Starting phenix.real_space_refine on Fri Jun 13 11:09:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jpp_22418/06_2025/7jpp_22418.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jpp_22418/06_2025/7jpp_22418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jpp_22418/06_2025/7jpp_22418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jpp_22418/06_2025/7jpp_22418.map" model { file = "/net/cci-nas-00/data/ceres_data/7jpp_22418/06_2025/7jpp_22418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jpp_22418/06_2025/7jpp_22418.cif" } resolution = 3.7 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= 0.003 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 69 5.16 5 C 9547 2.51 5 N 2516 2.21 5 O 2732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14872 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 790 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "B" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2515 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 8, 'TRANS': 298} Chain: "C" Number of atoms: 4886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4886 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 24, 'TRANS': 572} Chain breaks: 7 Chain: "D" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3305 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 13, 'TRANS': 392} Chain breaks: 1 Chain: "E" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3312 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 19, 'TRANS': 386} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.37, per 1000 atoms: 0.56 Number of scatterers: 14872 At special positions: 0 Unit cell: (93.09, 119.84, 154.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 69 16.00 P 6 15.00 Mg 2 11.99 O 2732 8.00 N 2516 7.00 C 9547 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: 3.12 Conformation dependent library (CDL) restraints added in 1.7 seconds 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3528 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 7 sheets defined 64.0% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 761 through 769 removed outlier: 3.602A pdb=" N THR A 765 " --> pdb=" O SER A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 789 Processing helix chain 'A' and resid 795 through 810 removed outlier: 3.664A pdb=" N ALA A 804 " --> pdb=" O SER A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 829 removed outlier: 3.602A pdb=" N ALA A 821 " --> pdb=" O SER A 817 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS A 829 " --> pdb=" O HIS A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 860 removed outlier: 4.176A pdb=" N ASP A 860 " --> pdb=" O TYR A 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 283 through 297 removed outlier: 3.937A pdb=" N GLN B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASN B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLN B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN B 293 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU B 297 " --> pdb=" O GLN B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 307 Processing helix chain 'B' and resid 319 through 330 Processing helix chain 'B' and resid 347 through 358 removed outlier: 4.120A pdb=" N GLU B 358 " --> pdb=" O SER B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 382 Processing helix chain 'B' and resid 397 through 401 Processing helix chain 'B' and resid 402 through 414 Processing helix chain 'B' and resid 428 through 432 Processing helix chain 'B' and resid 436 through 441 removed outlier: 3.717A pdb=" N LEU B 440 " --> pdb=" O ALA B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 483 removed outlier: 4.186A pdb=" N SER B 483 " --> pdb=" O HIS B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 503 removed outlier: 3.713A pdb=" N LEU B 495 " --> pdb=" O ILE B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 523 removed outlier: 3.519A pdb=" N ALA B 523 " --> pdb=" O GLN B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 542 removed outlier: 3.627A pdb=" N HIS B 542 " --> pdb=" O GLU B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 573 Processing helix chain 'C' and resid 25 through 31 removed outlier: 4.037A pdb=" N TYR C 29 " --> pdb=" O PRO C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 66 removed outlier: 4.034A pdb=" N PHE C 44 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU C 45 " --> pdb=" O LYS C 41 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 81 removed outlier: 3.575A pdb=" N PHE C 70 " --> pdb=" O ASN C 66 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 87 Processing helix chain 'C' and resid 113 through 129 removed outlier: 