Starting phenix.real_space_refine on Sat Aug 23 19:20:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rk5_19260/08_2025/8rk5_19260.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rk5_19260/08_2025/8rk5_19260.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rk5_19260/08_2025/8rk5_19260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rk5_19260/08_2025/8rk5_19260.map" model { file = "/net/cci-nas-00/data/ceres_data/8rk5_19260/08_2025/8rk5_19260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rk5_19260/08_2025/8rk5_19260.cif" } resolution = 4.54 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= 0.002 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 9177 2.51 5 N 2496 2.21 5 O 2703 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14424 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2470 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 295} Chain: "B" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2338 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 285} Restraints were copied for chains: C, D, E, F Time building chain proxies: 2.66, per 1000 atoms: 0.18 Number of scatterers: 14424 At special positions: 0 Unit cell: (118.371, 114.203, 145.046, 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 2703 8.00 N 2496 7.00 C 9177 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 174 " distance=2.03 Simple disulfide: pdb=" SG CYS E 142 " - pdb=" SG CYS E 174 " distance=2.03 Simple disulfide: pdb=" SG CYS F 142 " - pdb=" SG CYS F 174 " 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 491.2 milliseconds Enol-peptide restraints added in 1.2 microseconds 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3336 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 21 sheets defined 11.1% alpha, 29.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 10 through 25 Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.534A pdb=" N ILE A 98 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 223 removed outlier: 3.618A pdb=" N TYR A 222 " --> pdb=" O GLU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'B' and resid 10 through 25 removed outlier: 3.533A pdb=" N LEU B 14 " --> pdb=" O ASN B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 184 Processing helix chain 'B' and resid 217 through 223 removed outlier: 3.560A pdb=" N ILE B 221 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 25 Processing helix chain 'C' and resid 25 through 31 Processing helix chain 'C' and resid 94 through 98 removed outlier: 3.533A pdb=" N ILE C 98 " --> pdb=" O PRO C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 223 removed outlier: 3.618A pdb=" N TYR C 222 " --> pdb=" O GLU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 Processing helix chain 'C' and resid 308 through 310 No H-bonds generated for 'chain 'C' and resid 308 through 310' Processing helix chain 'E' and resid 10 through 25 removed outlier: 3.533A pdb=" N LEU E 14 " --> pdb=" O ASN E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 184 Processing helix chain 'E' and resid 217 through 223 removed outlier: 3.560A pdb=" N ILE E 221 " --> pdb=" O ASP E 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 25 Processing helix chain 'D' and resid 25 through 31 Processing helix chain 'D' and resid 94 through 98 removed outlier: 3.534A pdb=" N ILE D 98 " --> pdb=" O PRO D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 223 removed outlier: 3.618A pdb=" N TYR D 222 " --> pdb=" O GLU D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 308 through 310 No H-bonds generated for 'chain 'D' and resid 308 through 310' Processing helix chain 'F' and resid 10 through 25 removed outlier: 3.533A pdb=" N LEU F 14 " --> pdb=" O ASN F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 184 Processing helix chain 'F' and resid 217 through 223 removed outlier: 3.561A pdb=" N ILE F 221 " --> pdb=" O ASP F 217 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 8 removed outlier: 4.882A pdb=" N LEU A 166 " --> pdb=" O ARG A 201 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 41 removed outlier: 6.466A pdb=" N THR A 56 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP A 40 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLN A 54 " --> pdb=" O ASP A 40 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 116 " --> pdb=" O TYR A 172 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR A 172 " --> pdb=" O GLN A 116 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 225 through 227 removed outlier: 9.889A pdb=" N LYS A 256 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N GLY A 276 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LEU A 258 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY A 272 " --> pdb=" O PHE A 260 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N THR A 262 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N TYR A 270 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY A 276 " --> pdb=" O ARG A 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 246 through 247 removed outlier: 4.585A pdb=" N TYR B 250 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N TYR B 250 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA B 241 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY B 252 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 8 removed outlier: 5.719A pdb=" N ALA B 8 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR B 98 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N PHE B 97 " --> pdb=" O ALA B 116 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA B 116 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N HIS B 110 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE B 125 " --> pdb=" O HIS B 110 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N HIS B 112 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL B 123 " --> pdb=" O HIS B 112 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N GLU B 114 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ARG B 121 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLN B 139 " --> pdb=" O ARG B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 28 through 32 removed outlier: 5.031A pdb=" N THR B 29 " --> pdb=" O HIS B 40 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N HIS B 40 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR B 45 " --> pdb=" O ASN B 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 257 through 261 removed outlier: 4.310A pdb=" N THR B 277 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 3 through 8 removed outlier: 4.882A pdb=" N LEU C 166 " --> pdb=" O ARG C 201 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 36 through 41 removed outlier: 6.465A pdb=" N THR C 56 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP C 40 " --> pdb=" O GLN C 54 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLN C 54 " --> pdb=" O ASP C 40 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN C 116 " --> pdb=" O TYR C 172 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR C 172 " --> pdb=" O GLN C 116 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 225 through 227 removed outlier: 9.889A pdb=" N LYS C 256 " --> pdb=" O GLY C 276 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N GLY C 276 " --> pdb=" O LYS C 256 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LEU C 258 " --> pdb=" O PHE C 274 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY C 272 " --> pdb=" O PHE C 260 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N THR C 262 " --> pdb=" O TYR C 270 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N TYR C 270 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY C 276 " --> pdb=" O ARG C 316 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 246 through 247 removed outlier: 4.584A pdb=" N TYR E 250 " --> pdb=" O ARG C 247 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N TYR E 250 " --> pdb=" O ALA E 241 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA E 241 " --> pdb=" O TYR E 250 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY E 252 " --> pdb=" O ILE E 239 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 3 through 8 removed outlier: 5.719A pdb=" N ALA E 8 " --> pdb=" O THR E 98 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR E 98 " --> pdb=" O ALA E 8 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N PHE E 97 " --> pdb=" O ALA E 116 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA E 116 " --> pdb=" O PHE E 97 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N HIS E 110 " --> pdb=" O ILE E 125 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE E 125 " --> pdb=" O HIS E 110 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N HIS E 112 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL E 123 " --> pdb=" O HIS E 112 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLU E 114 " --> pdb=" O ARG E 121 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ARG E 121 " --> pdb=" O GLU E 114 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLN E 139 " --> pdb=" O ARG E 177 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 28 through 32 removed outlier: 5.031A pdb=" N THR E 29 " --> pdb=" O HIS E 40 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N HIS E 40 " --> pdb=" O THR E 29 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR E 45 " --> pdb=" O ASN E 60 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 257 through 261 removed outlier: 4.310A pdb=" N THR E 277 " --> pdb=" O VAL E 305 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 3 through 8 removed outlier: 4.882A pdb=" N LEU D 166 " --> pdb=" O ARG D 201 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 36 through 41 removed outlier: 6.466A pdb=" N THR D 56 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP D 40 " --> pdb=" O GLN D 54 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLN D 54 " --> pdb=" O ASP