Starting phenix.real_space_refine on Sat Aug 23 16:07:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vam_21143/08_2025/6vam_21143.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vam_21143/08_2025/6vam_21143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vam_21143/08_2025/6vam_21143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vam_21143/08_2025/6vam_21143.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vam_21143/08_2025/6vam_21143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vam_21143/08_2025/6vam_21143.map" } resolution = 3.63 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= 0.045 sd= 0.520 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 152 5.16 5 C 8704 2.51 5 N 2248 2.21 5 O 2256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s 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: 13360 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1670 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 13 Restraints were copied for chains: B, C, D, E, F, G, H Time building chain proxies: 1.81, per 1000 atoms: 0.14 Number of scatterers: 13360 At special positions: 0 Unit cell: (119.78, 119.78, 96.46, 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 152 16.00 O 2256 8.00 N 2248 7.00 C 8704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 126 " distance=2.02 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 126 " distance=2.02 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 126 " distance=2.02 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 126 " distance=2.02 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 126 " distance=2.02 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: 1.15 Conformation dependent library (CDL) restraints added in 625.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3280 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 0 sheets defined 78.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 22 through 35 Processing helix chain 'A' and resid 48 through 70 removed outlier: 3.920A pdb=" N LEU A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Proline residue: A 59 - end of helix removed outlier: 3.772A pdb=" N PHE A 68 " --> pdb=" O PHE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 83 removed outlier: 4.556A pdb=" N MET A 76 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 107 removed outlier: 3.841A pdb=" N GLN A 104 " --> pdb=" O CYS A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 121 removed outlier: 3.695A pdb=" N ALA A 111 " --> pdb=" O MET A 107 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 128 Processing helix chain 'A' and resid 147 through 157 Processing helix chain 'A' and resid 171 through 201 removed outlier: 3.535A pdb=" N LEU A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 246 removed outlier: 3.715A pdb=" N ASP A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 35 Processing helix chain 'B' and resid 48 through 70 removed outlier: 3.920A pdb=" N LEU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Proline residue: B 59 - end of helix removed outlier: 3.772A pdb=" N PHE B 68 " --> pdb=" O PHE B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 83 removed outlier: 4.556A pdb=" N MET B 76 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG B 83 " --> pdb=" O GLU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 107 removed outlier: 3.841A pdb=" N GLN B 104 " --> pdb=" O CYS B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 121 removed outlier: 3.696A pdb=" N ALA B 111 " --> pdb=" O MET B 107 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY B 121 " --> pdb=" O THR B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 128 Processing helix chain 'B' and resid 147 through 157 Processing helix chain 'B' and resid 171 through 201 removed outlier: 3.535A pdb=" N LEU B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 246 removed outlier: 3.715A pdb=" N ASP B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 35 Processing helix chain 'C' and