3.861A pdb=" N GLY C 119 " --> pdb=" O ASP C 115 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C 121 " --> pdb=" O THR C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 159 Processing helix chain 'C' and resid 180 through 192 Processing helix chain 'C' and resid 226 through 240 removed outlier: 3.563A pdb=" N LEU C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N HIS C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 263 removed outlier: 4.126A pdb=" N HIS C 260 " --> pdb=" O PRO C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 269 removed outlier: 3.521A pdb=" N SER C 269 " --> pdb=" O HIS C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 293 Processing helix chain 'C' and resid 303 through 316 removed outlier: 3.563A pdb=" N PHE C 314 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 339 removed outlier: 3.737A pdb=" N PHE C 324 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN C 339 " --> pdb=" O HIS C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 345 removed outlier: 3.714A pdb=" N VAL C 343 " --> pdb=" O PRO C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 357 removed outlier: 3.622A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 368 Processing helix chain 'C' and resid 369 through 378 removed outlier: 3.712A pdb=" N GLU C 377 " --> pdb=" O ARG C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 390 removed outlier: 3.816A pdb=" N VAL C 385 " --> pdb=" O SER C 381 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN C 390 " --> pdb=" O ALA C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 426 removed outlier: 3.536A pdb=" N LEU C 394 " --> pdb=" O ASN C 390 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN C 399 " --> pdb=" O LYS C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 445 removed outlier: 3.580A pdb=" N LEU C 438 " --> pdb=" O GLN C 434 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS C 445 " --> pdb=" O THR C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 462 removed outlier: 4.297A pdb=" N SER C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL C 456 " --> pdb=" O GLU C 452 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET C 462 " --> pdb=" O GLN C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 482 Processing helix chain 'C' and resid 487 through 501 removed outlier: 3.912A pdb=" N PHE C 501 " --> pdb=" O PHE C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 568 removed outlier: 3.633A pdb=" N LEU C 568 " --> pdb=" O VAL C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 574 Processing helix chain 'C' and resid 584 through 593 removed outlier: 3.641A pdb=" N LEU C 588 " --> pdb=" O ALA C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 606 removed outlier: 3.859A pdb=" N LEU C 600 " --> pdb=" O PRO C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 638 removed outlier: 3.812A pdb=" N LEU C 638 " --> pdb=" O TYR C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 661 Processing helix chain 'C' and resid 675 through 690 removed outlier: 3.689A pdb=" N LEU C 690 " --> pdb=" O SER C 686 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 29 Processing helix chain 'D' and resid 40 through 57 Processing helix chain 'D' and resid 72 through 87 removed outlier: 3.543A pdb=" N ILE D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 118 removed outlier: 3.520A pdb=" N LEU D 118 " --> pdb=" O ILE D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 removed outlier: 3.965A pdb=" N GLY D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 141 Processing helix chain 'D' and resid 160 through 166 Processing helix chain 'D' and resid 170 through 183 Processing helix chain 'D' and resid 197 through 202 removed outlier: 3.856A pdb=" N LEU D 202 " --> pdb=" O ILE D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 210 Processing helix chain 'D' and resid 222 through 234 Processing helix chain 'D' and resid 242 through 258 removed outlier: 3.842A pdb=" N LYS D 248 " --> pdb=" O VAL D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 273 removed outlier: 3.813A pdb=" N ILE D 272 " --> pdb=" O LYS D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 290 removed outlier: 3.786A pdb=" N LEU D 279 " --> pdb=" O ASN D 275 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL D 290 " --> pdb=" O ALA D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 310 removed outlier: 3.704A pdb=" N LEU D 302 " --> pdb=" O THR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 320 removed outlier: 3.567A pdb=" N GLY D 320 " --> pdb=" O ASN D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 339 Processing helix chain 'D' and resid 345 through 