Starting phenix.real_space_refine on Thu Jul 2 12:09:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yg5_72913/07_2026/9yg5_72913.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yg5_72913/07_2026/9yg5_72913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yg5_72913/07_2026/9yg5_72913.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yg5_72913/07_2026/9yg5_72913.map" model { file = "/net/cci-nas-00/data/ceres_data/9yg5_72913/07_2026/9yg5_72913.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yg5_72913/07_2026/9yg5_72913.cif" } resolution = 3.41 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= 1.000 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 5393 2.51 5 N 1356 2.21 5 O 1453 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8250 Number of models: 1 Model: "" Number of chains: 2 Chain: "D" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3103 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 14, 'TRANS': 369} Chain breaks: 1 Chain: "B" Number of atoms: 5147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5147 Classifications: {'peptide': 636} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 604} Chain breaks: 6 Time building chain proxies: 1.53, per 1000 atoms: 0.19 Number of scatterers: 8250 At special positions: 0 Unit cell: (125.632, 150.592, 99.008, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1453 8.00 N 1356 7.00 C 5393 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: 0.50 Conformation dependent library (CDL) restraints added in 287.3 milliseconds 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1956 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 8 sheets defined 38.7% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'D' and resid 4 through 32 removed outlier: 3.722A pdb=" N LEU D 8 " --> pdb=" O PRO D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 59 Proline residue: D 47 - end of helix removed outlier: 3.678A pdb=" N HIS D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 75 Processing helix chain 'D' and resid 77 through 93 Processing helix chain 'D' and resid 124 through 146 removed outlier: 3.533A pdb=" N LEU D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 161 Processing helix chain 'D' and resid 166 through 196 removed outlier: 3.674A pdb=" N LEU D 178 " --> pdb=" O THR D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 233 removed outlier: 3.832A pdb=" N VAL D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 260 removed outlier: 3.923A pdb=" N ILE D 241 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE D 243 " --> pdb=" O VAL D 239 " (cutoff:3.500A) Proline residue: D 252 - end of helix Processing helix chain 'D' and resid 272 through 294 Processing helix chain 'D' and resid 313 through 338 removed outlier: 3.669A pdb=" N LEU D 317 " --> pdb=" O ASN D 313 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL D 319 " --> pdb=" O TYR D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 346 removed outlier: 3.580A pdb=" N TYR D 343 " --> pdb=" O THR D 340 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR D 345 " --> pdb=" O ILE D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 373 Processing helix chain 'B' and resid 1611 through 1615 Processing helix chain 'B' and resid 1654 through 1669 Processing helix chain 'B' and resid 1736 through 1740 removed outlier: 3.593A pdb=" N ARG B1740 " --> pdb=" O ILE B1737 " (cutoff:3.500A) Processing helix chain 'B' and resid 1847 through 1866 Processing helix chain 'B' and resid 2570 through 2586 Processing helix chain 'B' and resid 2674 through 2678 Processing helix chain 'B' and resid 2717 through 2728 Processing helix chain 'B' and resid 3052 through 3064 Processing helix chain 'B' and resid 3153 through 3167 removed outlier: 3.550A pdb=" N THR B3162 " --> pdb=" O ARG B3158 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 122 through 123 Processing sheet with id=AA2, first strand: chain 'D' and resid 105 through 107 