resid 48 through 70 removed outlier: 3.920A pdb=" N LEU C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY C 54 " --> pdb=" O ALA C 50 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 3.772A pdb=" N PHE C 68 " --> pdb=" O PHE C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 83 removed outlier: 4.556A pdb=" N MET C 76 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG C 83 " --> pdb=" O GLU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 107 removed outlier: 3.841A pdb=" N GLN C 104 " --> pdb=" O CYS C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 121 removed outlier: 3.695A pdb=" N ALA C 111 " --> pdb=" O MET C 107 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL C 112 " --> pdb=" O ILE C 108 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY C 121 " --> pdb=" O THR C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 128 Processing helix chain 'C' and resid 147 through 157 Processing helix chain 'C' and resid 171 through 201 removed outlier: 3.535A pdb=" N LEU C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 246 removed outlier: 3.715A pdb=" N ASP C 223 " --> pdb=" O SER C 219 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN C 246 " --> pdb=" O LYS C 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 35 Processing helix chain 'D' and resid 48 through 70 removed outlier: 3.920A pdb=" N LEU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY D 54 " --> pdb=" O ALA D 50 " (cutoff:3.500A) Proline residue: D 59 - end of helix removed outlier: 3.771A pdb=" N PHE D 68 " --> pdb=" O PHE D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 83 removed outlier: 4.556A pdb=" N MET D 76 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG D 83 " --> pdb=" O GLU D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 107 removed outlier: 3.841A pdb=" N GLN D 104 " --> pdb=" O CYS D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 121 removed outlier: 3.695A pdb=" N ALA D 111 " --> pdb=" O MET D 107 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY D 121 " --> pdb=" O THR D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 128 Processing helix chain 'D' and resid 147 through 157 Processing helix chain 'D' and resid 171 through 201 removed outlier: 3.535A pdb=" N LEU D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 246 removed outlier: 3.715A pdb=" N ASP D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN D 246 " --> pdb=" O LYS D 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 35 Processing helix chain 'E' and resid 48 through 70 removed outlier: 3.920A pdb=" N LEU E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY E 54 " --> pdb=" O ALA E 50 " (cutoff:3.500A) Proline residue: E 59 - end of helix removed outlier: 3.772A pdb=" N PHE E 68 " --> pdb=" O PHE E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 83 removed outlier: 4.556A pdb=" N MET E 76 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG E 83 " --> pdb=" O GLU E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 107 removed outlier: 3.841A pdb=" N GLN E 104 " --> pdb=" O CYS E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 121 removed outlier: 3.695A pdb=" N ALA E 111 " --> pdb=" O MET E 107 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY E 121 " --> pdb=" O THR E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 128 Processing helix chain 'E' and resid 147 through 157 Processing helix chain 'E' and resid 171 through 201 removed outlier: 3.535A pdb=" N LEU E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 246 removed outlier: 3.715A pdb=" N ASP E 223 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN E 246 " --> pdb=" O LYS E 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 35 Processing helix chain 'F' and resid 48 through 70 removed outlier: 3.920A pdb=" N LEU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY F 54 " --> pdb=" O ALA F 50 " (cutoff:3.500A) Proline residue: F 59 - end of helix removed outlier: 3.772A pdb=" N PHE F 68 " --> pdb=" O PHE F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 83 removed outlier: 4.556A pdb=" N MET F 76 " --> pdb=" O ASN F 72 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG F 83 " --> pdb=" O GLU F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 107 removed outlier: 3.841A pdb=" N GLN F 104 " --> pdb=" O CYS F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 121 removed outlier: 3.696A pdb=" N ALA F 111 " --> pdb=" O MET F 107 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL F 112 " --> pdb=" O ILE F 108 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY F 121 " --> pdb=" O THR F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 128 Processing helix chain 'F' and resid 147 through 157 Processing helix chain 'F' and resid 171 through 201 removed outlier: 3.535A pdb=" N LEU F 178 " --> pdb=" O ALA F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 246 removed outlier: 3.715A pdb=" N ASP F 223 " --> pdb=" O SER F 219 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN F 246 " --> pdb=" O LYS F 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 35 Processing helix chain 'G' and resid 48 through 70 removed outlier: 3.920A pdb=" N LEU G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY G 54 " --> pdb=" O ALA G 50 " (cutoff:3.500A) Proline residue: G 59 - end of helix removed outlier: 3.772A pdb=" N PHE G 68 " --> pdb=" O PHE G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 83 removed outlier: 4.556A pdb=" N MET G 76 " --> pdb=" O ASN G 72 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG G 83 " --> pdb=" O GLU G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 107 removed outlier: 3.842A pdb=" N GLN G 104 " --> pdb=" O CYS G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 121 removed outlier: 3.695A pdb=" N ALA G 111 " --> pdb=" O MET G 107 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL G 112 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY G 121 " --> pdb=" O THR G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 128 Processing helix chain 'G' and resid 147 through 157 Processing helix chain 'G' and resid 171 through 201 removed outlier: 3.536A pdb=" N LEU G 178 " --> pdb=" O ALA G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 246 removed outlier: 3.715A pdb=" N ASP G 223 " --> pdb=" O SER G 219 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN G 246 " --> pdb=" O LYS G 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 35 Processing helix chain 'H' and resid 48 through 70 removed outlier: 3.920A pdb=" N LEU H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY H 54 " --> pdb=" O ALA H 50 " (cutoff:3.500A) Proline residue: H 59 - end of helix removed outlier: 3.772A pdb=" N PHE H 68 " --> pdb=" O PHE H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 83 removed outlier: 4.556A pdb=" N MET H 76 " --> pdb=" O ASN H 72 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG H 83 " --> pdb=" O GLU H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 107 removed outlier: 3.841A pdb=" N GLN H 104 " --> pdb=" O CYS H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 121 removed outlier: 3.695A pdb=" N ALA H 111 " --> pdb=" O MET H 107 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL H 112 " --> pdb=" O ILE H 108 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY H 121 " --> pdb=" O THR H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 128 Processing helix chain 'H' and resid 147 through 157 Processing helix chain 'H' and resid 171 through 201 removed outlier: 3.536A pdb=" N LEU H 178 " --> pdb=" O ALA H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 246 removed outlier: 3.715A pdb=" N ASP H 223 " --> pdb=" O SER H 219 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN H 246 " --> pdb=" O LYS H 242 " (cutoff:3.500A) 929 hydrogen bonds defined for protein. 