Starting phenix.real_space_refine on Fri Feb 6 19:08:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u6f_63904/02_2026/9u6f_63904.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u6f_63904/02_2026/9u6f_63904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9u6f_63904/02_2026/9u6f_63904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u6f_63904/02_2026/9u6f_63904.map" model { file = "/net/cci-nas-00/data/ceres_data/9u6f_63904/02_2026/9u6f_63904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u6f_63904/02_2026/9u6f_63904.cif" } resolution = 2.2 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= 0.001 sd= 0.037 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 5 5.49 5 Mg 2 5.21 5 S 101 5.16 5 C 17114 2.51 5 N 4643 2.21 5 O 5081 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26946 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4477 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4477 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "C" Number of atoms: 4477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4477 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} Chain: "E" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3668 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 441} Chain: "F" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3694 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" 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: 6.21, per 1000 atoms: 0.23 Number of scatterers: 26946 At special positions: 0 Unit cell: (134.706, 138.474, 153.546, 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 101 16.00 P 5 15.00 Mg 2 11.99 O 5081 8.00 N 4643 7.00 C 17114 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: 2.30 Conformation dependent library (CDL) restraints added in 1.1 seconds 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6278 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 27 sheets defined 45.6% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 90 through 99 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 258 through 269 removed outlier: 3.769A pdb=" N MET A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 297 through 316 removed outlier: 4.294A pdb=" N ALA A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 342 removed outlier: 3.961A pdb=" N TRP A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 351 through 352 No H-bonds generated for 'chain 'A' and resid 351 through 352' Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 393 through 401 Processing helix chain 'A' and resid 410 through 416 Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 446 through 472 removed outlier: 3.895A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 476 Processing helix chain 'A' and resid 477 through 494 Processing helix chain 'A' and resid 508 through 531 Processing helix chain 'A' and resid 535 through 540 removed outlier: 3.535A pdb=" N ILE A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 551 removed outlier: 4.072A pdb=" N GLU A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 554 No H-bonds generated for 'chain 'A' and resid 552 through 554' Processing helix chain 'A' and resid 558 through 577 removed outlier: 3.540A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 258 through 269 Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 295 through 316 removed outlier: 4.932A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.504A pdb=" N TRP B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 393 through 403 removed outlier: 3.832A pdb=" N ILE B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 416 removed outlier: 3.553A pdb=" N ALA B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 446 through 464 Processing helix chain 'B' and resid 464 through 471 Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 477 through 495 Processing helix chain 'B' and resid 508 through 532 Processing helix chain 'B' and resid 535 through 540 removed outlier: 3.935A pdb=" N ILE B 539 " --> pdb=" O SER B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 550 removed outlier: 4.340A pdb=" N GLU B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 554 removed outlier: 3.679A pdb=" N VAL B 554 " --> pdb=" O ALA B 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 551 through 554' Processing helix chain 'B' and resid 558 through 576 removed outlier: 3.719A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS B 575 " --> pdb=" O GLN B 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 