360 removed outlier: 3.584A pdb=" N VAL D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 382 removed outlier: 3.598A pdb=" N VAL D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 417 removed outlier: 3.589A pdb=" N LYS D 417 " --> pdb=" O ASN D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 431 Processing helix chain 'E' and resid 11 through 23 Processing helix chain 'E' and resid 43 through 55 removed outlier: 3.607A pdb=" N GLU E 55 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 85 Processing helix chain 'E' and resid 98 through 111 removed outlier: 3.779A pdb=" N THR E 111 " --> pdb=" O LYS E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 116 removed outlier: 3.905A pdb=" N LYS E 116 " --> pdb=" O GLU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 131 removed outlier: 3.882A pdb=" N TYR E 129 " --> pdb=" O LYS E 126 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG E 131 " --> pdb=" O GLU E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 143 Processing helix chain 'E' and resid 143 through 149 Processing helix chain 'E' and resid 161 through 165 removed outlier: 3.651A pdb=" N LYS E 164 " --> pdb=" O VAL E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 192 Processing helix chain 'E' and resid 200 through 216 Processing helix chain 'E' and resid 221 through 232 Processing helix chain 'E' and resid 232 through 237 Processing helix chain 'E' and resid 237 through 243 Processing helix chain 'E' and resid 249 through 267 Proline residue: E 259 - end of helix removed outlier: 4.010A pdb=" N LYS E 262 " --> pdb=" O GLU E 258 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS E 263 " --> pdb=" O PRO E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 284 Processing helix chain 'E' and resid 303 through 318 removed outlier: 3.811A pdb=" N LEU E 315 " --> pdb=" O ILE E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 329 Processing helix chain 'E' and resid 358 through 370 Processing helix chain 'E' and resid 377 through 390 removed outlier: 3.696A pdb=" N PHE E 381 " --> pdb=" O THR E 377 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR E 389 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 423 removed outlier: 3.666A pdb=" N ILE E 416 " --> pdb=" O SER E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 432 removed outlier: 3.956A pdb=" N TYR E 430 " --> pdb=" O ASP E 426 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR E 432 " --> pdb=" O ILE E 428 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 793 through 794 removed outlier: 3.928A pdb=" N ARG A 846 " --> pdb=" O LEU A 833 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 833 " --> pdb=" O ARG A 846 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 443 through 447 removed outlier: 6.558A pdb=" N ASN B 310 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N TYR B 446 " --> pdb=" O ASN B 310 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL B 312 " --> pdb=" O TYR B 446 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE B 311 " --> pdb=" O ALA B 422 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE B 424 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU B 313 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 421 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER B 423 " --> pdb=" O ILE B 392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 133 through 136 removed outlier: 6.581A pdb=" N VAL C 215 " --> pdb=" O ILE C 247 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ILE C 249 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL C 217 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N GLY C 251 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU C 219 " --> pdb=" O GLY C 251 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N PHE C 250 " --> pdb=" O PRO C 101 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA C 103 " --> pdb=" O PHE C 250 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE C 252 " --> pdb=" O ALA C 103 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU C 105 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 61 through 66 removed outlier: 6.737A pdb=" N LEU D 95 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE D 157 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL D 97 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ASP D 159 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU D 99 " --> pdb=" O ASP D 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 385 through 387 Processing sheet with id=AA6, first strand: chain 'E' and resid 58 through 62 removed outlier: 6.212A pdb=" N VAL E 59 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ASP