Processing sheet with id=AA3, first strand: chain 'D' and resid 299 through 300 removed outlier: 4.827A pdb=" N GLN D 299 " --> pdb=" O SER D 309 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1552 through 1559 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1552 through 1559 current: chain 'B' and resid 1576 through 1589 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1594 through 1598 current: chain 'B' and resid 1621 through 1626 Processing sheet with id=AA5, first strand: chain 'B' and resid 1640 through 1653 removed outlier: 6.955A pdb=" N VAL B1641 " --> pdb=" O GLU B1720 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE B1722 " --> pdb=" O VAL B1641 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASP B1643 " --> pdb=" O ILE B1722 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N MET B1724 " --> pdb=" O ASP B1643 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER B1645 " --> pdb=" O MET B1724 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE B1726 " --> pdb=" O SER B1645 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LYS B1647 " --> pdb=" O ILE B1726 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE B1730 " --> pdb=" O LEU B1649 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER B1728 " --> pdb=" O SER B1749 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N SER B1749 " --> pdb=" O SER B1728 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE B1730 " --> pdb=" O ALA B1747 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ALA B1747 " --> pdb=" O PHE B1730 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL B1732 " --> pdb=" O LEU B1745 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU B1745 " --> pdb=" O VAL B1732 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLU B1734 " --> pdb=" O PRO B1743 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N MET B1744 " --> pdb=" O TYR B1775 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TYR B1774 " --> pdb=" O PRO B1784 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASN B1776 " --> pdb=" O TRP B1782 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N TRP B1782 " --> pdb=" O ASN B1776 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1781 through 1786 current: chain 'B' and resid 1830 through 1846 removed outlier: 6.057A pdb=" N THR B1831 " --> pdb=" O GLN B2522 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ILE B2524 " --> pdb=" O THR B1831 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE B1833 " --> pdb=" O ILE B2524 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL B2526 " --> pdb=" O ILE B1833 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE B1835 " --> pdb=" O VAL B2526 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU B2528 " --> pdb=" O PHE B1835 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N SER B1837 " --> pdb=" O LEU B2528 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ASP B2530 " --> pdb=" O SER B1837 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ASP B1839 " --> pdb=" O ASP B2530 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N GLY B2532 " --> pdb=" O ASP B1839 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU B1841 " --> pdb=" O GLY B2532 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N SER B2534 " --> pdb=" O LEU B1841 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE B1843 " --> pdb=" O SER B2534 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N VAL B2536 " --> pdb=" O ILE B1843 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU B1845 " --> pdb=" O VAL B2536 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASN B2537 " --> pdb=" O GLU B2543 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N GLU B2543 " --> pdb=" O ASN B2537 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 2542 through 2550 current: chain 'B' and resid 2640 through 2647 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 2640 through 2647 current: chain 'B' and resid 2663 through 