233 through 245 Processing helix chain 'C' and resid 258 through 269 removed outlier: 3.722A pdb=" N MET C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 296 through 316 removed outlier: 4.295A pdb=" N GLU C 300 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 341 removed outlier: 3.920A pdb=" N TRP C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 393 through 401 removed outlier: 3.553A pdb=" N ARG C 401 " --> pdb=" O GLN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 416 Processing helix chain 'C' and resid 431 through 443 Proline residue: C 437 - end of helix Processing helix chain 'C' and resid 446 through 472 removed outlier: 4.150A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 476 removed outlier: 3.689A pdb=" N LEU C 476 " --> pdb=" O PRO C 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 473 through 476' Processing helix chain 'C' and resid 477 through 494 Processing helix chain 'C' and resid 508 through 532 Processing helix chain 'C' and resid 535 through 541 removed outlier: 3.679A pdb=" N ILE C 539 " --> pdb=" O SER C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 550 Processing helix chain 'C' and resid 551 through 554 Processing helix chain 'C' and resid 558 through 578 removed outlier: 3.515A pdb=" N ALA C 578 " --> pdb=" O PHE C 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.505A pdb=" N LEU D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 159 through 171 Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 197 through 210 Processing helix chain 'D' and resid 212 through 215 Processing helix chain 'D' and resid 227 through 250 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.560A pdb=" N TYR D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 283 Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 340 through 346 Processing helix chain 'D' and resid 361 through 366 removed outlier: 3.744A pdb=" N GLY D 365 " --> pdb=" O LEU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 400 removed outlier: 3.794A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 422 Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 455 through 463 Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.668A pdb=" N LEU E 89 " --> pdb=" O LYS E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 159 through 171 Processing helix chain 'E' and resid 174 through 179 removed outlier: 3.773A pdb=" N GLY E 179 " --> pdb=" O ASP E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 211 removed outlier: 3.987A pdb=" N THR E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 215 Processing helix chain 'E' and resid 227 through 250 removed outlier: 3.654A pdb=" N ARG E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE E 232 " --> pdb=" O THR E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 259 through 273 removed outlier: 3.577A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.605A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 320 Processing helix chain 'E' and resid 323 through 333 Processing helix chain 'E' and resid 340 through 346 Processing helix chain 'E' and resid 361 through 365 Processing helix chain 'E' and resid 374 through 400 removed outlier: 3.621A pdb=" N ALA E 397 " --> pdb=" O ARG E 393 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 422 Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 445 through 446 No H-bonds generated for 'chain 'E' and resid 445 through 446' Processing helix chain 'E' and resid 447 through 451 Processing helix chain 'E' and resid 455 through 463 Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.613A pdb=" N LEU F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 159 through 171 Processing helix chain 'F' and resid 174 through 179 Processing helix chain 'F' and resid 197 through 212 Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 228 through 232 Processing helix chain 'F' and resid 233 through 250 Processing helix chain 'F' and resid 259 through 274 removed outlier: 3.505A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 283 removed outlier: 4.336A pdb=" N GLY F 282 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 285 No H-bonds generated for 'chain 'F' and resid 284 through 285' Processing helix chain 'F' and resid 286 through 296 Processing helix chain 'F' and resid 317 through 320 Processing helix chain 'F' and resid 323 through 333 Processing helix chain 'F' and resid 340 through 346 Processing helix chain 'F' and resid 361 through 366 removed outlier: 3.782A