E 125 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL E 61 " --> pdb=" O ASP E 125 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE E 33 " --> pdb=" O PHE E 156 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N SER E 158 " --> pdb=" O ILE E 33 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE E 35 " --> pdb=" O SER E 158 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N SER E 32 " --> pdb=" O PHE E 175 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N LEU E 177 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE E 34 " --> pdb=" O LEU E 177 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N PHE E 179 " --> pdb=" O PHE E 34 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N TYR E 36 " --> pdb=" O PHE E 179 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 393 through 394 755 hydrogen bonds defined for protein. 2223 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: 3.91 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4256 1.34 - 1.46: 2834 1.46 - 1.58: 7980 1.58 - 1.70: 10 1.70 - 1.82: 104 Bond restraints: 15184 Sorted by residual: bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.42e+01 bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.87e+01 bond pdb=" C5 ATP D 901 " pdb=" C6 ATP D 901 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.33e+01 bond pdb=" C5 ATP E 501 " pdb=" C6 ATP E 501 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.93e+01 bond pdb=" C5 ATP E 501 " pdb=" N7 ATP E 501 " ideal model delta sigma weight residual 1.387 1.339 0.048 1.00e-02 1.00e+04 2.34e+01 ... (remaining 15179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.38: 20312 4.38 - 8.75: 222 8.75 - 13.13: 15 13.13 - 17.51: 1 17.51 - 21.88: 2 Bond angle restraints: 20552 Sorted by residual: angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 117.99 21.88 1.00e+00 1.00e+00 4.79e+02 angle pdb=" PA ATP E 501 " pdb=" O3A ATP E 501 " pdb=" PB ATP E 501 " ideal model delta sigma weight residual 136.83 118.19 18.64 1.00e+00 1.00e+00 3.47e+02 angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 123.89 15.98 1.00e+00 1.00e+00 2.55e+02 angle pdb=" PA ATP D 901 " pdb=" O3A ATP D 901 " pdb=" PB ATP D 901 " ideal model delta sigma weight residual 136.83 123.79 13.04 1.00e+00 1.00e+00 1.70e+02 angle pdb=" C5 ATP E 501 " pdb=" C4 ATP E 501 " pdb=" N3 ATP E 501 " ideal model delta sigma weight residual 126.80 118.19 8.61 1.00e+00 1.00e+00 7.41e+01 ... (remaining 20547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 8197 17.63 - 35.26: 814 35.26 - 52.88: 151 52.88 - 70.51: 45 70.51 - 88.14: 28 Dihedral angle restraints: 9235 sinusoidal: 3841 harmonic: 5394 Sorted by residual: dihedral pdb=" CA THR C 130 " pdb=" C THR C 130 " pdb=" N PRO C 131 " pdb=" CA PRO C 131 " ideal model delta harmonic sigma weight residual 180.00 159.49 20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA HIS D 34 " pdb=" C HIS D 34 " pdb=" N SER D 35 " pdb=" CA SER D 35 " ideal model delta harmonic sigma weight residual -180.00 -160.00 -20.00 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA GLN D 358 " pdb=" C GLN D 358 " pdb=" N ARG D 359 " pdb=" CA ARG D 359 " ideal model delta harmonic sigma weight residual -180.00 -160.83 -19.17 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 9232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2009 0.088 - 0.176: 303 0.176 - 0.264: 28 0.264 - 0.352: 2 0.352 - 0.441: 2 Chirality restraints: 2344 Sorted by residual: chirality pdb=" CB ILE C 435 " pdb=" CA ILE C 435 " pdb=" CG1 ILE C 435 " pdb=" CG2 ILE C 435 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" CA LEU A 832 " pdb=" N LEU A 832 " pdb=" C LEU A 832 " pdb=" CB LEU A 832 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CB THR B 449 " pdb=" CA THR B 449 " pdb=" OG1 THR B 449 " pdb=" CG2 THR B 449 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 2341 not shown) Planarity restraints: 2591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU E 238 " 0.063 5.00e-02 4.00e+02 9.40e-02 1.41e+01 pdb=" N PRO E 239 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO E 239 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO E 239 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 44 " -0.007 2.00e-02 2.50e+03 2.23e-02 9.93e+00 pdb=" CG TYR D 44 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR D 44 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR D 44 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR D 44 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 44 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR D 44 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 44 