Starting phenix.real_space_refine on Wed Jan 14 03:05:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h06_34409/01_2026/8h06_34409.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h06_34409/01_2026/8h06_34409.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8h06_34409/01_2026/8h06_34409.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h06_34409/01_2026/8h06_34409.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h06_34409/01_2026/8h06_34409.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h06_34409/01_2026/8h06_34409.map" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6345 atoms to isotropic. 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 Zn 1 6.06 5 S 37 5.16 5 C 4195 2.51 5 N 1079 2.21 5 O 1248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6560 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4869 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Conformer: "B" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} bond proxies already assigned to first conformer: 4990 Chain: "B" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1554 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.49, per 1000 atoms: 0.38 Number of scatterers: 6560 At special positions: 0 Unit cell: (82.72, 91.52, 119.68, 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) Zn 1 29.99 S 37 16.00 O 1248 8.00 N 1079 7.00 C 4195 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " BETA1-6 " NAG D 1 " - " FUC D 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 701 " - " ASN A 53 " " NAG A 702 " - " ASN A 90 " " NAG A 703 " - " ASN A 322 " " NAG A 704 " - " ASN A 432 " " NAG B 601 " - " ASN B 343 " " NAG C 1 " - " ASN A 103 " " NAG D 1 " - " ASN A 546 " Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 400.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 705 " pdb="ZN ZN A 705 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 705 " - pdb=" NE2 HIS A 374 " 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 6 sheets defined 55.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.547A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 removed outlier: 3.584A pdb=" N THR A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 80 " --> pdb=" O GLN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 92 through 101 removed outlier: 3.602A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.974A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 158 through 172 removed outlier: 3.763A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 176 through 194 removed outlier: 3.573A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 249 removed outlier: 3.975A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS A 234 " --> pdb=" O PHE A 230 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.677A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.768A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 412 removed outlier: 3.593A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 433 through 447 removed outlier: 3.768A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 481 removed outlier: 3.659A pdb=" N LYS A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS A 481 " --> pdb=" O TRP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.083A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.736A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.831A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.755A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 405 through 410 removed outlier: 5.218A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.590A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.098A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 283 hydrogen bonds defined for protein. 