Starting phenix.real_space_refine on Thu Feb 13 16:57:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jbj_9791/02_2025/6jbj_9791_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jbj_9791/02_2025/6jbj_9791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6jbj_9791/02_2025/6jbj_9791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jbj_9791/02_2025/6jbj_9791.map" model { file = "/net/cci-nas-00/data/ceres_data/6jbj_9791/02_2025/6jbj_9791_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jbj_9791/02_2025/6jbj_9791_neut.cif" } resolution = 3.6 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 40 5.16 5 C 5914 2.51 5 N 1534 2.21 5 O 1672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9166 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4552 Classifications: {'peptide': 565} Link IDs: {'PTRANS': 19, 'TRANS': 545} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 8.28, per 1000 atoms: 0.90 Number of scatterers: 9166 At special positions: 0 Unit cell: (75.92, 73.84, 130, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 6 15.00 O 1672 8.00 N 1534 7.00 C 5914 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: 2.46 Conformation dependent library (CDL) restraints added in 1.1 seconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 4 sheets defined 63.9% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 18 through 32 removed outlier: 4.193A pdb=" N GLN A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL A 30 " --> pdb=" O GLN A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 61 removed outlier: 3.936A pdb=" N THR A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 46 " --> pdb=" O MET A 42 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU A 52 " --> pdb=" O CYS A 48 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 75 through 124 removed outlier: 3.877A pdb=" N THR A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 95 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS A 118 " --> pdb=" O ASP A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 135 removed outlier: 3.786A pdb=" N ASN A 133 " --> pdb=" O TYR A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 159 removed outlier: 3.736A pdb=" N ASP A 149 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 180 removed outlier: 3.565A pdb=" N LEU A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL A 172 " --> pdb=" O PRO A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 203 removed outlier: 3.930A pdb=" N TYR A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 231 removed outlier: 3.905A pdb=" N HIS A 214 " --> pdb=" O MET A 210 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 218 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 241 through 289 removed outlier: 4.281A pdb=" N MET A 247 " --> pdb=" O HIS A 243 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG A 251 " --> pdb=" O MET A 247 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A 262 " --> pdb=" O GLN A 258 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N TRP A 269 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 270 " --> pdb=" O LYS A 266 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE A 283 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N TYR A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.608A pdb=" N PHE A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.778A pdb=" N VAL A 337 " --> pdb=" O THR A 333 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN A 346 " --> pdb=" O HIS A 342 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU A 349 " --> pdb=" O GLY A 345 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP A 353 " --> pdb=" O GLU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 426 through 435 removed outlier: 3.851A pdb=" N LEU A 430 " --> pdb=" O GLY A 426 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL A 433 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 475 removed outlier: 3.524A pdb=" N VAL A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A 475 " --> pdb=" O ARG A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 486 Processing helix chain 'A' and resid 490 through 501 removed outlier: 3.719A pdb=" N LEU A 494 " --> pdb=" O ASP A 490 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 509 removed outlier: 4.182A pdb=" N ALA A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG A 508 " --> pdb=" O ASN A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 540 removed outlier: 3.858A pdb=" N GLN A 530 " --> pdb=" O PRO A 526 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG A 531 " --> pdb=" O GLY A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 removed outlier: 3.545A pdb=" N ILE A 565 " --> pdb=" O GLU A 561 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 585 removed outlier: 3.912A pdb=" N LYS A 584 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 32 removed outlier: 4.194A pdb=" N GLN B 22 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE B 27 " --> pdb=" O ARG B 23 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL B 30 " --> pdb=" O GLN B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 61 removed outlier: 3.936A pdb=" N THR B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 46 " --> pdb=" O MET B 42 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU B 49 " --> pdb=" O THR B 45 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU B 52 " --> pdb=" O CYS B 48 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 67 through 72 Processing helix chain 'B' and resid 75 through 124 removed outlier: 3.877A pdb=" N THR B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 95 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE B 99 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS B 118 " --> pdb=" O ASP B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 135 removed outlier: 3.786A pdb=" N ASN B 133 " --> pdb=" O TYR B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 159 removed outlier: 3.736A pdb=" N ASP B 149 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 180 removed outlier: 3.565A pdb=" N LEU B 171 " --> pdb=" O SER B 167 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL B 172 " --> pdb=" O PRO B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 203 removed outlier: 3.930A pdb=" N TYR B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN B 201 " --> pdb=" O GLY B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 231 removed outlier: 3.905A pdb=" N HIS B 214 " --> pdb=" O MET B 210 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 218 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 241 through 289 removed outlier: 4.281A pdb=" N MET B 247 " --> pdb=" O HIS B 243 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG B 251 " --> pdb=" O MET B 247 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR B 259 " --> pdb=" O ARG B 255 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU B 262 " --> pdb=" O GLN B 258 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N TRP B 269 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 270 " --> pdb=" O LYS B 266 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE B 277 " --> pdb=" O GLY B 273 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE B 283 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER B 285 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N TYR B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE B 289 " --> pdb=" O SER B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 322 removed outlier: 3.608A pdb=" N PHE B 315 " --> pdb=" O SER B 311 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 316 " --> pdb=" O LYS B 312 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR B 319 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 331 through 353 removed outlier: 3.778A pdb=" N VAL B 337 " --> pdb=" O THR B 333 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN B 346 " --> pdb=" O HIS B 342 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU B 349 " --> pdb=" O GLY B 345 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR B 350 " --> pdb=" O GLN B 346 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 426 through 435 removed outlier: 3.852A pdb=" N LEU B 430 " --> pdb=" O GLY B 426 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU B 431 " --> pdb=" O LYS B 427 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL B 433 " --> pdb=" O SER B 429 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 434 " --> pdb=" O LEU B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 475 removed outlier: 3.524A pdb=" N VAL B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 475 " --> pdb=" O ARG B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 