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 122 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.23e+00 pdb=" C THR C 122 " 0.053 2.00e-02 2.50e+03 pdb=" O THR C 122 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU C 123 " -0.018 2.00e-02 2.50e+03 ... (remaining 2588 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 84 2.63 - 3.20: 12602 3.20 - 3.76: 22691 3.76 - 4.33: 30253 4.33 - 4.90: 49568 Nonbonded interactions: 115198 Sorted by model distance: nonbonded pdb=" O1B ATP E 501 " pdb="MG MG E 502 " model vdw 2.061 2.170 nonbonded pdb=" O1G ATP D 901 " pdb="MG MG D 902 " model vdw 2.148 2.170 nonbonded pdb=" OH TYR D 44 " pdb=" OE1 GLU D 83 " model vdw 2.235 3.040 nonbonded pdb=" O1A ATP E 501 " pdb="MG MG E 502 " model vdw 2.280 2.170 nonbonded pdb=" O LEU C 419 " pdb=" OG1 THR C 423 " model vdw 2.297 3.040 ... (remaining 115193 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.230 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 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:2.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 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 : 0.007 0.080 15184 Z= 0.383 Angle : 1.181 21.883 20552 Z= 0.700 Chirality : 0.064 0.441 2344 Planarity : 0.007 0.094 2591 Dihedral : 15.662 88.139 5707 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.90 (0.17), residues: 1786 helix: -0.84 (0.14), residues: 1054 sheet: -0.61 (0.41), residues: 131 loop : -1.96 (0.22), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP E 162 HIS 0.013 0.002 HIS C 81 PHE 0.043 0.004 PHE B 539 TYR 0.050 0.003 TYR D 44 ARG 0.019 0.002 ARG B 533 Details of bonding type rmsd hydrogen bonds : bond 0.17287 ( 755) hydrogen bonds : angle 6.44418 ( 2223) covalent geometry : bond 0.00704 (15184) covalent geometry : angle 1.18068 (20552) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 784 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7962 (tm-30) REVERT: A 815 THR cc_start: 0.7774 (p) cc_final: 0.7103 (p) REVERT: A 820 MET cc_start: 0.8113 (tpp) cc_final: 0.7855 (tpp) REVERT: B 288 LYS cc_start: 0.8007 (tppt) cc_final: 0.7687 (tptt) REVERT: B 557 LEU cc_start: 0.7192 (tp) cc_final: 0.6861 (tp) REVERT: C 29 TYR cc_start: 0.8132 (m-80) cc_final: 0.7926 (m-80) REVERT: C 148 LEU cc_start: 0.8794 (mp) cc_final: 0.8580 (mm) REVERT: C 369 LEU cc_start: 0.8532 (tp) cc_final: 0.8216 (mt) REVERT: C 372 PHE cc_start: 0.7773 (t80) cc_final: 0.7531 (t80) REVERT: C 467 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7922 (mp0) REVERT: C 673 MET cc_start: 0.4573 (tmm) cc_final: 0.4256 (tmm) REVERT: D 50 LEU cc_start: 0.8803 (tt) cc_final: 0.8171 (mp) REVERT: D 138 PHE cc_start: 0.6761 (t80) cc_final: 0.6541 (t80) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.2865 time to fit residues: 125.9771 Evaluate side-chains 177 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 151 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 75 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 0.3980 chunk 104 optimal weight: 1.9990 chunk 162 optimal weight: 0.0370 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 398 GLN B 411 GLN ** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN C 87 ASN C 128 ASN C 149 GLN E 48 GLN ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.131774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.107877 restraints weight = 24571.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.110349 restraints weight = 15217.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.111327 restraints weight = 11081.109| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15184 Z= 0.130 Angle : 0.588 10.033 20552 Z= 0.309 Chirality : 0.040 0.140 2344 Planarity : 0.004 0.067 2591 Dihedral : 8.121 83.433 2017 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.43 % Allowed : 7.63 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.52 (0.19), residues: 1786 helix: 0.45 (0.15), residues: 1085 sheet: 0.04 (0.45), residues: 114 loop : -1.86 (0.22), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 448 HIS 0.008 0.001 HIS C 406 PHE 0.036 0.002 PHE C 497 TYR 0.013 0.002 TYR B 508 ARG 0.006 0.001 ARG B 273 Details of bonding type rmsd hydrogen bonds : bond 0.04867 ( 755) hydrogen bonds : angle 4.30721 ( 2223) covalent geometry : bond 0.00282 (15184) covalent geometry : angle 0.58798 (20552) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 273 ARG cc_start: 0.6965 (tpm170) cc_final: 0.5873 (tpm170) REVERT: B 288 LYS cc_start: 0.8099 (tppt) cc_final: 0.7687 (tptt) REVERT: B 557 LEU cc_start: 0.6975 (tp) cc_final: 0.6737 (tp) REVERT: C 369 LEU cc_start: 0.8396 (tp) cc_final: 0.8145 (mt) REVERT: D 50 LEU cc_start: 0.8983 (tt) cc_final: 0.8341 (mp) outliers start: 24 outliers final: 11 residues processed: 231 average time/residue: 0.2653 time to fit residues: 90.1499 Evaluate side-chains 175 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 1.