798 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: 0.95 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2089 1.35 - 1.48: 1834 1.48 - 1.61: 2764 1.61 - 1.75: 0 1.75 - 1.88: 58 Bond restraints: 6745 Sorted by residual: bond pdb=" CA SER B 494 " pdb=" CB SER B 494 " ideal model delta sigma weight residual 1.528 1.473 0.055 1.48e-02 4.57e+03 1.40e+01 bond pdb=" CE1 HIS A 401 " pdb=" NE2 HIS A 401 " ideal model delta sigma weight residual 1.321 1.355 -0.034 1.00e-02 1.00e+04 1.19e+01 bond pdb=" N LYS B 378 " pdb=" CA LYS B 378 " ideal model delta sigma weight residual 1.454 1.495 -0.041 1.23e-02 6.61e+03 1.13e+01 bond pdb=" N CYS B 379 " pdb=" CA CYS B 379 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.22e-02 6.72e+03 8.84e+00 bond pdb=" N SER B 494 " pdb=" CA SER B 494 " ideal model delta sigma weight residual 1.452 1.484 -0.032 1.25e-02 6.40e+03 6.39e+00 ... (remaining 6740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 8741 1.36 - 2.72: 333 2.72 - 4.08: 76 4.08 - 5.45: 16 5.45 - 6.81: 5 Bond angle restraints: 9171 Sorted by residual: angle pdb=" CA LYS B 378 " pdb=" C LYS B 378 " pdb=" O LYS B 378 " ideal model delta sigma weight residual 121.11 116.78 4.33 1.13e+00 7.83e-01 1.47e+01 angle pdb=" CA GLN B 493 " pdb=" C GLN B 493 " pdb=" O GLN B 493 " ideal model delta sigma weight residual 121.06 117.29 3.77 1.16e+00 7.43e-01 1.06e+01 angle pdb=" CA SER B 494 " pdb=" C SER B 494 " pdb=" O SER B 494 " ideal model delta sigma weight residual 121.82 117.95 3.87 1.21e+00 6.83e-01 1.02e+01 angle pdb=" CA HIS A 401 " pdb=" C HIS A 401 " pdb=" O HIS A 401 " ideal model delta sigma weight residual 120.90 117.63 3.27 1.03e+00 9.43e-01 1.01e+01 angle pdb=" CA GLN A 24 " pdb=" C GLN A 24 " pdb=" O GLN A 24 " ideal model delta sigma weight residual 120.55 117.28 3.27 1.06e+00 8.90e-01 9.52e+00 ... (remaining 9166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 3723 16.71 - 33.41: 290 33.41 - 50.11: 66 50.11 - 66.82: 21 66.82 - 83.52: 7 Dihedral angle restraints: 4107 sinusoidal: 1781 harmonic: 2326 Sorted by residual: dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -125.66 39.66 1 1.00e+01 1.00e-02 2.21e+01 dihedral pdb=" CA ASN A 53 " pdb=" C ASN A 53 " pdb=" N ILE A 54 " pdb=" CA ILE A 54 " ideal model delta harmonic sigma weight residual 180.00 163.41 16.59 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA ALA A 396 " pdb=" C ALA A 396 " pdb=" N ASN A 397 " pdb=" CA ASN A 397 " ideal model delta harmonic sigma weight residual 180.00 163.44 16.56 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 4104 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 676 0.042 - 0.083: 235 0.083 - 0.125: 65 0.125 - 0.167: 7 0.167 - 0.209: 3 Chirality restraints: 986 Sorted by residual: chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 53 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB ILE B 410 " pdb=" CA ILE B 410 " pdb=" CG1 ILE B 410 " pdb=" CG2 ILE B 410 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.69e-01 chirality pdb=" CA GLN B 493 " pdb=" N GLN B 493 " pdb=" C GLN B 493 " pdb=" CB GLN B 493 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 983 not shown) Planarity restraints: 1184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 468 " -0.031 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO A 469 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 469 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 469 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 41 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.46e+00 pdb=" C TYR A 41 " -0.032 2.00e-02 2.50e+03 pdb=" O TYR A 41 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN A 42 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 400 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.18e+00 pdb=" C PHE A 400 " 0.031 2.00e-02 2.50e+03 pdb=" O PHE A 400 " -0.012 2.00e-02 2.50e+03 pdb=" N HIS A 401 " -0.010 2.00e-02 2.50e+03 ... (remaining 1181 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 21 2.58 - 3.16: 5095 3.16 - 3.74: 9347 3.74 - 4.32: 13290 4.32 - 4.90: 22854 Nonbonded interactions: 50607 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 705 " model vdw 2.005 2.230 nonbonded pdb=" OE2 GLU A 435 " pdb=" NE2 HIS A 540 " model vdw 2.270 3.120 nonbonded pdb=" O GLY A 268 " pdb=" ND2 ASN A 277 " model vdw 2.381 3.120 nonbonded pdb=" O THR A 118 " pdb=" OG1 THR A 122 " model vdw 2.420 3.040 nonbonded pdb=" NH1 ARG B 457 " pdb=" OD2 ASP B 467 " model vdw 2.449 3.120 ... (remaining 50602 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 17.