2787 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: 2.05 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4184 1.34 - 1.46: 2675 1.46 - 1.57: 6597 1.57 - 1.69: 0 1.69 - 1.81: 200 Bond restraints: 13656 Sorted by residual: bond pdb=" N PRO C 146 " pdb=" CD PRO C 146 " ideal model delta sigma weight residual 1.473 1.521 -0.048 1.40e-02 5.10e+03 1.20e+01 bond pdb=" N PRO E 146 " pdb=" CD PRO E 146 " ideal model delta sigma weight residual 1.473 1.521 -0.048 1.40e-02 5.10e+03 1.20e+01 bond pdb=" N PRO A 146 " pdb=" CD PRO A 146 " ideal model delta sigma weight residual 1.473 1.521 -0.048 1.40e-02 5.10e+03 1.20e+01 bond pdb=" N PRO B 146 " pdb=" CD PRO B 146 " ideal model delta sigma weight residual 1.473 1.521 -0.048 1.40e-02 5.10e+03 1.19e+01 bond pdb=" N PRO F 146 " pdb=" CD PRO F 146 " ideal model delta sigma weight residual 1.473 1.521 -0.048 1.40e-02 5.10e+03 1.19e+01 ... (remaining 13651 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 18171 2.57 - 5.14: 309 5.14 - 7.71: 40 7.71 - 10.28: 0 10.28 - 12.85: 16 Bond angle restraints: 18536 Sorted by residual: angle pdb=" C LEU B 203 " pdb=" N ARG B 204 " pdb=" CA ARG B 204 " ideal model delta sigma weight residual 120.06 132.91 -12.85 1.19e+00 7.06e-01 1.17e+02 angle pdb=" C LEU F 203 " pdb=" N ARG F 204 " pdb=" CA ARG F 204 " ideal model delta sigma weight residual 120.06 132.90 -12.84 1.19e+00 7.06e-01 1.16e+02 angle pdb=" C LEU A 203 " pdb=" N ARG A 204 " pdb=" CA ARG A 204 " ideal model delta sigma weight residual 120.06 132.88 -12.82 1.19e+00 7.06e-01 1.16e+02 angle pdb=" C LEU C 203 " pdb=" N ARG C 204 " pdb=" CA ARG C 204 " ideal model delta sigma weight residual 120.06 132.88 -12.82 1.19e+00 7.06e-01 1.16e+02 angle pdb=" C LEU E 203 " pdb=" N ARG E 204 " pdb=" CA ARG E 204 " ideal model delta sigma weight residual 120.06 132.88 -12.82 1.19e+00 7.06e-01 1.16e+02 ... (remaining 18531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.29: 7232 16.29 - 32.59: 760 32.59 - 48.88: 120 48.88 - 65.17: 24 65.17 - 81.47: 48 Dihedral angle restraints: 8184 sinusoidal: 3152 harmonic: 5032 Sorted by residual: dihedral pdb=" CB CYS G 41 " pdb=" SG CYS G 41 " pdb=" SG CYS G 126 " pdb=" CB CYS G 126 " ideal model delta sinusoidal sigma weight residual -86.00 -155.76 69.76 1 1.00e+01 1.00e-02 6.28e+01 dihedral pdb=" CB CYS H 41 " pdb=" SG CYS H 41 " pdb=" SG CYS H 126 " pdb=" CB CYS H 126 " ideal model delta sinusoidal sigma weight residual -86.00 -155.75 69.75 1 1.00e+01 1.00e-02 6.28e+01 dihedral pdb=" CB CYS D 41 " pdb=" SG CYS D 41 " pdb=" SG CYS D 126 " pdb=" CB CYS D 126 " ideal model delta sinusoidal sigma weight residual -86.00 -155.75 69.75 1 1.00e+01 1.00e-02 6.28e+01 ... (remaining 8181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1375 0.034 - 0.068: 620 0.068 - 0.102: 109 0.102 - 0.136: 41 0.136 - 0.170: 15 Chirality restraints: 2160 Sorted by residual: chirality pdb=" CA ILE B 169 " pdb=" N ILE B 169 " pdb=" C ILE B 169 " pdb=" CB ILE B 169 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CA ILE F 169 " pdb=" N ILE F 169 " pdb=" C ILE F 169 " pdb=" CB ILE F 169 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CA ILE H 169 " pdb=" N ILE H 169 " pdb=" C ILE H 169 " pdb=" CB ILE H 169 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.20e-01 ... (remaining 2157 not shown) Planarity restraints: 2296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 59 " 0.035 5.00e-02 4.00e+02 5.26e-02 4.43e+00 pdb=" N PRO D 60 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO D 60 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 60 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 59 " 0.035 5.00e-02 4.00e+02 5.25e-02 4.42e+00 pdb=" N PRO C 60 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 60 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 60 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 59 " 0.035 5.00e-02 4.00e+02 5.25e-02 4.42e+00 pdb=" N PRO E 60 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO E 60 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 60 " 0.030 5.00e-02 4.00e+02 ... (remaining 2293 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3850 