Starting phenix.real_space_refine on Sat Aug 3 22:30:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf6_34714/08_2024/8hf6_34714.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf6_34714/08_2024/8hf6_34714.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf6_34714/08_2024/8hf6_34714.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf6_34714/08_2024/8hf6_34714.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf6_34714/08_2024/8hf6_34714.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf6_34714/08_2024/8hf6_34714.cif" } resolution = 3.1 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= 0.004 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 28 5.16 5 C 5732 2.51 5 N 1464 2.21 5 O 1686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 469": "OE1" <-> "OE2" Residue "A GLU 657": "OE1" <-> "OE2" Residue "A GLU 685": "OE1" <-> "OE2" Residue "B PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 584": "OE1" <-> "OE2" Residue "B GLU 614": "OE1" <-> "OE2" Residue "B PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8916 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4427 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 12, 'TRANS': 550} Chain: "B" Number of atoms: 4427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4427 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 12, 'TRANS': 550} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.44, per 1000 atoms: 0.50 Number of scatterers: 8916 At special positions: 0 Unit cell: (83.226, 84.084, 138.996, 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 28 16.00 P 6 15.00 O 1686 8.00 N 1464 7.00 C 5732 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.64 Conformation dependent library (CDL) restraints added in 1.6 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: 2124 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 5 sheets defined 69.0% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 157 through 164 removed outlier: 3.923A pdb=" N LEU A 161 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 195 removed outlier: 3.656A pdb=" N LEU A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU A 189 " --> pdb=" O GLY A 185 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLN A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER A 191 " --> pdb=" O TYR A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 251 removed outlier: 4.075A pdb=" N ASP A 240 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A 243 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 260 removed outlier: 4.028A pdb=" N PHE A 257 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 258 " --> pdb=" O MET A 254 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 272 removed outlier: 3.622A pdb=" N ARG A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 304 removed outlier: 4.270A pdb=" N ASP A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N VAL A 290 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 312 removed outlier: 3.517A pdb=" N PHE A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 325 removed outlier: 3.992A pdb=" N ILE A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE A 325 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 353 removed outlier: 3.704A pdb=" N PHE A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU A 330 " --> pdb=" O MET A 326 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 353 " --> pdb=" O GLU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 361 Processing helix chain 'A' and resid 362 through 416 removed outlier: 4.087A pdb=" N ARG A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP A 416 " --> pdb=" O VAL A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 460 removed outlier: 3.731A pdb=" N VAL A 432 " --> pdb=" O ASN A 428 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N TYR A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Proline residue: A 437 - end of helix removed outlier: 3.616A pdb=" N ASN A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR A 446 " --> pdb=" O ILE A 442 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LYS A 447 " --> pdb=" O ASN A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 464 Processing helix chain 'A' and resid 522 through 531 removed outlier: 3.597A pdb=" N VAL A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 551 Processing helix chain 'A' and resid 553 through 559 Processing helix chain 'A' and resid 573 through 580 Processing helix chain 'A' and