pdb=" N GLY F 365 " --> pdb=" O LEU F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 400 removed outlier: 3.944A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 404 Processing helix chain 'F' and resid 405 through 422 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 445 through 446 No H-bonds generated for 'chain 'F' and resid 445 through 446' Processing helix chain 'F' and resid 447 through 451 removed outlier: 3.605A pdb=" N LEU F 451 " --> pdb=" O GLN F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 463 Processing helix chain 'F' and resid 466 through 471 removed outlier: 3.956A pdb=" N ILE F 470 " --> pdb=" O LYS F 466 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP F 471 " --> pdb=" O LEU F 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 466 through 471' Processing helix chain 'G' and resid 7 through 71 removed outlier: 3.615A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA G 63 " --> pdb=" O GLU G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 82 Processing helix chain 'G' and resid 122 through 167 removed outlier: 3.619A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 209 Processing helix chain 'H' and resid 6 through 16 removed outlier: 3.560A pdb=" N GLN H 11 " --> pdb=" O PRO H 7 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N GLY H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE H 13 " --> pdb=" O THR H 9 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG H 14 " --> pdb=" O ALA H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 38 Processing helix chain 'H' and resid 55 through 58 Processing helix chain 'H' and resid 59 through 64 Processing helix chain 'H' and resid 76 through 83 removed outlier: 3.650A pdb=" N PHE H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 98 removed outlier: 3.729A pdb=" N TYR H 89 " --> pdb=" O ASP H 85 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 10 removed outlier: 6.512A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ALA A 13 " --> pdb=" O ILE A 9 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 13 through 17 current: chain 'A' and resid 35 through 43 removed outlier: 5.586A pdb=" N ILE A 39 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLN A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 41 " --> pdb=" O PHE A 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 46 through 51 current: chain 'B' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 13 through 17 current: chain 'B' and resid 35 through 43 removed outlier: 5.762A pdb=" N ILE B 39 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLN B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG B 41 " --> pdb=" O PHE B 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 46 through 51 current: chain 'C' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 13 through 17 current: chain 'C' and resid 35 through 43 removed outlier: 5.659A pdb=" N ILE C 39 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLN C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG C 41 " --> pdb=" O PHE C 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 46 through 51 current: chain 'D' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 22 current: chain 'D' and resid 42 through 51 removed outlier: 5.622A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR D 54 " --> pdb=" O SER D 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 54 through 59 current: chain 'E' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 21 current: chain 'E' and resid 42 through 51 removed outlier: 5.828A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 55 through 59 current: chain 'F' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 21 current: chain 'F' and resid 42 through 51 removed outlier: 5.752A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 83 through 84 current: chain 'A' and resid 285 through 290 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 285 through 290 current: chain 'A' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 375 through 384 current: chain 'A' and resid 428 through 429 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 148 removed outlier: 6.559A pdb=" N PHE A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ALA A 118 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129 removed outlier: 6.914A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AA7, first strand: chain 'B' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 83 through 84 current: chain 'B' and resid 