2667 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 2663 through 2667 current: chain 'B' and resid 2699 through 2708 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 2699 through 2708 current: chain 'B' and resid 2822 through 2824 Processing sheet with id=AA6, first strand: chain 'B' and resid 1789 through 1790 Processing sheet with id=AA7, first strand: chain 'B' and resid 2567 through 2568 removed outlier: 3.978A pdb=" N ALA B2621 " --> pdb=" O LYS B2559 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS B2613 " --> pdb=" O ARG B2604 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL B2601 " --> pdb=" O LEU B2597 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 3075 through 3079 removed outlier: 6.860A pdb=" N ILE B3089 " --> pdb=" O PHE B3076 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N HIS B3078 " --> pdb=" O LEU B3087 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU B3087 " --> pdb=" O HIS B3078 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY B3093 " --> pdb=" O THR B3090 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL B3094 " --> pdb=" O GLN B3110 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLN B3110 " --> pdb=" O VAL B3094 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE B3096 " --> pdb=" O GLU B3108 " (cutoff:3.500A) 368 hydrogen bonds defined for protein. 1053 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: 1.26 Time building geometry restraints manager: 0.72 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: 2539 1.34 - 1.46: 1482 1.46 - 1.57: 4340 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 8439 Sorted by residual: bond pdb=" CG1 ILE D 142 " pdb=" CD1 ILE D 142 " ideal model delta sigma weight residual 1.513 1.469 0.044 3.90e-02 6.57e+02 1.25e+00 bond pdb=" CG GLN D 354 " pdb=" CD GLN D 354 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.18e+00 bond pdb=" CB GLU B3166 " pdb=" CG GLU B3166 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 7.86e-01 bond pdb=" CA ASN D 96 " pdb=" CB ASN D 96 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.67e-01 bond pdb=" CB ASN D 96 " pdb=" CG ASN D 96 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.41e-01 ... (remaining 8434 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 11320 2.69 - 5.37: 91 5.37 - 8.06: 12 8.06 - 10.75: 4 10.75 - 13.44: 1 Bond angle restraints: 11428 Sorted by residual: angle pdb=" CA LEU D 285 " pdb=" CB LEU D 285 " pdb=" CG LEU D 285 " ideal model delta sigma weight residual 116.30 129.74 -13.44 3.50e+00 8.16e-02 1.47e+01 angle pdb=" CA GLU B3166 " pdb=" CB GLU B3166 " pdb=" CG GLU B3166 " ideal model delta sigma weight residual 114.10 120.53 -6.43 2.00e+00 2.50e-01 1.03e+01 angle pdb=" N GLN D 354 " pdb=" CA GLN D 354 " pdb=" CB GLN D 354 " ideal model delta sigma weight residual 110.28 115.10 -4.82 1.55e+00 4.16e-01 9.69e+00 angle pdb=" N THR D 288 " pdb=" CA THR D 288 " pdb=" CB THR D 288 " ideal model delta sigma weight residual 110.16 114.61 -4.45 1.48e+00 4.57e-01 9.04e+00 angle pdb=" CA LEU D 75 " pdb=" CB LEU D 75 " pdb=" CG LEU D 75 " ideal model delta sigma weight residual 116.30 126.68 -10.38 3.50e+00 8.16e-02 8.79e+00 ... (remaining 11423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 4410 17.52 - 35.03: 510 35.03 - 52.54: 115 52.54 - 70.06: 26 70.06 - 87.57: 9 Dihedral angle restraints: 5070 sinusoidal: 2064 harmonic: 3006 Sorted by residual: dihedral pdb=" CA SER D 148 " pdb=" C SER D 148 " pdb=" N ALA D 149 " pdb=" CA ALA D 149 " ideal model delta harmonic sigma weight residual 180.00 162.82 17.18 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA ILE B3122 " pdb=" C ILE B3122 " pdb=" N VAL B3123 " pdb=" CA VAL B3123 " ideal model delta harmonic sigma weight residual -180.00 -163.10 -16.90 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA PHE D 248 " pdb=" C PHE D 248 " pdb=" N PHE D 249 " pdb=" CA PHE D 249 " ideal model delta harmonic sigma weight residual 180.00 163.62 16.38 