resid 588 through 598 Processing helix chain 'A' and resid 623 through 638 removed outlier: 3.865A pdb=" N THR A 638 " --> pdb=" O ARG A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 666 removed outlier: 3.697A pdb=" N ALA A 666 " --> pdb=" O ASP A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 683 removed outlier: 3.716A pdb=" N GLU A 682 " --> pdb=" O LEU A 678 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG A 683 " --> pdb=" O THR A 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 678 through 683' Processing helix chain 'A' and resid 701 through 706 Processing helix chain 'A' and resid 709 through 717 Processing helix chain 'B' and resid 157 through 164 removed outlier: 3.953A pdb=" N GLN B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 196 removed outlier: 3.634A pdb=" N TYR B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU B 189 " --> pdb=" O GLY B 185 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLN B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 250 removed outlier: 3.809A pdb=" N ILE B 207 " --> pdb=" O SER B 203 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASP B 240 " --> pdb=" O ARG B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 260 removed outlier: 4.202A pdb=" N PHE B 257 " --> pdb=" O PRO B 253 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA B 258 " --> pdb=" O MET B 254 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR B 259 " --> pdb=" O SER B 255 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B 260 " --> pdb=" O PHE B 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 253 through 260' Processing helix chain 'B' and resid 261 through 276 removed outlier: 3.635A pdb=" N ILE B 265 " --> pdb=" O ARG B 261 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER B 274 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE B 275 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 304 Processing helix chain 'B' and resid 305 through 312 removed outlier: 3.868A pdb=" N MET B 310 " --> pdb=" O ASN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 325 removed outlier: 4.064A pdb=" N ILE B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE B 325 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 352 removed outlier: 3.622A pdb=" N PHE B 329 " --> pdb=" O PHE B 325 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU B 330 " --> pdb=" O MET B 326 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B 331 " --> pdb=" O LYS B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 362 through 417 removed outlier: 4.122A pdb=" N ARG B 366 " --> pdb=" O SER B 362 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 431 Processing helix chain 'B' and resid 431 through 460 Proline residue: B 437 - end of helix removed outlier: 4.196A pdb=" N THR B 446 " --> pdb=" O ILE B 442 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS B 447 " --> pdb=" O ASN B 443 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA B 454 " --> pdb=" O THR B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 464 removed outlier: 3.646A pdb=" N VAL B 464 " --> pdb=" O VAL B 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 461 through 464' Processing helix chain 'B' and resid 522 through 531 removed outlier: 3.645A pdb=" N VAL B 531 " --> pdb=" O ALA B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 551 No H-bonds generated for 'chain 'B' and resid 549 through 551' Processing helix chain 'B' and resid 552 through 559 Processing helix chain 'B' and resid 573 through 579 Processing helix chain 'B' and resid 588 through 598 removed outlier: 3.684A pdb=" N ALA B 598 " --> pdb=" O ALA B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 638 removed outlier: 3.752A pdb=" N THR B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 666 removed outlier: 3.950A pdb=" N ALA B 666 " --> pdb=" O ASP B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 684 removed outlier: 4.593A pdb=" N ARG B 683 " --> pdb=" O THR B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 708 removed outlier: 3.557A pdb=" N LEU B 704 " --> pdb=" O LYS B 700 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 708 " --> pdb=" O LEU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 717 Processing sheet with id=AA1, first strand: chain 'A' and resid 500 through 503 removed outlier: 3.826A pdb=" N LEU A 500 " --> pdb=" O TYR A 491 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL A 489 " --> pdb=" O ASP A 502 