285 through 288 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 285 through 288 current: chain 'B' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 375 through 384 current: chain 'B' and resid 428 through 429 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 143 through 148 removed outlier: 6.935A pdb=" N PHE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ALA B 118 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 129 removed outlier: 6.867A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 204 through 205 removed outlier: 4.770A pdb=" N VAL B 218 " --> pdb=" O PHE B 205 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AB3, first strand: chain 'C' and resid 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 82 through 84 current: chain 'C' and resid 285 through 290 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 285 through 290 current: chain 'C' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 375 through 384 current: chain 'C' and resid 428 through 429 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 144 through 148 removed outlier: 6.503A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 128 through 129 removed outlier: 6.824A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.634A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 91 through 93 removed outlier: 6.599A pdb=" N ARG D 91 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LEU D 221 " --> pdb=" O ARG D 91 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N PHE D 93 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N LYS D 223 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N VAL D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ASN D 222 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ALA D 193 " --> pdb=" O ASN D 222 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 130 through 131 removed outlier: 4.579A pdb=" N LEU D 144 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 81 through 84 Processing sheet with id=AC1, first strand: chain 'E' and resid 92 through 93 removed outlier: 6.510A pdb=" N PHE E 93 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LYS E 223 " --> pdb=" O PHE E 93 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N VAL E 218 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N PHE E 220 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE E 191 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ASN E 222 " --> pdb=" O PHE E 191 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ALA E 193 " --> pdb=" O ASN E 222 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 124 through 125 removed outlier: 4.707A pdb=" N VAL E 300 " --> pdb=" O ARG E 125 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.484A pdb=" N LEU E 144 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 81 through 84 Processing sheet with id=AC5, first strand: chain 'F' and resid 92 through 94 removed outlier: 6.511A pdb=" N PHE F 93 " --> pdb=" O LEU F 221 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LYS F 223 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ASN F 222 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ALA F 193 " --> pdb=" O ASN F 222 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA F 188 " --> pdb=" O LEU F 254 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE F 256 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL F 190 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU F 257 " --> pdb=" O ILE F 311 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 124 through 125 removed outlier: 4.714A pdb=" N VAL F 300 " --> pdb=" O ARG F 125 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.649A pdb=" N LEU F 144 " --> pdb=" O ILE F 131 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 89 through 96 Processing sheet with id=AC9, first strand: chain 'H' and resid 19 through 22 removed outlier: 4.249A pdb=" N ASP H 48 " --> pdb=" O ILE H 4 " (cutoff:3.500A) 1150 hydrogen bonds defined for protein. 