2.81 - 3.33: 13724 3.33 - 3.86: 20744 3.86 - 4.38: 21377 4.38 - 4.90: 37590 Nonbonded interactions: 97285 Sorted by model distance: nonbonded pdb=" OE1 GLU F 225 " pdb=" NH1 ARG F 226 " model vdw 2.290 3.120 nonbonded pdb=" OE1 GLU B 225 " pdb=" NH1 ARG B 226 " model vdw 2.290 3.120 nonbonded pdb=" OE1 GLU A 225 " pdb=" NH1 ARG A 226 " model vdw 2.290 3.120 nonbonded pdb=" OE1 GLU G 225 " pdb=" NH1 ARG G 226 " model vdw 2.290 3.120 nonbonded pdb=" OE1 GLU C 225 " pdb=" NH1 ARG C 226 " model vdw 2.290 3.120 ... (remaining 97280 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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 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: 1.640 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.730 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13664 Z= 0.251 Angle : 0.844 12.848 18552 Z= 0.538 Chirality : 0.041 0.170 2160 Planarity : 0.005 0.053 2296 Dihedral : 14.629 81.467 4880 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.89 (0.19), residues: 1664 helix: -0.64 (0.12), residues: 1304 sheet: None (None), residues: 0 loop : -3.16 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 226 TYR 0.014 0.002 TYR H 97 PHE 0.008 0.001 PHE H 229 TRP 0.020 0.001 TRP F 218 HIS 0.001 0.000 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00534 (13656) covalent geometry : angle 0.84314 (18536) SS BOND : bond 0.00656 ( 8) SS BOND : angle 1.59915 ( 16) hydrogen bonds : bond 0.08586 ( 929) hydrogen bonds : angle 4.32021 ( 2787) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.659 Fit side-chains REVERT: A 102 MET cc_start: 0.8083 (ttp) cc_final: 0.7852 (ttm) REVERT: B 26 MET cc_start: 0.7340 (mmm) cc_final: 0.6989 (tpt) REVERT: B 235 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8523 (mm-30) REVERT: C 102 MET cc_start: 0.8084 (ttp) cc_final: 0.7851 (ttm) REVERT: D 26 MET cc_start: 0.7335 (mmm) cc_final: 0.6978 (tpt) REVERT: D 235 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8519 (mm-30) REVERT: E 102 MET cc_start: 0.8081 (ttp) cc_final: 0.7847 (ttm) REVERT: F 26 MET cc_start: 0.7331 (mmm) cc_final: 0.6980 (tpt) REVERT: F 235 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8515 (mm-30) REVERT: G 102 MET cc_start: 0.8081 (ttp) cc_final: 0.7846 (ttm) REVERT: H 26 MET cc_start: 0.7333 (mmm) cc_final: 0.6985 (tpt) REVERT: H 235 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8520 (mm-30) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.1093 time to fit residues: 43.8760 Evaluate side-chains 213 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN A 73 ASN A 147 GLN B 40 ASN C 40 ASN C 73 ASN C 147 GLN D 40 ASN E 40 ASN E 73 ASN E 147 GLN F 40 ASN G 40 ASN G 73 ASN G 147 GLN H 40 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.116292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.098178 restraints weight = 28060.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.100956 restraints weight = 13000.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.103027 restraints weight = 8052.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.104251 restraints weight = 5869.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.105273 restraints weight = 4813.720| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13664 Z= 0.138 Angle : 0.599 5.778 18552 Z= 0.325 Chirality : 0.038 0.181 2160 Planarity : 0.005 0.054 2296 Dihedral : 5.180 22.720 1856 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.40 % Allowed : 14.04 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.32 (0.21), residues: 1664 helix: 0.94 (0.14), residues: 1328 sheet: None (None), residues: 0 loop : -2.63 (0.39), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 179 TYR 0.008 0.001 TYR A 34 PHE 0.008 0.001 PHE D 128 TRP 0.009 0.001 TRP D 218 HIS 0.000 0.000 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00345 (13656) covalent geometry : angle 0.59823 (18536) SS BOND : bond 0.00285 ( 8) SS BOND : angle 0.99722 ( 16) hydrogen bonds : bond 0.04001 ( 