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 637 HIS Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 384 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 147 optimal weight: 0.0040 chunk 136 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN B 416 HIS ** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.131362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.106855 restraints weight = 24461.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.109716 restraints weight = 15216.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.111672 restraints weight = 10975.160| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15184 Z= 0.116 Angle : 0.525 8.920 20552 Z= 0.277 Chirality : 0.039 0.163 2344 Planarity : 0.004 0.050 2591 Dihedral : 7.282 88.359 2017 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.91 % Allowed : 9.72 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.17 (0.19), residues: 1786 helix: 1.04 (0.16), residues: 1093 sheet: 0.22 (0.45), residues: 114 loop : -1.70 (0.23), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 448 HIS 0.006 0.001 HIS C 637 PHE 0.021 0.001 PHE E 328 TYR 0.021 0.001 TYR B 508 ARG 0.005 0.000 ARG A 786 Details of bonding type rmsd hydrogen bonds : bond 0.04004 ( 755) hydrogen bonds : angle 3.93119 ( 2223) covalent geometry : bond 0.00254 (15184) covalent geometry : angle 0.52516 (20552) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 273 ARG cc_start: 0.6981 (tpm170) cc_final: 0.5962 (tpm170) REVERT: B 288 LYS cc_start: 0.8088 (tppt) cc_final: 0.7741 (tptt) REVERT: B 498 TYR cc_start: 0.8149 (t80) cc_final: 0.7831 (t80) REVERT: B 557 LEU cc_start: 0.7004 (tp) cc_final: 0.6736 (tp) REVERT: C 29 TYR cc_start: 0.8195 (m-80) cc_final: 0.7915 (m-10) REVERT: C 369 LEU cc_start: 0.8397 (tp) cc_final: 0.8161 (mp) REVERT: C 572 GLU cc_start: 0.7585 (pm20) cc_final: 0.7317 (pm20) REVERT: D 50 LEU cc_start: 0.8986 (tt) cc_final: 0.8340 (mp) outliers start: 32 outliers final: 15 residues processed: 206 average time/residue: 0.2685 time to fit residues: 82.2247 Evaluate side-chains 168 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 687 GLU Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 384 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 21 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 134 optimal weight: 0.0470 chunk 31 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 71 optimal weight: 0.0980 chunk 124 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 411 GLN B 416 HIS ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.131325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.107144 restraints weight = 24360.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.109973 restraints weight = 15066.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.111835 restraints weight = 10856.098| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15184 Z= 0.106 Angle : 0.499 8.628 20552 Z= 0.262 Chirality : 0.038 0.153 2344 Planarity : 0.003 0.046 2591 Dihedral : 6.976 87.678 2017 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.85 % Allowed : 11.33 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.49 (0.20), residues: 1786 helix: 1.32 (0.16), residues: 1094 sheet: 0.38 (0.45), residues: 114 loop : -1.65 (0.23), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 162 HIS 0.006 0.001 HIS C 637 PHE 0.021 0.001 PHE E 328 TYR 0.021 0.001 TYR C 179 ARG 0.006 0.000 ARG A 786 Details of bonding type rmsd hydrogen bonds : bond 0.03651 ( 755) hydrogen bonds : angle 3.77441 ( 2223) covalent geometry : bond 0.00230 (15184) covalent geometry : angle 0.49852 (20552) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 1.787 Fit side-chains REVERT: B 273 ARG cc_start: 0.6977 (tpm170) cc_final: 0.5931 (tpm170) REVERT: B 288 LYS cc_start: 0.8080 (tppt) cc_final: 0.7739 (tptt) REVERT: B 557 LEU cc_start: 0.6972 (tp) cc_final: 0.6735 (tp) REVERT: C 262 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8285 (mp) REVERT: C 369 LEU cc_start: 0.8424 (tp) cc_final: 0.8190 (mp) REVERT: C 572 GLU cc_start: 0.7522 (pm20) cc_final: 0.7294 (pm20) REVERT: D 50 LEU cc_start: 0.8981 (tt) cc_final: 0.8310 (mp) REVERT: E 94 ILE cc_start: 0.7605 (mm) cc_final: 0.7285 (pt) outliers start: 31 outliers final: 18 residues processed: 203 average time/residue: 0.2678 time to fit residues: 82.5524 Evaluate side-chains 171 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 610 TYR Chi-restraints excluded: chain C residue 637 HIS Chi-restraints excluded: chain C residue 687 GLU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 384 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 50 optimal weight: 0.1980 chunk 172 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN B 416 HIS C 379 GLN D 104 GLN ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.131093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.106120 restraints weight = 24495.