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET A 484 " --> pdb=" O VAL A 507 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 500 through 503 removed outlier: 3.826A pdb=" N LEU A 500 " --> pdb=" O TYR A 491 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL A 489 " --> pdb=" O ASP A 502 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 540 " --> pdb=" O LYS A 487 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL A 489 " --> pdb=" O GLN A 538 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLN A 538 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 560 through 563 removed outlier: 6.367A pdb=" N ASN A 561 " --> pdb=" O ILE A 644 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASP A 646 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU A 563 " --> pdb=" O ASP A 646 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE A 643 " --> pdb=" O ILE A 672 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILE A 674 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU A 645 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL A 513 " --> pdb=" O PHE A 673 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS A 512 " --> pdb=" O LYS A 686 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N VAL A 688 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ALA A 514 " --> pdb=" O VAL A 688 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU A 690 " --> pdb=" O ALA A 514 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL A 516 " --> pdb=" O LEU A 690 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL A 687 " --> pdb=" O GLU A 698 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU A 698 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL A 689 " --> pdb=" O VAL A 696 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 506 through 507 removed outlier: 4.172A pdb=" N VAL B 489 " --> pdb=" O GLN B 538 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLN B 538 " --> pdb=" O VAL B 489 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 546 " --> pdb=" O LEU B 543 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 560 through 563 removed outlier: 6.627A pdb=" N ASN B 561 " --> pdb=" O ILE B 644 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL B 513 " --> pdb=" O PHE B 673 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N VAL B 688 " --> pdb=" O LYS B 512 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ALA B 514 " --> pdb=" O VAL B 688 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU B 690 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL B 516 " --> pdb=" O LEU B 690 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU B 697 " --> pdb=" O VAL B 689 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1593 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: 2.55 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1466 1.29 - 1.42: 2144 1.42 - 1.55: 5371 1.55 - 1.68: 13 1.68 - 1.81: 56 Bond restraints: 9050 Sorted by residual: bond pdb=" CA ILE B 158 " pdb=" C ILE B 158 " ideal model delta sigma weight residual 1.524 1.442 0.082 1.05e-02 9.07e+03 6.12e+01 bond pdb=" CA ILE B 286 " pdb=" C ILE B 286 " ideal model delta sigma weight residual 1.524 1.426 0.098 1.39e-02 5.18e+03 4.95e+01 bond pdb=" CA GLN A 647 " pdb=" CB GLN A 647 " ideal model delta sigma weight residual 1.530 1.427 0.103 1.48e-02 4.57e+03 4.87e+01 bond pdb=" CA SER A 156 " pdb=" C SER A 156 " ideal model delta sigma weight residual 1.523 1.431 0.092 1.34e-02 5.57e+03 4.70e+01 bond pdb=" C4 ATP A 801 " pdb=" C5 ATP A 801 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.58e+01 ... (remaining 9045 not shown) Histogram of bond angle deviations from ideal: 97.71 - 105.62: 154 105.62 - 113.54: 5271 113.54 - 121.46: 5079 121.46 - 129.38: 1744 129.38 - 137.29: 30 Bond angle restraints: 12278 Sorted by residual: angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 123.00 16.87 1.00e+00 1.00e+00 2.85e+02 angle pdb=" PB ATP B 801 " pdb=" O3B ATP B 801 " pdb=" PG ATP B 801 " ideal model delta sigma weight residual 139.87 123.01 16.86 1.00e+00 1.00e+00 2.84e+02 angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 121.58 15.25 1.00e+00 1.00e+00 2.33e+02 angle pdb=" PA ATP B 801 " pdb=" O3A ATP B 801 " pdb=" PB ATP B 801 " ideal model delta sigma weight residual 136.83 121.60 15.23 1.00e+00 1.00e+00 2.32e+02 angle pdb=" N SER A 156 " pdb=" CA SER A 156 " pdb=" C SER A 156 " ideal model delta sigma weight residual 112.88 99.00 13.88 