426 " pdb=" CG1 VAL A 426 " pdb=" CG2 VAL A 426 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 1651 not shown) Planarity restraints: 1585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 301 " -0.047 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO B 302 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 302 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 302 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 301 " -0.046 5.00e-02 4.00e+02 6.93e-02 7.68e+00 pdb=" N PRO C 302 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 302 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 302 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 301 " -0.042 5.00e-02 4.00e+02 6.21e-02 6.17e+00 pdb=" N PRO A 302 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 302 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 302 " -0.035 5.00e-02 4.00e+02 ... (remaining 1582 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 82 2.65 - 3.21: 8339 3.21 - 3.77: 14585 3.77 - 4.34: 20502 4.34 - 4.90: 33380 Nonbonded interactions: 76888 Sorted by model distance: nonbonded pdb=" OD1 ASP A 368 " pdb="NA NA A 603 " model vdw 2.083 2.470 nonbonded pdb=" OD1 ASN A 366 " pdb="NA NA A 603 " model vdw 2.228 2.470 nonbonded pdb=" O ASN A 366 " pdb="NA NA A 601 " model vdw 2.293 2.470 nonbonded pdb=" O PRO B 69 " pdb=" OG SER B 73 " model vdw 2.301 3.040 nonbonded pdb=" O ALA A 456 " pdb=" OG1 THR A 459 " model vdw 2.317 3.040 ... (remaining 76883 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 'A' and (resid 19 through 121 or resid 137 through 474)) selection = chain 'B' selection = chain 'C' } 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: 1.270 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: 0.030 Set scattering table: 0.020 Process input model: 7.150 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 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 : 0.006 0.063 9603 Z= 0.245 Angle : 0.904 8.675 13027 Z= 0.500 Chirality : 0.055 0.352 1654 Planarity : 0.007 0.070 1585 Dihedral : 14.423 89.473 3454 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 11.31 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -6.06 (0.15), residues: 1223 helix: -4.16 (0.08), residues: 954 sheet: -2.40 (0.81), residues: 54 loop : -1.89 (0.34), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 39 TYR 0.024 0.002 TYR C 373 PHE 0.022 0.003 PHE B 159 TRP 0.008 0.001 TRP C 276 HIS 0.003 0.001 HIS C 41 Details of bonding type rmsd covalent geometry : bond 0.00559 ( 9603) covalent geometry : angle 0.90410 (13027) hydrogen bonds : bond 0.29788 ( 595) hydrogen bonds : angle 10.37458 ( 1761) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.9037 (mp) cc_final: 0.8808 (tp) REVERT: A 112 LEU cc_start: 0.8818 (mt) cc_final: 0.8537 (mt) REVERT: A 277 GLU cc_start: 0.8270 (tp30) cc_final: 0.7885 (tp30) REVERT: B 19 TRP cc_start: 0.7039 (t60) cc_final: 0.5389 (m100) REVERT: B 93 ARG cc_start: 0.8504 (mtt180) cc_final: 0.7722 (mtt180) REVERT: B 140 ASP cc_start: 0.7915 (m-30) cc_final: 0.7557 (m-30) REVERT: B 228 LYS cc_start: 0.8135 (mmtt) cc_final: 0.7889 (mmmt) REVERT: B 280 ARG cc_start: 0.8240 (ttp80) cc_final: 0.7459 (tpt170) REVERT: B 354 ILE cc_start: 0.8661 (mt) cc_final: 0.8310 (mm) REVERT: B 444 ASP cc_start: 0.8898 (t0) cc_final: 0.8466 (t0) REVERT: B 465 LEU cc_start: 0.8761 (mt) cc_final: 0.8457 (mt) REVERT: C 97 TYR cc_start: 0.9153 (t80) cc_final: 0.8689 (t80) REVERT: C 397 ILE cc_start: 0.9506 (mm) cc_final: 0.9256 (mm) REVERT: C 446 PHE cc_start: 0.8519 (m-80) cc_final: 0.8242 (m-80) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.0747 time to fit residues: 31.0653 Evaluate side-chains 198 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 ASN B 348 ASN C 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.130273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.095577 restraints weight = 