486 Processing helix chain 'B' and resid 490 through 501 removed outlier: 3.719A pdb=" N LEU B 494 " --> pdb=" O ASP B 490 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 509 removed outlier: 4.182A pdb=" N ALA B 507 " --> pdb=" O SER B 503 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG B 508 " --> pdb=" O ASN B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 540 removed outlier: 3.858A pdb=" N GLN B 530 " --> pdb=" O PRO B 526 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG B 531 " --> pdb=" O GLY B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 570 removed outlier: 3.545A pdb=" N ILE B 565 " --> pdb=" O GLU B 561 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY B 566 " --> pdb=" O LEU B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 585 removed outlier: 3.912A pdb=" N LYS B 584 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 408 through 410 Processing sheet with id=AA2, first strand: chain 'A' and resid 456 through 458 removed outlier: 7.228A pdb=" N LEU A 457 " --> pdb=" O VAL A 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 408 through 410 Processing sheet with id=AA4, first strand: chain 'B' and resid 456 through 458 removed outlier: 7.227A pdb=" N LEU B 457 " --> pdb=" O VAL B 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 424 hydrogen bonds defined for protein. 1260 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: 2.58 Time building geometry restraints manager: 2.73 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: 2872 1.34 - 1.46: 1899 1.46 - 1.57: 4521 1.57 - 1.69: 10 1.69 - 1.81: 66 Bond restraints: 9368 Sorted by residual: bond pdb=" C SER B 302 " pdb=" N PRO B 303 " ideal model delta sigma weight residual 1.336 1.376 -0.040 9.80e-03 1.04e+04 1.64e+01 bond pdb=" C SER A 302 " pdb=" N PRO A 303 " ideal model delta sigma weight residual 1.336 1.375 -0.039 9.80e-03 1.04e+04 1.62e+01 bond pdb=" C LEU B 524 " pdb=" N SER B 525 " ideal model delta sigma weight residual 1.333 1.281 0.052 1.39e-02 5.18e+03 1.41e+01 bond pdb=" C LEU A 524 " pdb=" N SER A 525 " ideal model delta sigma weight residual 1.333 1.281 0.052 1.39e-02 5.18e+03 1.39e+01 bond pdb=" N PHE A 387 " pdb=" CA PHE A 387 " ideal model delta sigma weight residual 1.455 1.487 -0.033 1.29e-02 6.01e+03 6.45e+00 ... (remaining 9363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 12164 2.26 - 4.52: 449 4.52 - 6.78: 59 6.78 - 9.05: 24 9.05 - 11.31: 6 Bond angle restraints: 12702 Sorted by residual: angle pdb=" PB ATP B 701 " pdb=" O3B ATP B 701 " pdb=" PG ATP B 701 " ideal model delta sigma weight residual 139.87 132.60 7.27 1.00e+00 1.00e+00 5.28e+01 angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 132.63 7.24 1.00e+00 1.00e+00 5.25e+01 angle pdb=" C SER B 307 " pdb=" N THR B 308 " pdb=" CA THR B 308 " ideal model delta sigma weight residual 121.54 131.38 -9.84 1.91e+00 2.74e-01 2.65e+01 angle pdb=" C SER A 307 " pdb=" N THR A 308 " pdb=" CA THR A 308 " ideal model delta sigma weight residual 121.54 131.37 -9.83 1.91e+00 2.74e-01 2.65e+01 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 132.53 4.30 1.00e+00 1.00e+00 1.85e+01 ... (remaining 12697 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 4813 17.67 - 35.33: 600 35.33 - 53.00: 135 53.00 - 70.66: 40 70.66 - 88.33: 10 Dihedral angle restraints: 5598 sinusoidal: 2316 harmonic: 3282 Sorted by residual: dihedral pdb=" CA MET A 227 " pdb=" C MET A 227 " pdb=" N GLN A 228 " pdb=" CA GLN A 228 " ideal model delta harmonic sigma weight residual 180.00 157.12 22.88 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA MET B 227 " pdb=" C MET B 227 " pdb=" N GLN B 228 " pdb=" CA GLN B 228 " ideal model delta harmonic sigma weight residual 180.00 157.15 22.85 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA ILE A 475 " pdb=" C ILE A 475 " pdb=" N TYR A 476 " pdb=" CA TYR A 476 " ideal model delta harmonic sigma weight residual 180.00 -158.64 -21.36 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 5595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1017 0.057 - 0.114: 360 0.114 - 0.171: 49 0.171 - 0.228: 18 0.228 - 0.285: 4 Chirality restraints: 1448 Sorted by residual: chirality pdb=" CB ILE A 574 " pdb=" CA ILE A 574 " pdb=" CG1 ILE A 574 " pdb=" CG2 ILE A 574 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB ILE B 574 " pdb=" CA ILE