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 5067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 796 0.031 - 0.062: 328 0.062 - 0.093: 112 0.093 - 0.124: 76 0.124 - 0.155: 10 Chirality restraints: 1322 Sorted by residual: chirality pdb=" CB THR D 54 " pdb=" CA THR D 54 " pdb=" OG1 THR D 54 " pdb=" CG2 THR D 54 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" CB ILE B3122 " pdb=" CA ILE B3122 " pdb=" CG1 ILE B3122 " pdb=" CG2 ILE B3122 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA GLN D 354 " pdb=" N GLN D 354 " pdb=" C GLN D 354 " pdb=" CB GLN D 354 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 1319 not shown) Planarity restraints: 1407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 245 " -0.020 2.00e-02 2.50e+03 2.10e-02 7.74e+00 pdb=" CG PHE D 245 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE D 245 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE D 245 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE D 245 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 245 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE D 245 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B3166 " -0.007 2.00e-02 2.50e+03 1.52e-02 2.30e+00 pdb=" CD GLU B3166 " 0.026 2.00e-02 2.50e+03 pdb=" OE1 GLU B3166 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU B3166 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET D 109 " 0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO D 110 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 110 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 110 " 0.020 5.00e-02 4.00e+02 ... (remaining 1404 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 12 2.62 - 3.19: 7257 3.19 - 3.76: 13074 3.76 - 4.33: 17173 4.33 - 4.90: 28411 Nonbonded interactions: 65927 Sorted by model distance: nonbonded pdb=" OE2 GLU D 327 " pdb=" CD1 LEU D 331 " model vdw 2.044 3.460 nonbonded pdb=" CG1 VAL D 225 " pdb=" OD1 ASN D 328 " model vdw 2.092 3.460 nonbonded pdb=" CD1 LEU B3087 " pdb=" O LEU B3095 " model vdw 2.184 3.460 nonbonded pdb=" CG1 VAL B3097 " pdb=" CD1 LEU B3105 " model vdw 2.265 3.880 nonbonded pdb=" SG CYS D 347 " pdb=" CB LEU D 350 " model vdw 2.343 3.800 ... (remaining 65922 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 31.660 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.300 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 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 : 0.003 0.044 8439 Z= 0.142 Angle : 0.640 13.437 11428 Z= 0.317 Chirality : 0.044 0.155 1322 Planarity : 0.004 0.054 1407 Dihedral : 16.031 87.574 3114 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.54 % Allowed : 21.49 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.23 (0.28), residues: 1002 helix: 1.96 (0.26), residues: 372 sheet: -0.67 (0.31), residues: 302 loop : -1.07 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 215 TYR 0.016 0.001 TYR B3073 PHE 0.049 0.001 PHE D 245 TRP 0.006 0.001 TRP D 295 HIS 0.004 0.001 HIS D 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 8439) covalent geometry : angle 0.63970 / 0.32 (11428) hydrogen bonds : bond 0.11812 / 8.54 ( 368) hydrogen bonds : angle 5.83321 / 4.00 ( 1053) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.327 Fit side-chains REVERT: D 17 GLU cc_start: 0.7344 (mm-30) cc_final: 0.7085 (tm-30) REVERT: D 120 LYS cc_start: 0.8252 (mmtt) cc_final: 0.7996 (mmtt) REVERT: D 164 ASP cc_start: 0.6166 (m-30) cc_final: 0.5952 (t0) REVERT: D 199 TYR cc_start: 0.8131 (m-80) cc_final: 0.7676 (m-80) REVERT: D 284 THR cc_start: 0.8462 (m) cc_final: 0.8165 (p) REVERT: D 357 ILE cc_start: 0.8023 (pt) cc_final: 0.7805 (pt) REVERT: D 360 CYS cc_start: 0.7866 (m) cc_final: 0.7601 (m) REVERT: B 1572 ASN cc_start: 0.8278 (p0) cc_final: 0.8032 (t0) REVERT: B 1596 MET cc_start: 0.8219 (tmm) cc_final: 0.7927 (tpp) REVERT: B 1761 LEU cc_start: 0.8522 (mp) cc_final: 0.8244 (tt) REVERT: B 1854 ASN cc_start: 0.8477 (t0) cc_final: 0.8042 (m-40) REVERT: B 