D 40 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN D 116 " --> pdb=" O TYR D 172 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR D 172 " --> pdb=" O GLN D 116 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 225 through 227 removed outlier: 9.890A pdb=" N LYS D 256 " --> pdb=" O GLY D 276 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N GLY D 276 " --> pdb=" O LYS D 256 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LEU D 258 " --> pdb=" O PHE D 274 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY D 272 " --> pdb=" O PHE D 260 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N THR D 262 " --> pdb=" O TYR D 270 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N TYR D 270 " --> pdb=" O THR D 262 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY D 276 " --> pdb=" O ARG D 316 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 246 through 247 removed outlier: 4.585A pdb=" N TYR F 250 " --> pdb=" O ARG D 247 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N TYR F 250 " --> pdb=" O ALA F 241 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA F 241 " --> pdb=" O TYR F 250 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY F 252 " --> pdb=" O ILE F 239 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 3 through 8 removed outlier: 5.719A pdb=" N ALA F 8 " --> pdb=" O THR F 98 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR F 98 " --> pdb=" O ALA F 8 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N PHE F 97 " --> pdb=" O ALA F 116 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA F 116 " --> pdb=" O PHE F 97 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N HIS F 110 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE F 125 " --> pdb=" O HIS F 110 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N HIS F 112 " --> pdb=" O VAL F 123 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL F 123 " --> pdb=" O HIS F 112 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLU F 114 " --> pdb=" O ARG F 121 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ARG F 121 " --> pdb=" O GLU F 114 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLN F 139 " --> pdb=" O ARG F 177 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 28 through 32 removed outlier: 5.031A pdb=" N THR F 29 " --> pdb=" O HIS F 40 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N HIS F 40 " --> pdb=" O THR F 29 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR F 45 " --> pdb=" O ASN F 60 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 257 through 261 removed outlier: 4.309A pdb=" N THR F 277 " --> pdb=" O VAL F 305 " (cutoff:3.500A) 459 hydrogen bonds defined for protein. 1224 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: 2.08 Time building geometry restraints manager: 1.27 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: 4731 1.34 - 1.46: 2990 1.46 - 1.57: 7078 1.57 - 1.69: 0 1.69 - 1.81: 69 Bond restraints: 14868 Sorted by residual: bond pdb=" C ILE D 43 " pdb=" N PRO D 44 " ideal model delta sigma weight residual 1.329 1.346 -0.017 1.20e-02 6.94e+03 1.99e+00 bond pdb=" C ILE C 43 " pdb=" N PRO C 44 " ideal model delta sigma weight residual 1.329 1.345 -0.017 1.20e-02 6.94e+03 1.89e+00 bond pdb=" C ILE A 43 " pdb=" N PRO A 44 " ideal model delta sigma weight residual 1.329 1.345 -0.016 1.20e-02 6.94e+03 1.87e+00 bond pdb=" N GLU D 288 " pdb=" CA GLU D 288 " ideal model delta sigma weight residual 1.458 1.475 -0.017 1.37e-02 5.33e+03 1.53e+00 bond pdb=" CB TRP F 37 " pdb=" CG TRP F 37 " ideal model delta sigma weight residual 1.498 1.460 0.038 3.10e-02 1.04e+03 1.48e+00 ... (remaining 14863 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 19329 1.40 - 2.80: 822 2.80 - 4.20: 137 4.20 - 5.60: 25 5.60 - 7.00: 9 Bond angle restraints: 20322 Sorted by residual: angle pdb=" C ALA D 287 " pdb=" N GLU D 288 " pdb=" CA GLU D 288 " ideal model delta sigma weight residual 125.02 131.23 -6.21 1.76e+00 3.23e-01 1.25e+01 angle pdb=" C ALA C 287 " pdb=" N GLU C 288 " pdb=" CA GLU C 288 " ideal model delta sigma weight residual 125.02 131.21 -6.19 1.76e+00 3.23e-01 1.24e+01 angle pdb=" C ALA A 287 " pdb=" N GLU A 288 " pdb=" CA GLU A 288 " ideal model delta sigma weight residual 125.02 131.20 -6.18 1.76e+00 3.23e-01 1.23e+01 angle pdb=" CA GLU D 288 " pdb=" CB GLU D 288 " pdb=" CG GLU D 288 " ideal model delta sigma weight residual 114.10 120.17 -6.07 2.00e+00 2.50e-01 9.23e+00 angle pdb=" CA GLU C 288 " pdb=" CB GLU C 288 " pdb=" CG GLU C 288 " ideal model delta sigma weight residual 114.10 120.15 -6.05 2.00e+00 2.50e-01 9.16e+00 ... (remaining 20317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7901 17.96 - 35.92: 499 35.92 - 53.88: 90 53.88 - 71.84: 6 71.84 - 89.80: 9 Dihedral angle restraints: 8505 sinusoidal: 3201 harmonic: 5304 Sorted by residual: dihedral pdb=" CA TRP F 37 " pdb=" C TRP F 37 " pdb=" N LEU F 38 " pdb=" CA LEU F 38 " ideal model delta