15406.064| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.04 r_work: 0.2959 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9603 Z= 0.123 Angle : 0.601 8.191 13027 Z= 0.305 Chirality : 0.040 0.148 1654 Planarity : 0.005 0.037 1585 Dihedral : 4.580 18.303 1302 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.21 % Allowed : 16.20 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -3.08 (0.20), residues: 1223 helix: -1.78 (0.14), residues: 953 sheet: -2.19 (0.77), residues: 54 loop : -2.05 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 342 TYR 0.010 0.001 TYR B 305 PHE 0.019 0.002 PHE C 306 TRP 0.030 0.002 TRP B 441 HIS 0.000 0.000 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 9603) covalent geometry : angle 0.60070 (13027) hydrogen bonds : bond 0.04346 ( 595) hydrogen bonds : angle 4.98315 ( 1761) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 224 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: A 30 LEU cc_start: 0.9056 (mp) cc_final: 0.8750 (tp) REVERT: A 40 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: A 112 LEU cc_start: 0.8353 (mt) cc_final: 0.8103 (mt) REVERT: A 205 MET cc_start: 0.8566 (pmm) cc_final: 0.8333 (ptm) REVERT: A 277 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7269 (tp30) REVERT: A 463 GLU cc_start: 0.8569 (tt0) cc_final: 0.7876 (tm-30) REVERT: A 473 MET cc_start: 0.4468 (mtt) cc_final: 0.4162 (ptp) REVERT: B 19 TRP cc_start: 0.7199 (t60) cc_final: 0.5420 (m100) REVERT: B 220 LEU cc_start: 0.9231 (tt) cc_final: 0.8352 (mt) REVERT: B 320 MET cc_start: 0.8357 (mmm) cc_final: 0.8044 (mpp) REVERT: B 354 ILE cc_start: 0.8641 (mt) cc_final: 0.8347 (mm) REVERT: B 368 ASP cc_start: 0.9265 (m-30) cc_final: 0.8956 (m-30) REVERT: B 449 MET cc_start: 0.8447 (tmm) cc_final: 0.8173 (tmm) REVERT: C 97 TYR cc_start: 0.8971 (t80) cc_final: 0.8635 (t80) REVERT: C 206 TYR cc_start: 0.8648 (OUTLIER) cc_final: 0.7502 (t80) REVERT: C 446 PHE cc_start: 0.8872 (m-80) cc_final: 0.8656 (m-80) outliers start: 23 outliers final: 13 residues processed: 235 average time/residue: 0.0588 time to fit residues: 20.5927 Evaluate side-chains 193 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 373 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 11 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 96 optimal weight: 0.1980 chunk 76 optimal weight: 0.0970 chunk 50 optimal weight: 0.5980 chunk 22 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 118 optimal weight: 0.2980 chunk 7 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.131495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.097212 restraints weight = 15245.572| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.98 r_work: 0.2990 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9603 Z= 0.103 Angle : 0.541 8.215 13027 Z= 0.270 Chirality : 0.038 0.152 1654 Planarity : 0.004 0.028 1585 Dihedral : 4.145 17.668 1302 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.40 % Allowed : 19.18 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.24 (0.23), residues: 1223 helix: -0.33 (0.17), residues: 947 sheet: -1.86 (0.77), residues: 54 loop : -2.04 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 342 TYR 0.014 0.001 TYR A 305 PHE 0.020 0.001 PHE B 357 TRP 0.030 0.002 TRP B 441 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 9603) covalent geometry : angle 0.54134 (13027) hydrogen bonds : bond 0.03524 ( 595) hydrogen bonds : angle 4.36734 ( 1761) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.9015 (mp) cc_final: 0.8679 (tp) REVERT: A 277 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8274 (tp30) REVERT: A 345 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: A 455 ASP cc_start: 0.8096 (m-30) cc_final: 0.7817 (m-30) REVERT: A 473 MET cc_start: 0.4342 (mtt) cc_final: 0.4041 (ptp) REVERT: B 19 TRP cc_start: 0.7279 (t60) cc_final: 0.5391 (m100) REVERT: B 220 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8319 (mt) REVERT: B 354 ILE cc_start: 0.8582 (mt) cc_final: 0.8356 (mm) REVERT: B 367 MET cc_start: 0.8473 (mmm) cc_final: 0.8134 (mmp) REVERT: B 413 GLN cc_start: 0.7570 (mm-40) cc_final: 0.7291 (mm110) REVERT: B 449 MET cc_start: 0.8350 (tmm) cc_final: 0.8027 (tmm) REVERT: C 97 TYR cc_start: 0.8903 (t80) cc_final: 0.8562 (t80) REVERT: C 206 TYR cc_start: 0.8587 (OUTLIER) cc_final: 0.7602 (t80) outliers start: 25 outliers final: 9 residues processed: 219 average time/residue: 0.0583 time to fit residues: 18.9831 Evaluate side-chains 187 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 174 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 373 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 20 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 chunk 118 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 99 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 ASN B 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.130638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.095594 restraints weight = 15334.186| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.05 r_work: 0.2959 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9603 Z= 0.107 Angle : 0.534 10.171 13027 Z= 0.266 Chirality : 0.039 0.152 1654 Planarity : 0.003 0.027 1585 Dihedral : 4.006 18.022 1302 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.49 % Allowed : 20.04 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.34 (0.25), residues: 1223 helix: 0.30 (0.17), residues: 954 sheet: -1.59 (0.78), residues: 54 loop : -1.79 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 342 TYR 0.017 0.001 TYR C 98 PHE 0.021 0.001 PHE A 306 TRP 0.032 0.002 TRP B 441 HIS 0.001 0.000 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 9603) covalent geometry : angle 0.53394 (13027) hydrogen bonds : bond 0.03275 ( 595) hydrogen bonds : angle 4.21833 ( 1761) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8276 (tp30) REVERT: A 455 ASP cc_start: 0.8008 (m-30) cc_final: 0.7758 (m-30) REVERT: A 473 MET cc_start: 0.4366 (mtt) cc_final: 0.4072 (ptp) REVERT: B 19 TRP cc_start: 0.7333 (t60) cc_final: 0.5416 (m100) REVERT: B 220 LEU cc_start: 0.9210 (tt) cc_final: 0.8280 (mt) REVERT: B 280 ARG cc_start: 0.8541 (ttp80) cc_final: 0.7574 (tpt170) REVERT: B 354 ILE cc_start: 0.8634 (mt) cc_final: 0.8407 (mm) REVERT: B 367 MET cc_start: 0.8452 (mmm) cc_final: 0.8136 (mmp) REVERT: B 449 MET cc_start: 0.8355 (tmm) cc_final: 0.8031 (tmm) REVERT: B 467 LYS cc_start: 0.8208 (ptmt) cc_final: 0.7603 (pttm) REVERT: B 472 GLN cc_start: 0.7328 (mt0) cc_final: 0.7041 (mm110) REVERT: C 206 TYR cc_start: 0.8604 (OUTLIER) cc_final: 0.7520 (t80) REVERT: C 320 MET cc_start: 0.7800 (mmm) cc_final: 0.7549 (mmm) REVERT: C 399 ILE cc_start: 0.9407 (OUTLIER) cc_final: 0.9194 (mp) outliers start: 26 outliers final: 13 residues processed: 194 average time/residue: 0.0789 time to fit residues: 22.3996 Evaluate side-chains 177 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 399 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 95 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 94 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.127918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.092604 restraints weight = 15300.138| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.97 r_work: 0.2922 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9603 Z= 0.147 Angle : 0.565 10.299 13027 Z= 0.282 Chirality : 0.040 0.143 1654 Planarity : 0.003 0.031 1585 Dihedral : 4.033 18.751 1302 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.45 % Allowed : 19.46 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.03 (0.25), residues: 1223 helix: 0.50 (0.17), residues: 967 sheet: -1.47 (0.76), residues: 54 loop : -1.65 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 342 TYR 0.017 0.001 TYR C 98 PHE 0.022 0.002 PHE B 357 TRP 0.034 0.002 TRP B 441 