2690 MET cc_start: 0.7171 (ptm) cc_final: 0.6788 (ppp) outliers start: 5 outliers final: 3 residues processed: 119 average time/residue: 0.0632 time to fit residues: 11.1293 Evaluate side-chains 100 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 97 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain B residue 3036 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.0370 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 ASN B3067 ASN B3150 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.138133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.095620 restraints weight = 14236.616| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.99 r_work: 0.3289 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8439 Z= 0.130 Angle : 0.549 7.740 11428 Z= 0.278 Chirality : 0.043 0.162 1322 Planarity : 0.004 0.042 1407 Dihedral : 4.797 50.595 1102 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.27 % Allowed : 23.22 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.42 (0.28), residues: 1002 helix: 2.30 (0.26), residues: 371 sheet: -0.66 (0.31), residues: 300 loop : -1.09 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 215 TYR 0.032 0.001 TYR D 320 PHE 0.036 0.001 PHE D 245 TRP 0.007 0.001 TRP D 214 HIS 0.005 0.001 HIS D 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 8439) covalent geometry : angle 0.54872 / 0.28 (11428) hydrogen bonds : bond 0.03651 / 2.39 ( 368) hydrogen bonds : angle 4.48532 / 3.14 ( 1053) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: D 17 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7172 (tm-30) REVERT: D 120 LYS cc_start: 0.8274 (mmtt) cc_final: 0.8000 (mmtt) REVERT: D 199 TYR cc_start: 0.8154 (m-80) cc_final: 0.7796 (m-80) REVERT: D 357 ILE cc_start: 0.7932 (pt) cc_final: 0.7674 (pt) REVERT: D 360 CYS cc_start: 0.7742 (m) cc_final: 0.7479 (m) REVERT: B 1572 ASN cc_start: 0.8311 (p0) cc_final: 0.8095 (t0) REVERT: B 1596 MET cc_start: 0.8153 (tmm) cc_final: 0.7856 (tpp) REVERT: B 1854 ASN cc_start: 0.8453 (t0) cc_final: 0.8048 (m-40) REVERT: B 2690 MET cc_start: 0.7164 (ptm) cc_final: 0.6803 (ppp) REVERT: B 3127 ARG cc_start: 0.8389 (mmm-85) cc_final: 0.7872 (mtp85) REVERT: B 3162 THR cc_start: 0.9259 (p) cc_final: 0.8907 (t) outliers start: 21 outliers final: 10 residues processed: 123 average time/residue: 0.0710 time to fit residues: 12.7725 Evaluate side-chains 107 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 354 GLN Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain B residue 1611 LEU Chi-restraints excluded: chain B residue 1791 ILE Chi-restraints excluded: chain B residue 2676 MET Chi-restraints excluded: chain B residue 3036 LEU Chi-restraints excluded: chain B residue 3077 THR Chi-restraints excluded: chain B residue 3087 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 27 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 73 optimal weight: 0.0970 chunk 52 optimal weight: 0.4980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2625 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.139611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.093731 restraints weight = 13812.942| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.82 r_work: 0.3313 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8439 Z= 0.131 Angle : 0.566 12.084 11428 Z= 0.280 Chirality : 0.043 0.142 1322 Planarity : 0.004 0.040 1407 Dihedral : 4.463 39.674 1100 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.02 % Allowed : 23.43 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.50 (0.28), residues: 1002 helix: 2.40 (0.26), residues: 371 sheet: -0.66 (0.31), residues: 299 loop : -1.05 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B2623 TYR 0.033 0.001 TYR D 320 PHE 0.040 0.001 PHE D 245 TRP 0.007 0.001 TRP D 214 HIS 0.004 0.001 HIS D 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 8439) covalent geometry : angle 0.56577 / 0.28 (11428) hydrogen bonds : bond 0.03414 / 2.24 ( 368) hydrogen