harmonic sigma weight residual 180.00 162.92 17.08 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA TRP E 37 " pdb=" C TRP E 37 " pdb=" N LEU E 38 " pdb=" CA LEU E 38 " ideal model delta harmonic sigma weight residual 180.00 162.94 17.06 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA TRP B 37 " pdb=" C TRP B 37 " pdb=" N LEU B 38 " pdb=" CA LEU B 38 " ideal model delta harmonic sigma weight residual 180.00 162.96 17.04 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 8502 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1098 0.027 - 0.054: 654 0.054 - 0.082: 181 0.082 - 0.109: 117 0.109 - 0.136: 62 Chirality restraints: 2112 Sorted by residual: chirality pdb=" CA ILE D 144 " pdb=" N ILE D 144 " pdb=" C ILE D 144 " pdb=" CB ILE D 144 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA ILE A 144 " pdb=" N ILE A 144 " pdb=" C ILE A 144 " pdb=" CB ILE A 144 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA ILE F 125 " pdb=" N ILE F 125 " pdb=" C ILE F 125 " pdb=" CB ILE F 125 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 2109 not shown) Planarity restraints: 2694 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 204 " -0.039 5.00e-02 4.00e+02 5.98e-02 5.73e+00 pdb=" N PRO B 205 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 205 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 205 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY F 204 " 0.039 5.00e-02 4.00e+02 5.98e-02 5.73e+00 pdb=" N PRO F 205 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO F 205 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO F 205 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 204 " 0.039 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO E 205 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO E 205 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 205 " 0.033 5.00e-02 4.00e+02 ... (remaining 2691 not shown) Histogram of nonbonded interaction distances: 0.55 - 1.42: 69 1.42 - 2.29: 236 2.29 - 3.16: 13060 3.16 - 4.03: 36671 4.03 - 4.90: 68628 Warning: very small nonbonded interaction distances. Nonbonded interactions: 118664 Sorted by model distance: nonbonded pdb=" OE1 GLN B 245 " pdb=" CA ALA C 79 " model vdw 0.555 3.470 nonbonded pdb=" CD ARG A 306 " pdb=" CB VAL C 183 " model vdw 0.573 3.870 nonbonded pdb=" CA ALA A 79 " pdb=" CD GLN E 245 " model vdw 0.605 3.700 nonbonded pdb=" N PRO A 99 " pdb=" NH1 ARG F 286 " model vdw 0.652 3.200 nonbonded pdb=" CA ALA A 79 " pdb=" OE1 GLN E 245 " model vdw 0.664 3.470 ... (remaining 118659 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.230 Find NCS groups from input model: 0.110 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4375 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 : 0.013 1.030 14881 Z= 1.256 Angle : 0.675 7.003 20328 Z= 0.391 Chirality : 0.044 0.136 2112 Planarity : 0.006 0.060 2694 Dihedral : 12.152 89.798 5160 Min Nonbonded Distance : 0.555 Molprobity Statistics. All-atom Clashscore : 21.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 aren not related in a simple way. whole: -1.01 (0.18), residues: 1854 helix: 0.02 (0.38), residues: 153 sheet: 0.08 (0.20), residues: 597 loop : -1.23 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 179 TYR 0.019 0.002 TYR E 82 PHE 0.018 0.001 PHE A 128 TRP 0.019 0.001 TRP B 189 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00289 (14868) covalent geometry : angle 0.67393 (20322) SS BOND : bond 0.00546 ( 3) SS BOND : angle 2.12715 ( 6) hydrogen bonds : bond 0.12721 ( 459) hydrogen bonds : angle 6.81945 ( 1224) Misc. bond : bond 0.48083 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 TRP cc_start: 0.6618 (m100) cc_final: 0.6279 (m100) REVERT: A 200 LEU cc_start: 0.8144 (tp) cc_final: 0.7925 (tp) REVERT: A 260 PHE cc_start: 0.7328 (m-80) cc_final: 0.6391 (m-80) REVERT: A 269 ARG cc_start: 0.6735 (ptp90) cc_final: 0.6003 (ttm170) REVERT: A 288 GLU cc_start: 0.4162 (pp20) cc_final: 0.3907 (pp20) REVERT: A 318 ASP cc_start: 0.7451 (t70) cc_final: 0.7221 (t0) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0435 time to fit residues: 3.4334 Evaluate side-chains 46 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.092 Evaluate side-chains 62 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 70 ASN cc_start: 0.7275 (p0) cc_final: 0.7062 (t0) REVERT: B 286 ARG cc_start: 0.3551 (ttt-90) cc_final: 0.3028 (tpt170) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0374 time to fit residues: 2.8685 Evaluate side-chains 40 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.0870 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.0470 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 309 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.129625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.119694 restraints weight = 7374.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.122085 restraints weight = 4779.