3249 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: 4.96 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4936 1.32 - 1.45: 6582 1.45 - 1.57: 15757 1.57 - 1.70: 8 1.70 - 1.82: 190 Bond restraints: 27473 Sorted by residual: bond pdb=" CA SER B 232 " pdb=" CB SER B 232 " ideal model delta sigma weight residual 1.532 1.478 0.054 1.74e-02 3.30e+03 9.66e+00 bond pdb=" CA SER A 232 " pdb=" CB SER A 232 " ideal model delta sigma weight residual 1.532 1.487 0.046 1.79e-02 3.12e+03 6.47e+00 bond pdb=" C THR A 235 " pdb=" O THR A 235 " ideal model delta sigma weight residual 1.237 1.206 0.030 1.19e-02 7.06e+03 6.45e+00 bond pdb=" CA SER C 232 " pdb=" CB SER C 232 " ideal model delta sigma weight residual 1.532 1.491 0.041 1.65e-02 3.67e+03 6.19e+00 bond pdb=" C LYS A 234 " pdb=" O LYS A 234 " ideal model delta sigma weight residual 1.236 1.210 0.027 1.15e-02 7.56e+03 5.51e+00 ... (remaining 27468 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 36756 2.30 - 4.60: 423 4.60 - 6.90: 43 6.90 - 9.20: 10 9.20 - 11.50: 1 Bond angle restraints: 37233 Sorted by residual: angle pdb=" C PHE A 230 " pdb=" CA PHE A 230 " pdb=" CB PHE A 230 " ideal model delta sigma weight residual 109.65 117.15 -7.50 1.71e+00 3.42e-01 1.92e+01 angle pdb=" CA PHE A 230 " pdb=" CB PHE A 230 " pdb=" CG PHE A 230 " ideal model delta sigma weight residual 113.80 118.09 -4.29 1.00e+00 1.00e+00 1.84e+01 angle pdb=" C PHE C 230 " pdb=" CA PHE C 230 " pdb=" CB PHE C 230 " ideal model delta sigma weight residual 109.65 116.78 -7.13 1.71e+00 3.42e-01 1.74e+01 angle pdb=" CA PHE C 230 " pdb=" CB PHE C 230 " pdb=" CG PHE C 230 " ideal model delta sigma weight residual 113.80 117.58 -3.78 1.00e+00 1.00e+00 1.43e+01 angle pdb=" N ILE H 98 " pdb=" CA ILE H 98 " pdb=" C ILE H 98 " ideal model delta sigma weight residual 111.81 108.77 3.04 8.60e-01 1.35e+00 1.25e+01 ... (remaining 37228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 14884 17.81 - 35.63: 1286 35.63 - 53.44: 383 53.44 - 71.26: 98 71.26 - 89.07: 50 Dihedral angle restraints: 16701 sinusoidal: 6852 harmonic: 9849 Sorted by residual: dihedral pdb=" CA VAL A 368 " pdb=" C VAL A 368 " pdb=" N ILE A 369 " pdb=" CA ILE A 369 " ideal model delta harmonic sigma weight residual 180.00 158.54 21.46 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" C5' ADP A 602 " pdb=" O5' ADP A 602 " pdb=" PA ADP A 602 " pdb=" O2A ADP A 602 " ideal model delta sinusoidal sigma weight residual -60.00 13.71 -73.71 1 2.00e+01 2.50e-03 1.73e+01 dihedral pdb=" CA VAL F 21 " pdb=" C VAL F 21 " pdb=" N GLU F 22 " pdb=" CA GLU F 22 " ideal model delta harmonic sigma weight residual 180.00 -159.69 -20.31 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 16698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3346 0.056 - 0.111: 736 0.111 - 0.167: 70 0.167 - 0.222: 3 0.222 - 0.278: 2 Chirality restraints: 4157 Sorted by residual: chirality pdb=" CA SER C 232 " pdb=" N SER C 232 " pdb=" C SER C 232 " pdb=" CB SER C 232 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA THR A 235 " pdb=" N THR A 235 " pdb=" C THR A 235 " pdb=" CB THR A 235 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA THR B 235 " pdb=" N THR B 235 " pdb=" C THR B 235 " pdb=" CB THR B 235 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 4154 not shown) Planarity restraints: 4867 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO C 229 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.73e+00 pdb=" C PRO C 229 " 0.038 2.00e-02 2.50e+03 pdb=" O PRO C 229 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE C 230 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 565 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" CD GLU B 565 " -0.038 2.00e-02 2.50e+03 pdb=" OE1 GLU B 565 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU B 565 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 446 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.13e+00 pdb=" CG ASP B 446 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP B 446 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP B 446 " -0.012 2.00e-02 2.50e+03 ... (remaining 4864 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 148 2.56 - 3.15: 21342 3.15 - 3.73: 43621 3.73 - 4.32: 62663 4.32 - 4.90: 103723 Nonbonded interactions: 231497 Sorted by model distance: nonbonded pdb=" OG1 THR C 235 " pdb="MG MG C 601 " model vdw 1.976 2.170 nonbonded pdb=" OG1 THR A 235 " pdb="MG MG A 601 " model vdw 2.056 2.170 nonbonded pdb="MG MG C 601 " pdb=" O2G ATP C 602 " model vdw 2.061 2.170 nonbonded pdb=" O MET C 220 " pdb=" OG1 THR C 379 " model vdw 2.105 3.040 nonbonded pdb=" O MET A 220 " pdb=" OG1 THR A 379 " model vdw 2.128 3.040 ... (remaining 231492 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 1 through 578) selection = chain 'B' selection = (chain 'C' and resid 1 through 578) } ncs_group { reference = (chain 'D' and resid 5 through 470) selection = (chain 'E' and resid 5 through 470) selection = (chain 'F' and resid 5 through 470) } 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: 2.820 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: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 23.800 Find NCS groups from input model: 0.680 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: 0.010 Load rotamer database and sin/cos tables:8.