bonds : angle 4.28173 / 3.00 ( 1053) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: D 17 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7182 (tm-30) REVERT: D 120 LYS cc_start: 0.8301 (mmtt) cc_final: 0.8072 (mmtt) REVERT: D 199 TYR cc_start: 0.8135 (m-80) cc_final: 0.7775 (m-80) REVERT: D 324 ARG cc_start: 0.5402 (OUTLIER) cc_final: 0.5187 (ttm170) REVERT: D 344 MET cc_start: 0.6812 (ppp) cc_final: 0.6405 (ppp) REVERT: B 1596 MET cc_start: 0.8138 (tmm) cc_final: 0.7859 (tpp) REVERT: B 1854 ASN cc_start: 0.8416 (t0) cc_final: 0.7993 (m-40) REVERT: B 2623 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7715 (ptt-90) REVERT: B 2690 MET cc_start: 0.7134 (ptm) cc_final: 0.6813 (ppp) REVERT: B 3127 ARG cc_start: 0.8362 (mmm-85) cc_final: 0.7763 (mtp85) outliers start: 28 outliers final: 14 residues processed: 113 average time/residue: 0.0721 time to fit residues: 11.5968 Evaluate side-chains 104 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 324 ARG Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain B residue 1611 LEU Chi-restraints excluded: chain B residue 1645 SER Chi-restraints excluded: chain B residue 1791 ILE Chi-restraints excluded: chain B residue 2623 ARG Chi-restraints excluded: chain B residue 2676 MET Chi-restraints excluded: chain B residue 2684 THR Chi-restraints excluded: chain B residue 3036 LEU Chi-restraints excluded: chain B residue 3077 THR Chi-restraints excluded: chain B residue 3087 LEU Chi-restraints excluded: chain B residue 3101 THR Chi-restraints excluded: chain B residue 3145 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.4333 > 50: distance: 2 - 17: 3.815 distance: 6 - 23: 17.823 distance: 10 - 30: 11.134 distance: 15 - 41: 15.007 distance: 17 - 18: 3.467 distance: 18 - 19: 6.502 distance: 18 - 21: 5.006 distance: 19 - 20: 5.860 distance: 19 - 23: 5.782 distance: 20 - 49: 28.318 distance: 21 - 22: 28.396 distance: 23 - 24: 13.753 distance: 24 - 25: 6.972 distance: 24 - 27: 10.061 distance: 25 - 26: 9.040 distance: 25 - 30: 6.998 distance: 26 - 60: 26.067 distance: 27 - 28: 16.840 distance: 27 - 29: 19.819 distance: 30 - 31: 5.267 distance: 31 - 32: 4.415 distance: 31 - 34: 8.982 distance: 32 - 33: 6.569 distance: 32 - 41: 7.663 distance: 33 - 67: 19.925 distance: 34 - 35: 9.446 distance: 35 - 36: 8.572 distance: 35 - 37: 7.526 distance: 36 - 38: 7.003 distance: 37 - 39: 8.377 distance: 38 - 40: 6.042 distance: 39 - 40: 4.432 distance: 41 - 42: 3.392 distance: 42 - 43: 3.466 distance: 42 - 45: 4.543 distance: 43 - 44: 19.996 distance: 43 - 49: 12.306 distance: 44 - 72: 32.198 distance: 45 - 46: 7.861 distance: 46 - 47: 16.340 distance: 46 - 48: 9.002 distance: 49 - 50: 10.053 distance: 50 - 51: 12.326 distance: 50 - 53: 5.463 distance: 51 - 52: 17.660 distance: 51 - 60: 15.191 distance: 52 - 81: 11.867 distance: 54 - 55: 19.756 distance: 54 - 56: 12.294 distance: 55 - 57: 3.006 distance: 56 - 58: 8.576 distance: 57 - 59: 9.404 distance: 58 - 59: 20.100 distance: 60 - 61: 9.458 distance: 61 - 62: 16.686 distance: 61 - 64: 14.054 distance: 62 - 63: 33.295 distance: 62 - 67: 18.476 distance: 63 - 88: 16.200 distance: 64 - 65: 30.546 distance: 64 - 66: 22.216 distance: 67 - 68: 39.341 distance: 68 - 69: 16.209 distance: 68 - 71: 14.478 distance: 69 - 70: 8.287 distance: 69 - 72: 23.837 distance: 70 - 95: 13.910 distance: 72 - 73: 6.501 distance: 73 - 74: 7.407 distance: 73 - 76: 8.876 distance: 74 - 75: 3.963 distance: 74 - 81: 4.358 distance: 75 - 100: 18.312 distance: 76 - 77: 13.882 distance: 78 - 79: 14.772 distance: 78 - 80: 11.583 distance: 81 - 82: 4.956 distance: 82 - 83: 3.287 distance: 82 - 85: 4.912 distance: 83 - 84: 8.155 distance: 83 - 88: 5.724 distance: 84 - 105: 10.632 distance: 85 - 86: 13.819 distance: 85 - 87: 16.840 distance: 88 - 89: 6.475 distance: 89 - 90: 4.857 distance: 89 - 92: 10.389 distance: 90 - 91: 7.157 distance: 90 - 95: 6.552 distance: 91 - 113: 11.349 distance: 92 - 93: 23.714 distance: 92 - 94: 20.107