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.123934 restraints weight = 3280.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.125233 restraints weight = 2334.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.126246 restraints weight = 1717.581| |-----------------------------------------------------------------------------| r_work (final): 0.3890 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.135020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.126854 restraints weight = 7934.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.129285 restraints weight = 4960.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.130781 restraints weight = 3217.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.132044 restraints weight = 2224.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.132887 restraints weight = 1523.877| |-----------------------------------------------------------------------------| r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4518 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 14881 Z= 0.222 Angle : 0.727 11.258 20328 Z= 0.387 Chirality : 0.048 0.191 2112 Planarity : 0.006 0.067 2694 Dihedral : 4.843 21.875 2079 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 aren not related in a simple way. whole: -1.03 (0.18), residues: 1854 helix: 0.10 (0.38), residues: 138 sheet: 0.05 (0.20), residues: 606 loop : -1.23 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 268 TYR 0.021 0.002 TYR D 126 PHE 0.061 0.003 PHE B 264 TRP 0.024 0.002 TRP D 127 HIS 0.003 0.001 HIS E 21 Details of bonding type rmsd covalent geometry : bond 0.00403 (14868) covalent geometry : angle 0.72615 (20322) SS BOND : bond 0.00313 ( 3) SS BOND : angle 2.61674 ( 6) hydrogen bonds : bond 0.03764 ( 459) hydrogen bonds : angle 6.56540 ( 1224) Misc. bond : bond 0.05503 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.054 Fit side-chains REVERT: A 120 TRP cc_start: 0.6768 (p90) cc_final: 0.5266 (p90) REVERT: A 136 TRP cc_start: 0.6560 (m100) cc_final: 0.6181 (m100) REVERT: A 169 VAL cc_start: 0.5773 (p) cc_final: 0.5365 (p) REVERT: A 180 TRP cc_start: 0.6467 (p-90) cc_final: 0.4765 (p-90) REVERT: A 269 ARG cc_start: 0.6225 (ptp90) cc_final: 0.5823 (mmt90) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0560 time to fit residues: 3.2705 Evaluate side-chains 41 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.079 Evaluate side-chains 48 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.055 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0517 time to fit residues: 3.0103 Evaluate side-chains 33 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 794, in minimization_ncs weight = real_space_weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 394, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 126, in refine minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 424, in __init__ minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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-2.0-5787/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-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 456, in compute_functional_and_gradients t,g = self.target_and_grads_object.target_and_gradients( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 242, in target_and_gradients t_restraints, g_restraints = restraints_target_and_grads( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 110, in restraints_target_and_grads ef = restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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-2.0-5787/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-2.0-5787/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: 71.5738 > 50: distance: 7 - 8: 39.279 distance: 8 - 9: 56.237 distance: 8 - 11: 57.650 distance: 9 - 10: 40.304 distance: 11 - 12: 40.071 distance: 12 - 13: 57.203 distance: 12 - 14: 55.504 distance: 16 - 19: 40.116 distance: 17 - 18: 57.487 distance: 17 - 23: 56.100 distance: 20 - 21: 39.201 distance: 20 - 22: 40.709 distance: 25 - 26: 40.668 distance: 27 - 28: 56.185 distance: 28 - 29: 55.327 distance: 29 - 30: 38.761 distance: 30 - 31: 56.967 distance: 31 - 33: 39.174 distance: 34 - 35: 54.143 distance: 35 - 36: 28.654 distance: 35 - 38: 3.298 distance: 36 - 37: 31.932 distance: 36 - 42: 32.854 distance: 38 - 39: 40.069 distance: 39 - 41: 56.813 distance: 43 - 44: 69.440 distance: 44 - 50: 39.955 distance: 46 - 47: 60.378 distance: 47 - 48: 40.460 distance: 48 - 49: 46.648 distance: 50 - 51: 57.202 distance: 51 - 52: 37.658 distance: 52 - 53: 39.817 distance: 52 - 54: 40.651 distance: 54 - 55: 69.767 distance: 55 - 56: 56.194 distance: 56 - 57: 56.269 distance: 56 - 58: 57.183 distance: 58 - 59: 16.696 distance: 59 - 60: 22.619 distance: 59 - 62: 62.293 distance: 60 - 61: 65.371 distance: 60 - 65: 41.435 distance: 62 - 63: 55.992 distance: 62 - 64: 55.930 distance: 65 - 66: 41.211 distance: 66 - 67: 18.403 distance: 66 - 69: 56.266 distance: 67 - 68: 46.016