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 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 : 0.004 0.054 27473 Z= 0.178 Angle : 0.612 11.496 37233 Z= 0.345 Chirality : 0.045 0.278 4157 Planarity : 0.005 0.060 4867 Dihedral : 15.921 89.069 10423 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.52 % Allowed : 13.17 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.15), residues: 3437 helix: 1.64 (0.15), residues: 1334 sheet: 0.28 (0.23), residues: 542 loop : 0.65 (0.16), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 154 TYR 0.014 0.001 TYR F 54 PHE 0.019 0.001 PHE C 415 TRP 0.007 0.001 TRP C 119 HIS 0.008 0.001 HIS C 145 Details of bonding type rmsd covalent geometry : bond 0.00371 (27473) covalent geometry : angle 0.61242 (37233) hydrogen bonds : bond 0.15617 ( 1150) hydrogen bonds : angle 6.35390 ( 3249) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 296 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 446 ASP cc_start: 0.7422 (t0) cc_final: 0.7080 (OUTLIER) REVERT: C 264 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7940 (t70) REVERT: D 402 ASP cc_start: 0.8764 (m-30) cc_final: 0.8519 (m-30) REVERT: E 409 ARG cc_start: 0.8595 (ttm110) cc_final: 0.8374 (ttp-170) REVERT: F 98 LYS cc_start: 0.8973 (mmtt) cc_final: 0.8677 (mmmt) REVERT: G 152 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7820 (tp30) REVERT: H 87 GLU cc_start: 0.8408 (mp0) cc_final: 0.8191 (mp0) REVERT: H 91 ARG cc_start: 0.8107 (mtp85) cc_final: 0.7811 (mtp85) outliers start: 43 outliers final: 28 residues processed: 327 average time/residue: 0.8494 time to fit residues: 312.2854 Evaluate side-chains 306 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 277 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 98 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN B 202 ASN B 397 GLN B 459 GLN B 496 GLN D 465 GLN G 181 GLN G 185 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.095626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.067190 restraints weight = 40148.282| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.03 r_work: 0.2715 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 27473 Z= 0.224 Angle : 0.590 11.394 37233 Z= 0.306 Chirality : 0.047 0.171 4157 Planarity : 0.005 0.054 4867 Dihedral : 6.690 85.428 3903 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.33 % Allowed : 12.04 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.15), residues: 3437 helix: 1.59 (0.15), residues: 1331 sheet: 0.18 (0.22), residues: 548 loop : 0.55 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 481 TYR 0.015 0.002 TYR F 54 PHE 0.020 0.002 PHE C 559 TRP 0.016 0.002 TRP B 119 HIS 0.006 0.001 HIS C 145 Details of bonding type rmsd covalent geometry : bond 0.00525 (27473) covalent geometry : angle 0.58982 (37233) hydrogen bonds : bond 0.05529 ( 1150) hydrogen bonds : angle 5.21019 ( 3249) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 295 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 MET cc_start: 0.9247 (OUTLIER) cc_final: 0.8183 (mmt) REVERT: B 294 MET cc_start: 0.8984 (mmm) cc_final: 0.8768 (mtt) REVERT: C 541 GLN cc_start: 0.8545 (mm110) cc_final: 0.8293 (mm110) REVERT: D 275 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8676 (mt-10) REVERT: F 98 LYS cc_start: 0.9065 (mmtt) cc_final: 0.8705 (mmmt) REVERT: F 206 GLN cc_start: 0.8866 (mt0) cc_final: 0.8639 (mt0) REVERT: G 152 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7895 (tp30) REVERT: G 165 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8123 (mt-10) REVERT: H 87 GLU cc_start: 0.8457 (mp0) cc_final: 0.8163 (mp0) REVERT: H 91 ARG cc_start: 0.8235 (mtp85) cc_final: 0.7825 (mtp85) outliers start: 66 outliers final: 32 residues processed: 340 average time/residue: 0.8797 time to fit residues: 335.2379 Evaluate side-chains 318 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 283 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 568 LYS Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 98 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 199 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 274 optimal weight: 7.9990 chunk 251 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 