B 574 " pdb=" CG1 ILE B 574 " pdb=" CG2 ILE B 574 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB ILE A 419 " pdb=" CA ILE A 419 " pdb=" CG1 ILE A 419 " pdb=" CG2 ILE A 419 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1445 not shown) Planarity restraints: 1580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 167 " -0.055 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO A 168 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 168 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 168 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 167 " 0.055 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO B 168 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO B 168 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 168 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 291 " -0.044 5.00e-02 4.00e+02 6.61e-02 6.99e+00 pdb=" N PRO A 292 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 292 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 292 " -0.038 5.00e-02 4.00e+02 ... (remaining 1577 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1327 2.75 - 3.28: 9119 3.28 - 3.82: 15961 3.82 - 4.36: 19573 4.36 - 4.90: 31882 Nonbonded interactions: 77862 Sorted by model distance: nonbonded pdb=" O THR B 423 " pdb=" O1B ATP B 701 " model vdw 2.206 3.040 nonbonded pdb=" O THR A 423 " pdb=" O1B ATP A 701 " model vdw 2.206 3.040 nonbonded pdb=" O ILE A 291 " pdb=" OG SER A 295 " model vdw 2.312 3.040 nonbonded pdb=" O ILE B 291 " pdb=" OG SER B 295 " model vdw 2.312 3.040 nonbonded pdb=" OH TYR A 108 " pdb=" OE1 GLN B 260 " model vdw 2.316 3.040 ... (remaining 77857 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.230 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 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 : 0.008 0.053 9368 Z= 0.503 Angle : 1.036 11.308 12702 Z= 0.555 Chirality : 0.059 0.285 1448 Planarity : 0.007 0.082 1580 Dihedral : 16.772 88.329 3490 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.00 % Allowed : 12.25 % Favored : 87.75 % 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: -6.19 (0.15), residues: 1122 helix: -4.17 (0.09), residues: 720 sheet: None (None), residues: 0 loop : -3.61 (0.23), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 520 HIS 0.004 0.001 HIS A 118 PHE 0.032 0.003 PHE A 324 TYR 0.021 0.003 TYR B 319 ARG 0.002 0.000 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.9050 (mt) cc_final: 0.8779 (mt) REVERT: A 55 PHE cc_start: 0.7354 (t80) cc_final: 0.6893 (m-10) REVERT: A 68 TYR cc_start: 0.7741 (m-80) cc_final: 0.7426 (m-10) REVERT: A 217 LYS cc_start: 0.8455 (tttt) cc_final: 0.8248 (tttp) REVERT: A 247 MET cc_start: 0.7616 (mmt) cc_final: 0.7366 (mmt) REVERT: A 465 PHE cc_start: 0.9099 (m-80) cc_final: 0.8878 (m-10) REVERT: A 567 GLN cc_start: 0.7960 (mp10) cc_final: 0.7664 (pm20) REVERT: B 55 PHE cc_start: 0.7394 (t80) cc_final: 0.6830 (m-10) REVERT: B 315 PHE cc_start: 0.7541 (t80) cc_final: 0.7050 (t80) REVERT: B 388 LEU cc_start: 0.8653 (mt) cc_final: 0.8401 (mt) REVERT: B 422 ASN cc_start: 0.8214 (t0) cc_final: 0.7305 (m-40) REVERT: B 465 PHE cc_start: 0.9070 (m-80) cc_final: 0.8856 (m-10) REVERT: B 495 ARG cc_start: 0.8205 (ttt180) cc_final: 0.7997 (ttt90) REVERT: B 517 ASP cc_start: 0.7162 (m-30) cc_final: 0.6952 (m-30) REVERT: B 518 TRP cc_start: 0.7900 (m-10) cc_final: 0.7395 (m-10) REVERT: B 567 GLN cc_start: 0.7880 (mp10) cc_final: 0.7636 (pm20) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.2190 time to fit residues: 83.5300 Evaluate side-chains 201 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 ASN A 201 ASN A 228 GLN ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN B 228 GLN ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.129591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.102813 restraints weight = 14504.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.106198 restraints weight = 7118.