HIS 0.002 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9603) covalent geometry : angle 0.56483 (13027) hydrogen bonds : bond 0.03540 ( 595) hydrogen bonds : angle 4.30727 ( 1761) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 277 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8028 (tp30) REVERT: A 285 TYR cc_start: 0.7851 (t80) cc_final: 0.7519 (t80) REVERT: A 473 MET cc_start: 0.4647 (mtt) cc_final: 0.4217 (ptp) REVERT: B 19 TRP cc_start: 0.7357 (t60) cc_final: 0.5416 (m100) REVERT: B 164 THR cc_start: 0.9027 (OUTLIER) cc_final: 0.8785 (p) REVERT: B 220 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8268 (mt) REVERT: B 280 ARG cc_start: 0.8553 (ttp80) cc_final: 0.7706 (tpt170) REVERT: B 354 ILE cc_start: 0.8608 (mt) cc_final: 0.8405 (mm) REVERT: B 447 ARG cc_start: 0.8538 (mtm-85) cc_final: 0.8113 (mtm-85) REVERT: B 449 MET cc_start: 0.8339 (tmm) cc_final: 0.7997 (tmm) REVERT: B 472 GLN cc_start: 0.7415 (mt0) cc_final: 0.7116 (mm110) REVERT: C 206 TYR cc_start: 0.8661 (OUTLIER) cc_final: 0.7290 (t80) REVERT: C 320 MET cc_start: 0.7812 (mmm) cc_final: 0.7536 (mmm) REVERT: C 399 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.9191 (mp) outliers start: 36 outliers final: 24 residues processed: 195 average time/residue: 0.0592 time to fit residues: 17.5143 Evaluate side-chains 193 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 276 TRP Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 19 TRP Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 367 MET Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 399 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.0811 > 50: distance: 15 - 31: 25.720 distance: 20 - 39: 11.951 distance: 24 - 44: 10.584 distance: 29 - 31: 28.220 distance: 30 - 52: 15.981 distance: 31 - 32: 33.343 distance: 32 - 33: 12.014 distance: 32 - 35: 45.323 distance: 33 - 34: 27.694 distance: 33 - 39: 21.195 distance: 34 - 62: 10.430 distance: 35 - 36: 42.813 distance: 36 - 37: 7.653 distance: 36 - 38: 27.961 distance: 39 - 40: 23.360 distance: 40 - 41: 10.423 distance: 40 - 43: 22.912 distance: 41 - 42: 26.833 distance: 41 - 44: 26.676 distance: 42 - 68: 46.669 distance: 44 - 45: 15.248 distance: 45 - 46: 29.241 distance: 45 - 48: 35.741 distance: 46 - 47: 39.862 distance: 46 - 52: 48.842 distance: 47 - 76: 21.773 distance: 48 - 49: 30.349 distance: 48 - 50: 25.357 distance: 49 - 51: 13.768 distance: 52 - 53: 38.552 distance: 53 - 54: 14.881 distance: 53 - 56: 14.223 distance: 54 - 55: 41.684 distance: 56 - 57: 18.714 distance: 57 - 58: 16.237 distance: 57 - 59: 43.783 distance: 58 - 60: 11.357 distance: 59 - 61: 16.732 distance: 60 - 61: 35.678 distance: 62 - 63: 18.141 distance: 63 - 64: 24.147 distance: 63 - 66: 15.787 distance: 64 - 65: 18.084 distance: 64 - 68: 22.782 distance: 66 - 67: 16.046 distance: 68 - 69: 27.233 distance: 69 - 70: 25.897 distance: 69 - 72: 24.988 distance: 70 - 71: 18.369 distance: 70 - 76: 36.285 distance: 72 - 73: 26.844 distance: 72 - 74: 35.520 distance: 73 - 75: 38.314 distance: 76 - 77: 34.179 distance: 77 - 78: 40.408 distance: 77 - 80: 40.378 distance: 78 - 79: 17.733 distance: 78 - 83: 13.585 distance: 80 - 81: 15.064 distance: 80 - 82: 5.954 distance: 83 - 84: 20.122 distance: 84 - 85: 23.142 distance: 84 - 87: 35.305 distance: 85 - 86: 28.916 distance: 85 - 91: 48.509 distance: 86 - 114: 12.935 distance: 87 - 88: 16.470 distance: 87 - 89: 17.080 distance: 88 - 90: 7.026 distance: 91 - 92: 46.557 distance: 92 - 93: 5.767 distance: 92 - 95: 40.476 distance: 93 - 94: 35.915 distance: 93 - 99: 17.933 distance: 94 - 120: 13.883 distance: 95 - 96: 18.219 distance: 96 - 97: 11.762 distance: 96 - 98: 24.566 distance: 99 - 100: 16.448 distance: 99 - 105: 27.981 distance: 100 - 101: 5.470 distance: 100 - 103: 22.485 distance: 101 - 102: 15.269 distance: 101 - 106: 13.363 distance: 102 - 125: 3.664 distance: 103 - 104: 11.921 distance: 104 - 105: 17.891