1.29e+00 6.01e-01 1.16e+02 ... (remaining 12273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4901 17.91 - 35.82: 488 35.82 - 53.73: 91 53.73 - 71.64: 28 71.64 - 89.55: 10 Dihedral angle restraints: 5518 sinusoidal: 2224 harmonic: 3294 Sorted by residual: dihedral pdb=" C SER A 156 " pdb=" N SER A 156 " pdb=" CA SER A 156 " pdb=" CB SER A 156 " ideal model delta harmonic sigma weight residual -122.60 -104.93 -17.67 0 2.50e+00 1.60e-01 4.99e+01 dihedral pdb=" C TYR A 188 " pdb=" N TYR A 188 " pdb=" CA TYR A 188 " pdb=" CB TYR A 188 " ideal model delta harmonic sigma weight residual -122.60 -138.22 15.62 0 2.50e+00 1.60e-01 3.90e+01 dihedral pdb=" N TYR A 188 " pdb=" C TYR A 188 " pdb=" CA TYR A 188 " pdb=" CB TYR A 188 " ideal model delta harmonic sigma weight residual 122.80 136.78 -13.98 0 2.50e+00 1.60e-01 3.13e+01 ... (remaining 5515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 1445 0.154 - 0.307: 45 0.307 - 0.461: 6 0.461 - 0.615: 1 0.615 - 0.768: 1 Chirality restraints: 1498 Sorted by residual: chirality pdb=" CA TYR A 188 " pdb=" N TYR A 188 " pdb=" C TYR A 188 " pdb=" CB TYR A 188 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" CA THR B 361 " pdb=" N THR B 361 " pdb=" C THR B 361 " pdb=" CB THR B 361 " both_signs ideal model delta sigma weight residual False 2.53 1.96 0.57 2.00e-01 2.50e+01 8.04e+00 chirality pdb=" CA ALA B 620 " pdb=" N ALA B 620 " pdb=" C ALA B 620 " pdb=" CB ALA B 620 " both_signs ideal model delta sigma weight residual False 2.48 2.05 0.43 2.00e-01 2.50e+01 4.68e+00 ... (remaining 1495 not shown) Planarity restraints: 1522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 647 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" C GLN A 647 " -0.052 2.00e-02 2.50e+03 pdb=" O GLN A 647 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA A 648 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 268 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.85e+00 pdb=" C ARG A 268 " -0.051 2.00e-02 2.50e+03 pdb=" O ARG A 268 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE A 269 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 196 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.63e+00 pdb=" C TYR A 196 " -0.045 2.00e-02 2.50e+03 pdb=" O TYR A 196 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL A 197 " 0.015 2.00e-02 2.50e+03 ... (remaining 1519 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1308 2.75 - 3.28: 9189 3.28 - 3.82: 14266 3.82 - 4.36: 15970 4.36 - 4.90: 27576 Nonbonded interactions: 68309 Sorted by model distance: nonbonded pdb=" OD1 ASP A 653 " pdb=" OG1 THR A 656 " model vdw 2.207 3.040 nonbonded pdb=" N THR A 195 " pdb=" O THR A 195 " model vdw 2.282 2.496 nonbonded pdb=" OG1 THR B 524 " pdb=" O2G ATP B 801 " model vdw 2.288 3.040 nonbonded pdb=" O ALA B 640 " pdb=" NZ LYS B 669 " model vdw 2.290 3.120 nonbonded pdb=" N SER A 156 " pdb=" N PHE A 157 " model vdw 2.309 2.560 ... (remaining 68304 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' 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 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: 4.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 26.770 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 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 : 0.009 0.103 9050 Z= 0.573 Angle : 1.048 16.871 12278 Z= 0.713 Chirality : 0.067 0.768 1498 Planarity : 0.005 0.056 1522 Dihedral : 15.338 89.551 3394 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.63 % Favored : 95.10 % Rotamer: Outliers : 3.23 % Allowed : 2.83 % Favored : 93.94 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.26), residues: 1122 helix: 2.03 (0.20), residues: 698 sheet: 0.32 (0.66), residues: 66 loop : -1.70 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 408 HIS 0.003 0.001 HIS A 248 PHE 0.025 0.002 PHE A 269 TYR 0.016 0.001 TYR B 493 ARG 0.006 0.001 ARG A 593 *********************** 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 134 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 102 time to evaluate : 1.097 Fit side-chains REVERT: A 201 MET cc_start: 0.8298 (ttm) cc_final: 0.8030 (ttm) REVERT: A 212 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8898 (mp) REVERT: B 678 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9145 (mt) outliers start: 32 outliers final: 15 residues processed: 129 average time/residue: 0.1905 time to fit residues: 35.2068 Evaluate side-chains 86 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 