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.109094 restraints weight = 14961.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.111083 restraints weight = 10712.390| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15184 Z= 0.122 Angle : 0.511 9.407 20552 Z= 0.268 Chirality : 0.038 0.137 2344 Planarity : 0.003 0.043 2591 Dihedral : 6.842 82.572 2017 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.73 % Allowed : 12.88 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.64 (0.20), residues: 1786 helix: 1.45 (0.16), residues: 1100 sheet: 0.47 (0.45), residues: 114 loop : -1.66 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 448 HIS 0.006 0.001 HIS C 637 PHE 0.035 0.001 PHE E 328 TYR 0.020 0.001 TYR B 508 ARG 0.006 0.000 ARG A 786 Details of bonding type rmsd hydrogen bonds : bond 0.03828 ( 755) hydrogen bonds : angle 3.75742 ( 2223) covalent geometry : bond 0.00280 (15184) covalent geometry : angle 0.51052 (20552) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 1.738 Fit side-chains REVERT: B 273 ARG cc_start: 0.7013 (tpm170) cc_final: 0.5938 (tpm170) REVERT: B 288 LYS cc_start: 0.8120 (tppt) cc_final: 0.7744 (tptt) REVERT: B 557 LEU cc_start: 0.6871 (tp) cc_final: 0.6648 (tp) REVERT: B 562 ASP cc_start: 0.7237 (t0) cc_final: 0.6912 (t0) REVERT: C 262 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8329 (mp) REVERT: C 572 GLU cc_start: 0.7564 (pm20) cc_final: 0.7344 (pm20) REVERT: D 50 LEU cc_start: 0.8966 (tt) cc_final: 0.8292 (mp) outliers start: 29 outliers final: 19 residues processed: 190 average time/residue: 0.2530 time to fit residues: 73.1240 Evaluate side-chains 166 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 446 ASN Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 610 TYR Chi-restraints excluded: chain C residue 637 HIS Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 396 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.4525 > 50: distance: 47 - 66: 8.335 distance: 52 - 78: 21.104 distance: 56 - 84: 19.144 distance: 60 - 66: 11.822 distance: 61 - 92: 18.468 distance: 66 - 67: 14.934 distance: 67 - 68: 10.640 distance: 67 - 70: 7.948 distance: 68 - 69: 32.111 distance: 68 - 78: 26.347 distance: 70 - 71: 18.022 distance: 71 - 72: 33.362 distance: 71 - 73: 21.146 distance: 72 - 74: 30.403 distance: 73 - 75: 24.381 distance: 74 - 76: 10.624 distance: 75 - 76: 17.341 distance: 76 - 77: 10.865 distance: 78 - 79: 9.266 distance: 79 - 80: 9.093 distance: 79 - 82: 17.805 distance: 80 - 81: 17.778 distance: 80 - 84: 8.652 distance: 82 - 83: 24.908 distance: 84 - 85: 17.579 distance: 85 - 86: 15.226 distance: 85 - 88: 22.015 distance: 86 - 87: 39.253 distance: 86 - 92: 30.902 distance: 88 - 89: 21.511 distance: 88 - 90: 29.020 distance: 89 - 91: 22.805 distance: 92 - 93: 6.531 distance: 93 - 94: 33.123 distance: 93 - 96: 11.980 distance: 94 - 95: 39.089 distance: 94 - 99: 41.349 distance: 96 - 97: 12.258 distance: 96 - 98: 17.762 distance: 99 - 100: 21.272 distance: 100 - 101: 10.588 distance: 101 - 102: 17.690 distance: 101 - 107: 39.325 distance: 103 - 104: 30.464 distance: 104 - 105: 14.679 distance: 104 - 106: 12.746 distance: 107 - 108: 20.601 distance: 108 - 109: 12.754 distance: 108 - 111: 33.601 distance: 109 - 110: 15.868 distance: 109 - 113: 20.473 distance: 111 - 112: 8.217 distance: 113 - 114: 16.794 distance: 114 - 115: 16.505 distance: 114 - 117: 11.807 distance: 115 - 116: 25.027 distance: 115 - 124: 20.626 distance: 117 - 118: 21.429 distance: 118 - 119: 29.362 distance: 119 - 120: 24.794 distance: 120 - 121: 11.959 distance: 121 - 122: 10.608 distance: 121 - 123: 10.946 distance: 124 - 125: 37.954 distance: 125 - 126: 16.233 distance: 125 - 128: 26.540 distance: 126 - 127: 11.974 distance: 126 - 131: 10.212 distance: 128 - 129: 23.425 distance: 128 - 130: 41.835 distance: 131 - 132: 5.732 distance: 132 - 133: 22.167 distance: 132 - 135: 40.131 distance: 133 - 134: 33.344 distance: 133 - 136: 28.808 distance: 136 - 137: 33.027 distance: 136 - 142: 34.254 distance: 137 - 138: 44.632 distance: 137 - 140: 41.542 distance: 138 - 139: 13.045 distance: 138 - 143: 25.900 distance: 140 - 141: 25.872 distance: 141 - 142: 32.365