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.640 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:6.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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 : 0.005 0.205 6764 Z= 0.240 Angle : 0.652 6.872 9215 Z= 0.370 Chirality : 0.044 0.209 986 Planarity : 0.004 0.048 1177 Dihedral : 13.274 83.525 2594 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.43 % Favored : 96.44 % Rotamer: Outliers : 0.58 % Allowed : 0.14 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.20 (0.30), residues: 788 helix: 0.63 (0.28), residues: 385 sheet: 1.50 (0.81), residues: 46 loop : -1.21 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 115 TYR 0.018 0.001 TYR B 495 PHE 0.017 0.001 PHE A 512 TRP 0.007 0.001 TRP A 168 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 6745) covalent geometry : angle 0.64152 ( 9171) SS BOND : bond 0.01212 ( 7) SS BOND : angle 1.73003 ( 14) hydrogen bonds : bond 0.15971 ( 283) hydrogen bonds : angle 5.73530 ( 798) metal coordination : bond 0.20091 ( 2) link_BETA1-4 : bond 0.00556 ( 2) link_BETA1-4 : angle 1.22629 ( 6) link_BETA1-6 : bond 0.00361 ( 1) link_BETA1-6 : angle 1.50140 ( 3) link_NAG-ASN : bond 0.00294 ( 7) link_NAG-ASN : angle 2.06048 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 179 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.8326 (ptpp) cc_final: 0.8051 (ptpp) REVERT: A 137 ASN cc_start: 0.7251 (t0) cc_final: 0.6941 (t0) REVERT: A 150 GLU cc_start: 0.7270 (tm-30) cc_final: 0.6981 (tm-30) REVERT: A 568 LEU cc_start: 0.8204 (tp) cc_final: 0.7698 (tp) REVERT: B 438 SER cc_start: 0.8431 (p) cc_final: 0.8137 (p) outliers start: 4 outliers final: 2 residues processed: 181 average time/residue: 0.5417 time to fit residues: 103.0241 Evaluate side-chains 158 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 156 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 378 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 0.0670 chunk 45 optimal weight: 0.0470 chunk 74 optimal weight: 0.0980 overall best weight: 0.1816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 121 ASN A 154 ASN A 287 GLN A 572 ASN A 586 ASN B 409 GLN B 477 ASN B 481 ASN B 493 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.113497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.101195 restraints weight = 11705.883| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.13 r_work: 0.3213 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6764 Z= 0.142 Angle : 0.557 7.783 9215 Z= 0.284 Chirality : 0.043 0.243 986 Planarity : 0.004 0.046 1177 Dihedral : 6.491 56.882 1074 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.59 % Allowed : 9.80 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.03 (0.30), residues: 788 helix: 0.79 (0.28), residues: 392 sheet: 1.56 (0.78), residues: 44 loop : -1.05 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 454 TYR 0.013 0.001 TYR A 50 PHE 0.027 0.001 PHE A 512 TRP 0.013 0.001 TRP A 165 HIS 0.003 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 6745) covalent geometry : angle 0.54177 ( 9171) SS BOND : bond 0.00470 ( 7) SS BOND : angle 1.79731 ( 14) hydrogen bonds : bond 0.06000 ( 283) hydrogen bonds : angle 4.46443 ( 798) metal coordination : bond 0.00236 ( 2) link_BETA1-4 : bond 0.00404 ( 2) link_BETA1-4 : angle 1.20014 ( 6) link_BETA1-6 : bond 0.00267 ( 1) link_BETA1-6 : angle 1.68622 ( 3) link_NAG-ASN : bond 0.00329 ( 7) link_NAG-ASN : angle 2.20679 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.279 Fit side-chains REVERT: A 131 LYS cc_start: 0.8758 (ptpp) cc_final: 0.8491 (ptpp) REVERT: A 137 ASN cc_start: 0.7344 (t0) cc_final: 0.6910 (t0) REVERT: A 152 MET cc_start: 0.8575 (mmm) cc_final: 0.8368 (mmt) REVERT: A 401 HIS cc_start: 0.8595 (OUTLIER) cc_final: 0.8101 (m-70) outliers start: 11 outliers final: 4 residues processed: 157 average time/residue: 0.5952 