Starting phenix.real_space_refine on Thu Jun 12 17:59:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rk5_19260/06_2025/8rk5_19260.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rk5_19260/06_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_19260/06_2025/8rk5_19260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rk5_19260/06_2025/8rk5_19260.map" model { file = "/net/cci-nas-00/data/ceres_data/8rk5_19260/06_2025/8rk5_19260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rk5_19260/06_2025/8rk5_19260.cif" } resolution = 4.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: E, F, C, D Time building chain proxies: 8.38, per 1000 atoms: 0.58 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: 4.29 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.00 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: 4.76 Time building geometry restraints manager: 4.87 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: 0.10 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.740 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 36.340 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.030 ------------------------------------------------------------------------------- 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 : 21.86 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (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 TRP 0.019 0.001 TRP B 189 HIS 0.003 0.001 HIS A 298 PHE 0.018 0.001 PHE A 128 TYR 0.019 0.002 TYR E 82 ARG 0.011 0.001 ARG A 179 Details of bonding type rmsd hydrogen bonds : bond 0.12721 ( 459) hydrogen bonds : angle 6.81945 ( 1224) SS BOND : bond 0.00546 ( 3) SS BOND : angle 2.12715 ( 6) covalent geometry : bond 0.00289 (14868) covalent geometry : angle 0.67393 (20322) 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 62 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.233 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: 0.1278 time to fit residues: 9.5262 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 : 0.264 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 : 0.283 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: 0.1391 time to fit residues: 10.9916 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 : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 76 optimal weight: 0.0980 chunk 47 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 74 optimal weight: 0.0040 chunk 143 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 166 optimal weight: 9.9990 overall best weight: 2.0196 ------------------------------------------------------------------------------- NQH flips ********* 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 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 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.134315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.126154 restraints weight = 7823.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.128500 restraints weight = 4899.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.130232 restraints weight = 3184.154| |-----------------------------------------------------------------------------| r_work (final): 0.3974 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.128891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.119179 restraints weight = 7208.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.121544 restraints weight = 4680.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.123361 restraints weight = 3208.595| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4563 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 14881 Z= 0.225 Angle : 0.732 11.668 20328 Z= 0.390 Chirality : 0.048 0.202 2112 Planarity : 0.006 0.062 2694 Dihedral : 4.883 22.905 2079 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.18), residues: 1854 helix: 0.08 (0.38), residues: 138 sheet: 0.03 (0.20), residues: 576 loop : -1.27 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 127 HIS 0.003 0.001 HIS A 298 PHE 0.065 0.003 PHE B 264 TYR 0.021 0.002 TYR D 126 ARG 0.010 0.001 ARG A 268 Details of bonding type rmsd hydrogen bonds : bond 0.03787 ( 459) hydrogen bonds : angle 6.59527 ( 1224) SS BOND : bond 0.00277 ( 3) SS BOND : angle 2.63675 ( 6) covalent geometry : bond 0.00417 (14868) covalent geometry : angle 0.73035 (20322) Misc. bond : bond 0.05418 ( 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 48 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.236 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1227 time to fit residues: 7.2225 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 : 0.264 Evaluate side-chains 51 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.276 Fit side-chains REVERT: A 136 TRP cc_start: 0.6539 (m100) cc_final: 0.6186 (m100) REVERT: A 169 VAL cc_start: 0.5815 (p) cc_final: 0.5395 (p) REVERT: A 269 ARG cc_start: 0.6219 (ptp90) cc_final: 0.5713 (mmt90) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1599 time to fit residues: 9.6366 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 : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 801, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.6153 > 50: distance: 2 - 3: 57.035 distance: 3 - 4: 41.603 distance: 4 - 5: 13.567 distance: 4 - 6: 48.195 distance: 6 - 7: 48.079 distance: 7 - 8: 27.125 distance: 7 - 10: 13.882 distance: 8 - 9: 40.443 distance: 8 - 15: 19.186 distance: 10 - 11: 13.235 distance: 11 - 12: 28.453 distance: 12 - 13: 38.897 distance: 12 - 14: 26.932 distance: 15 - 16: 45.719 distance: 16 - 17: 65.977 distance: 17 - 18: 16.008 distance: 17 - 20: 33.858 distance: 20 - 21: 34.560 distance: 21 - 22: 55.524 distance: 21 - 24: 65.635 distance: 22 - 23: 4.532 distance: 22 - 32: 12.948 distance: 24 - 25: 14.049 distance: 25 - 26: 16.563 distance: 25 - 27: 15.124 distance: 26 - 28: 27.491 distance: 27 - 29: 15.843 distance: 28 - 30: 5.810 distance: 29 - 30: 37.109 distance: 30 - 31: 4.678 distance: 32 - 33: 22.931 distance: 33 - 36: 57.103 distance: 36 - 37: 59.391 distance: 37 - 38: 13.732 distance: 38 - 39: 40.652 distance: 38 - 40: 41.344 distance: 42 - 43: 47.772 distance: 43 - 44: 25.358 distance: 43 - 50: 34.413 distance: 45 - 46: 19.479 distance: 46 - 47: 20.117 distance: 47 - 48: 38.705 distance: 48 - 49: 28.364 distance: 51 - 54: 7.923 distance: 52 - 53: 69.299 distance: 54 - 55: 40.040 distance: 54 - 56: 14.669 distance: 57 - 58: 44.684 distance: 58 - 59: 20.329 distance: 58 - 61: 55.872 distance: 59 - 68: 28.757 distance: 61 - 62: 46.090 distance: 62 - 63: 8.206 distance: 62 - 64: 41.212 distance: 63 - 65: 43.630 distance: 64 - 66: 30.447 distance: 66 - 67: 28.948 distance: 68 - 69: 14.900 distance: 69 - 70: 44.423 distance: 69 - 72: 27.805 distance: 70 - 76: 39.634 distance: 72 - 73: 46.012 distance: 73 - 74: 14.994 distance: 73 - 75: 21.942 distance: 76 - 77: 57.132 distance: 77 - 78: 39.744