69 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 201 MET Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 680 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 676 HIS B 200 GLN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9050 Z= 0.229 Angle : 0.586 9.755 12278 Z= 0.314 Chirality : 0.041 0.309 1498 Planarity : 0.003 0.038 1522 Dihedral : 9.100 85.070 1309 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.92 % Favored : 95.90 % Rotamer: Outliers : 2.42 % Allowed : 8.99 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.26), residues: 1122 helix: 2.41 (0.20), residues: 700 sheet: 0.34 (0.65), residues: 66 loop : -1.60 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 408 HIS 0.008 0.001 HIS A 676 PHE 0.013 0.001 PHE B 468 TYR 0.010 0.001 TYR B 228 ARG 0.005 0.000 ARG B 683 *********************** 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 106 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 82 time to evaluate : 1.029 Fit side-chains REVERT: A 607 MET cc_start: 0.7624 (pmm) cc_final: 0.7216 (pmm) outliers start: 24 outliers final: 16 residues processed: 101 average time/residue: 0.1649 time to fit residues: 25.2028 Evaluate side-chains 89 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 713 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 84 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 0.0010 chunk 101 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 overall best weight: 1.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 HIS A 676 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9050 Z= 0.223 Angle : 0.548 10.185 12278 Z= 0.293 Chirality : 0.040 0.327 1498 Planarity : 0.003 0.029 1522 Dihedral : 7.709 74.655 1291 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.02 % Allowed : 11.52 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.26), residues: 1122 helix: 2.54 (0.20), residues: 704 sheet: 0.25 (0.64), residues: 66 loop : -1.65 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 408 HIS 0.005 0.001 HIS A 676 PHE 0.011 0.001 PHE B 468 TYR 0.016 0.001 TYR A 559 ARG 0.003 0.000 ARG B 683 *********************** REFINEMENT MACRO_CYCLE 3 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 96 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 76 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: A 606 ARG cc_start: 0.8648 (mtm110) cc_final: 0.8113 (mpp80) REVERT: A 607 MET cc_start: 0.7773 (pmm) cc_final: 0.7472 (pmm) outliers start: 20 outliers final: 13 residues processed: 90 average time/residue: 0.1790 time to fit residues: 23.9691 Evaluate side-chains 84 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 713 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.0877 > 50: distance: 38 - 98: 26.910 distance: 92 - 98: 29.438 distance: 98 - 99: 50.376 distance: 99 - 100: 43.170 distance: 99 - 102: 32.951 distance: 100 - 101: 42.647 distance: 100 - 106: 40.231 distance: 102 - 103: 42.426 distance: 102 - 104: 26.477 distance: 103 - 105: 16.972 distance: 106 - 107: 21.191 distance: 107 - 110: 40.911 distance: 108 - 109: 31.193 distance: 108 - 111: 39.600 distance: 111 - 112: 39.585 distance: 112 - 115: 8.850 distance: 115 - 116: 33.102 distance: 116 - 117: 55.454 distance: 116 - 118: 56.467 distance: 117 - 119: 37.424 distance: 119 - 120: 36.599 distance: 123 - 124: 39.875 distance: 123 - 132: 9.754 distance: 126 - 127: 39.047 distance: 127 - 128: 40.639 distance: 128 - 129: 8.407 distance: 129 - 130: 8.175 distance: 129 - 131: 50.414 distance: 132 - 133: 31.288 distance: 133 - 136: 40.003 distance: 134 - 135: 44.626 distance: 134 - 140: 20.037 distance: 136 - 137: 33.100 distance: 137 - 138: 35.388 distance: 137 - 139: 40.193 distance: 140 - 141: 18.928 distance: 141 - 142: 39.731 distance: 142 - 147: 46.995 distance: 144 - 145: 42.675 distance: 147 - 148: 43.586 distance: 149 - 155: 40.326 distance: 150 - 180: 32.421 distance: 151 - 152: 39.863 distance: 152 - 154: 40.210 distance: 156 - 159: 40.219 distance: 157 - 158: 39.164 distance: 157 - 160: 40.718 distance: 160 - 161: 56.758 distance: 161 - 162: 6.998 distance: 161 - 164: 39.781 distance: 162 - 163: 32.326 distance: 162 - 169: 31.296 distance: 166 - 167: 39.960 distance: 166 - 168: 45.201 distance: 169 - 170: 39.134 distance: 170 - 171: 48.283 distance: 170 - 173: 41.324 distance: 171 - 180: 34.377 distance: 175 - 176: 48.745 distance: 176 - 177: 29.234 distance: 177 - 178: 3.720 distance: 177 - 179: 41.106