time to fit residues: 97.8175 Evaluate side-chains 150 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 145 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 0.0980 chunk 67 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 16 optimal weight: 0.0870 chunk 8 optimal weight: 0.9990 chunk 56 optimal weight: 0.3980 chunk 68 optimal weight: 0.2980 chunk 14 optimal weight: 0.8980 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN B 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.111460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.098734 restraints weight = 13464.114| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.29 r_work: 0.3169 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 6764 Z= 0.200 Angle : 0.595 8.765 9215 Z= 0.301 Chirality : 0.045 0.272 986 Planarity : 0.004 0.046 1177 Dihedral : 6.151 58.465 1074 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.17 % Allowed : 10.66 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.01 (0.30), residues: 788 helix: 0.80 (0.28), residues: 393 sheet: 0.93 (0.74), residues: 49 loop : -1.07 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 559 TYR 0.015 0.002 TYR A 385 PHE 0.022 0.002 PHE A 512 TRP 0.016 0.001 TRP A 165 HIS 0.004 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 6745) covalent geometry : angle 0.57640 ( 9171) SS BOND : bond 0.00585 ( 7) SS BOND : angle 2.43383 ( 14) hydrogen bonds : bond 0.06695 ( 283) hydrogen bonds : angle 4.34502 ( 798) metal coordination : bond 0.00285 ( 2) link_BETA1-4 : bond 0.00378 ( 2) link_BETA1-4 : angle 1.18356 ( 6) link_BETA1-6 : bond 0.00019 ( 1) link_BETA1-6 : angle 1.72276 ( 3) link_NAG-ASN : bond 0.00303 ( 7) link_NAG-ASN : angle 2.35554 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 131 LYS cc_start: 0.8790 (ptpp) cc_final: 0.8536 (ptpp) REVERT: A 137 ASN cc_start: 0.7400 (t0) cc_final: 0.6937 (t0) REVERT: A 401 HIS cc_start: 0.8761 (OUTLIER) cc_final: 0.8327 (m-70) REVERT: A 568 LEU cc_start: 0.8530 (tt) cc_final: 0.8326 (tp) REVERT: B 405 ASN cc_start: 0.8655 (OUTLIER) cc_final: 0.8303 (p0) outliers start: 22 outliers final: 9 residues processed: 162 average time/residue: 0.6147 time to fit residues: 104.3107 Evaluate side-chains 161 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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-2.0-5927/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: 51.4985 > 50: distance: 43 - 44: 3.944 distance: 44 - 47: 4.510 distance: 45 - 46: 4.026 distance: 45 - 51: 6.659 distance: 47 - 48: 7.493 distance: 47 - 49: 10.796 distance: 48 - 50: 3.098 distance: 51 - 52: 7.453 distance: 52 - 53: 6.416 distance: 52 - 55: 9.401 distance: 53 - 54: 13.460 distance: 53 - 60: 4.129 distance: 56 - 57: 7.778 distance: 57 - 58: 4.772 distance: 60 - 61: 7.238 distance: 61 - 62: 11.626 distance: 62 - 63: 34.258 distance: 62 - 68: 17.298 distance: 64 - 65: 6.673 distance: 65 - 66: 9.765 distance: 65 - 67: 13.839 distance: 67 - 168: 3.223 distance: 68 - 69: 13.945 distance: 69 - 70: 11.610 distance: 69 - 72: 11.795 distance: 70 - 71: 8.028 distance: 70 - 76: 5.103 distance: 72 - 73: 11.437 distance: 73 - 74: 12.946 distance: 73 - 75: 3.081 distance: 77 - 78: 3.910 distance: 77 - 80: 5.668 distance: 78 - 79: 6.695 distance: 78 - 83: 3.924 distance: 80 - 81: 4.573 distance: 84 - 85: 4.168 distance: 84 - 87: 5.939 distance: 85 - 90: 3.928 distance: 86 - 116: 6.741 distance: 87 - 88: 6.406 distance: 87 - 89: 3.817 distance: 90 - 91: 3.488 distance: 91 - 92: 3.846 distance: 91 - 94: 6.188 distance: 93 - 124: 4.595 distance: 94 - 95: 4.435 distance: 96 - 97: 5.575 distance: 102 - 131: 3.073 distance: 104 - 105: 3.269 distance: 104 - 106: 3.660 distance: 107 - 108: 5.367 distance: 108 - 109: 3.221 distance: 108 - 111: 4.705 distance: 109 - 110: 4.238 distance: 110 - 136: 6.226 distance: 111 - 112: 7.781 distance: 113 - 115: 7.811 distance: 116 - 117: 4.377 distance: 117 - 120: 3.376 distance: 118 - 124: 3.151 distance: 119 - 143: 4.572 distance: 120 - 121: 4.198 distance: 121 - 122: 9.666 distance: 121 - 123: 6.033