262 optimal weight: 0.9980 chunk 283 optimal weight: 0.3980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN B 202 ASN B 459 GLN D 465 GLN E 129 GLN E 428 GLN G 180 GLN G 181 GLN G 185 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.095702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.067260 restraints weight = 40369.583| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.04 r_work: 0.2715 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 27473 Z= 0.200 Angle : 0.562 9.933 37233 Z= 0.290 Chirality : 0.046 0.169 4157 Planarity : 0.005 0.050 4867 Dihedral : 6.658 83.336 3887 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.30 % Allowed : 12.68 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.15), residues: 3437 helix: 1.64 (0.15), residues: 1314 sheet: -0.01 (0.22), residues: 559 loop : 0.51 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 481 TYR 0.016 0.001 TYR H 21 PHE 0.018 0.002 PHE C 559 TRP 0.013 0.001 TRP A 119 HIS 0.005 0.001 HIS C 145 Details of bonding type rmsd covalent geometry : bond 0.00470 (27473) covalent geometry : angle 0.56169 (37233) hydrogen bonds : bond 0.05030 ( 1150) hydrogen bonds : angle 5.04731 ( 3249) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 305 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 MET cc_start: 0.9231 (OUTLIER) cc_final: 0.8133 (mmt) REVERT: B 269 PHE cc_start: 0.9239 (OUTLIER) cc_final: 0.8687 (t80) REVERT: B 294 MET cc_start: 0.9028 (mmm) cc_final: 0.8810 (mtt) REVERT: B 537 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8305 (OUTLIER) REVERT: C 336 GLU cc_start: 0.8065 (tp30) cc_final: 0.7812 (mp0) REVERT: C 481 ARG cc_start: 0.8341 (mmm-85) cc_final: 0.7963 (ttp-110) REVERT: C 541 GLN cc_start: 0.8617 (mm110) cc_final: 0.8318 (mm110) REVERT: D 61 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7707 (mp0) REVERT: D 275 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8693 (mt-10) REVERT: D 394 LYS cc_start: 0.8952 (ttmm) cc_final: 0.8442 (mppt) REVERT: F 206 GLN cc_start: 0.8840 (mt0) cc_final: 0.8572 (mt0) REVERT: G 152 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8010 (tp30) REVERT: G 165 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8069 (mt-10) REVERT: H 19 GLU cc_start: 0.5416 (tm-30) cc_final: 0.5115 (tm-30) REVERT: H 87 GLU cc_start: 0.8459 (mp0) cc_final: 0.8144 (mp0) REVERT: H 91 ARG cc_start: 0.8319 (mtp85) cc_final: 0.7985 (mtp85) outliers start: 65 outliers final: 35 residues processed: 349 average time/residue: 0.8999 time to fit residues: 351.0986 Evaluate side-chains 323 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 283 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 305 LYS Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 98 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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: 70.523 > 50: distance: 28 - 33: 29.768 distance: 33 - 34: 57.555 distance: 33 - 39: 9.916 distance: 34 - 35: 40.891 distance: 35 - 40: 41.190 distance: 38 - 39: 57.698 distance: 40 - 41: 29.683 distance: 40 - 136: 32.610 distance: 41 - 42: 56.647 distance: 41 - 44: 41.374 distance: 42 - 43: 39.084 distance: 43 - 148: 37.321 distance: 44 - 45: 39.775 distance: 44 - 46: 45.983 distance: 45 - 47: 19.702 distance: 48 - 49: 57.327 distance: 48 - 198: 34.132 distance: 49 - 50: 40.172 distance: 50 - 51: 40.670 distance: 50 - 59: 12.577 distance: 52 - 53: 48.115 distance: 53 - 54: 8.352 distance: 53 - 55: 28.986 distance: 54 - 56: 28.378 distance: 55 - 57: 39.143 distance: 56 - 58: 56.485 distance: 57 - 58: 14.822 distance: 59 - 60: 47.071 distance: 59 - 151: 27.368 distance: 61 - 65: 4.418 distance: 63 - 64: 57.757 distance: 65 - 66: 54.086 distance: 66 - 67: 29.684 distance: 67 - 68: 10.655 distance: 67 - 69: 30.083 distance: 70 - 71: 40.596 distance: 71 - 72: 39.837 distance: 71 - 75: 40.173 distance: 75 - 76: 3.304 distance: 76 - 77: 39.905 distance: 77 - 78: 41.006 distance: 77 - 79: 56.611 distance: 80 - 81: 56.109 distance: 80 - 83: 57.932 distance: 81 - 87: 39.433 distance: 83 - 84: 40.905 distance: 84 - 85: 31.651 distance: 84 - 86: 64.279 distance: 87 - 88: 55.768 distance: 87 - 93: 69.891 distance: 88 - 89: 70.426 distance: 88 - 91: 38.960 distance: 89 - 90: 56.284 distance: 89 - 94: 68.574 distance: 90 - 115: 34.872 distance: 91 - 92: 56.936 distance: 94 - 95: 57.350 distance: 95 - 96: 69.310 distance: 95 - 98: 41.394 distance: 96 - 97: 48.999 distance: 96 - 99: 34.144 distance: 97 - 123: 29.307