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.108327 restraints weight = 4595.078| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9368 Z= 0.215 Angle : 0.697 8.566 12702 Z= 0.357 Chirality : 0.042 0.147 1448 Planarity : 0.005 0.059 1580 Dihedral : 10.022 76.813 1310 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 1.98 % Allowed : 20.45 % Favored : 77.57 % 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: -4.43 (0.19), residues: 1122 helix: -2.51 (0.15), residues: 700 sheet: None (None), residues: 0 loop : -3.54 (0.24), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 111 HIS 0.004 0.001 HIS B 342 PHE 0.022 0.002 PHE B 451 TYR 0.013 0.001 TYR A 319 ARG 0.004 0.001 ARG B 145 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 235 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.9098 (mt) cc_final: 0.8875 (mt) REVERT: A 52 LEU cc_start: 0.9376 (tp) cc_final: 0.9011 (tp) REVERT: A 55 PHE cc_start: 0.7520 (t80) cc_final: 0.7033 (m-10) REVERT: A 84 PHE cc_start: 0.7904 (t80) cc_final: 0.7599 (t80) REVERT: A 217 LYS cc_start: 0.8563 (tttt) cc_final: 0.8292 (tttp) REVERT: A 234 GLU cc_start: 0.8577 (tp30) cc_final: 0.8194 (mm-30) REVERT: A 247 MET cc_start: 0.7757 (mmt) cc_final: 0.7508 (mmt) REVERT: A 271 TYR cc_start: 0.9064 (m-10) cc_final: 0.8760 (m-80) REVERT: A 312 LYS cc_start: 0.8235 (tmmt) cc_final: 0.7856 (ptmm) REVERT: A 422 ASN cc_start: 0.8221 (t0) cc_final: 0.7525 (m-40) REVERT: A 518 TRP cc_start: 0.7860 (m-10) cc_final: 0.7617 (m-10) REVERT: B 38 GLN cc_start: 0.7690 (tm-30) cc_final: 0.7327 (tm-30) REVERT: B 55 PHE cc_start: 0.7537 (t80) cc_final: 0.6757 (m-10) REVERT: B 247 MET cc_start: 0.7874 (mmt) cc_final: 0.7663 (mmt) REVERT: B 252 ARG cc_start: 0.8843 (mmt90) cc_final: 0.8633 (mtp85) REVERT: B 312 LYS cc_start: 0.8236 (tmmt) cc_final: 0.7821 (ptmm) REVERT: B 315 PHE cc_start: 0.7697 (t80) cc_final: 0.7141 (t80) REVERT: B 422 ASN cc_start: 0.8082 (t0) cc_final: 0.7647 (m110) REVERT: B 465 PHE cc_start: 0.9070 (m-80) cc_final: 0.8860 (m-10) outliers start: 20 outliers final: 8 residues processed: 242 average time/residue: 0.2155 time to fit residues: 73.7494 Evaluate side-chains 200 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 192 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 574 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/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-5592/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-5592/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-5592/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: 53.2348 > 50: distance: 30 - 54: 6.052 distance: 39 - 70: 17.830 distance: 49 - 54: 5.280 distance: 50 - 77: 27.727 distance: 54 - 55: 13.187 distance: 55 - 56: 15.452 distance: 55 - 58: 4.870 distance: 56 - 57: 14.259 distance: 56 - 62: 14.366 distance: 58 - 59: 15.856 distance: 59 - 60: 28.913 distance: 59 - 61: 13.446 distance: 62 - 63: 8.347 distance: 63 - 64: 12.775 distance: 63 - 66: 19.611 distance: 64 - 65: 18.235 distance: 64 - 70: 17.549 distance: 66 - 67: 11.726 distance: 67 - 68: 7.883 distance: 67 - 69: 8.713 distance: 70 - 71: 25.726 distance: 71 - 72: 23.277 distance: 71 - 74: 18.002 distance: 72 - 73: 14.887 distance: 72 - 77: 22.908 distance: 74 - 75: 12.561 distance: 74 - 76: 25.729 distance: 77 - 78: 8.374 distance: 78 - 79: 9.514 distance: 78 - 81: 11.115 distance: 79 - 80: 9.444 distance: 81 - 82: 12.406 distance: 82 - 83: 19.252 distance: 82 - 84: 14.103 distance: 86 - 87: 7.120 distance: 86 - 89: 18.956 distance: 87 - 88: 5.178 distance: 87 - 96: 11.882 distance: 89 - 90: 4.972 distance: 90 - 91: 20.048 distance: 92 - 93: 11.482 distance: 93 - 94: 14.442 distance: 93 - 95: 26.538 distance: 96 - 97: 14.429 distance: 97 - 98: 12.880 distance: 97 - 100: 12.416 distance: 98 - 104: 7.438 distance: 100 - 101: 36.947 distance: 101 - 102: 29.256 distance: 101 - 103: 22.805 distance: 104 - 105: 18.187 distance: 105 - 106: 6.103 distance: 105 - 108: 6.768 distance: 106 - 107: 8.765 distance: 106 - 112: 27.114 distance: 108 - 109: 12.959 distance: 109 - 110: 7.589 distance: 109 - 111: 3.275 distance: 112 - 113: 24.472 distance: 113 - 114: 12.338 distance: 113 - 116: 14.847 distance: 114 - 120: 16.536 distance: 116 - 117: 41.789 distance: 116 - 118: 9.565 distance: 117 - 119: 10.123 distance: 120 - 121: 19.158 distance: 121 - 122: 16.150 distance: 121 - 124: 7.529 distance: 122 - 123: 6.316 distance: 122 - 128: 32.261 distance: 124 - 125: 27.956 distance: 125 - 126: 25.711 distance: 125 - 127: 14.286 distance: 128 - 129: 16.135 distance: 129 - 130: 9.736 distance: 129 - 132: 5.173 distance: 130 - 131: 12.756 distance: 130 - 136: 9.046 distance: 131 - 157: 21.618 distance: 132 - 133: 18.992 distance: 133 - 134: 10.489 distance: 133 - 135: 16.321