929) hydrogen bonds : angle 3.43698 ( 2787) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 252 time to evaluate : 0.549 Fit side-chains REVERT: A 76 MET cc_start: 0.8798 (ttp) cc_final: 0.8482 (tmm) REVERT: B 26 MET cc_start: 0.5948 (mmm) cc_final: 0.5576 (tpt) REVERT: B 107 MET cc_start: 0.8858 (tpp) cc_final: 0.8578 (ttt) REVERT: B 147 GLN cc_start: 0.8249 (tp40) cc_final: 0.7993 (tp-100) REVERT: B 235 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8547 (mm-30) REVERT: C 76 MET cc_start: 0.8793 (ttp) cc_final: 0.8475 (tmm) REVERT: D 26 MET cc_start: 0.5929 (mmm) cc_final: 0.5562 (tpt) REVERT: D 107 MET cc_start: 0.8855 (tpp) cc_final: 0.8576 (ttt) REVERT: D 147 GLN cc_start: 0.8255 (tp40) cc_final: 0.7997 (tp-100) REVERT: D 235 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8548 (mm-30) REVERT: E 76 MET cc_start: 0.8789 (ttp) cc_final: 0.8472 (tmm) REVERT: F 26 MET cc_start: 0.5905 (mmm) cc_final: 0.5533 (tpt) REVERT: F 107 MET cc_start: 0.8854 (tpp) cc_final: 0.8578 (ttt) REVERT: F 147 GLN cc_start: 0.8272 (tp40) cc_final: 0.8011 (tp-100) REVERT: F 235 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8546 (mm-30) REVERT: G 76 MET cc_start: 0.8798 (ttp) cc_final: 0.8480 (tmm) REVERT: H 26 MET cc_start: 0.5913 (mmm) cc_final: 0.5537 (tpt) REVERT: H 107 MET cc_start: 0.8851 (tpp) cc_final: 0.8575 (ttt) REVERT: H 147 GLN cc_start: 0.8264 (tp40) cc_final: 0.8004 (tp-100) REVERT: H 235 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8551 (mm-30) outliers start: 20 outliers final: 8 residues processed: 260 average time/residue: 0.0996 time to fit residues: 39.3956 Evaluate side-chains 225 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 217 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain H residue 243 VAL 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 702, in refine_xyz self.minimization_no_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 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( 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 44, in __init__ self.weight = mmtbx.refinement.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 362, 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 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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: 59.6579 > 50: distance: 20 - 26: 35.530 distance: 26 - 27: 19.137 distance: 27 - 28: 10.240 distance: 27 - 30: 21.499 distance: 28 - 29: 14.436 distance: 28 - 32: 13.682 distance: 30 - 31: 21.943 distance: 31 - 132: 22.065 distance: 32 - 33: 17.769 distance: 32 - 38: 18.631 distance: 33 - 34: 6.767 distance: 33 - 36: 10.116 distance: 34 - 35: 3.710 distance: 34 - 39: 20.374 distance: 36 - 37: 8.999 distance: 37 - 38: 17.895 distance: 39 - 40: 18.515 distance: 40 - 41: 26.817 distance: 40 - 43: 41.464 distance: 41 - 42: 53.532 distance: 41 - 45: 7.655 distance: 43 - 44: 26.687 distance: 45 - 46: 24.247 distance: 46 - 47: 28.226 distance: 46 - 49: 18.846 distance: 47 - 48: 21.908 distance: 47 - 53: 41.683 distance: 49 - 50: 36.684 distance: 50 - 51: 24.644 distance: 50 - 52: 25.728 distance: 53 - 54: 8.130 distance: 53 - 59: 15.430 distance: 54 - 55: 23.683 distance: 54 - 57: 26.010 distance: 55 - 56: 28.534 distance: 55 - 60: 27.957 distance: 57 - 58: 30.054 distance: 58 - 59: 27.139 distance: 60 - 61: 40.503 distance: 61 - 62: 26.241 distance: 61 - 64: 44.408 distance: 62 - 63: 41.619 distance: 62 - 71: 32.042 distance: 64 - 65: 16.337 distance: 65 - 66: 19.543 distance: 66 - 67: 10.452 distance: 67 - 68: 11.933 distance: 68 - 69: 8.135 distance: 68 - 70: 7.283 distance: 71 - 72: 25.327 distance: 72 - 73: 5.401 distance: 72 - 75: 34.023 distance: 73 - 74: 12.889 distance: 73 - 83: 10.930 distance: 75 - 76: 12.875 distance: 76 - 77: 7.218 distance: 76 - 78: 4.610 distance: 77 - 79: 15.992 distance: 78 - 80: 10.114 distance: 79 - 81: 7.956 distance: 80 - 81: 8.287 distance: 81 - 82: 9.854 distance: 83 - 84: 12.170 distance: 84 - 85: 15.766 distance: 84 - 87: 12.173 distance: 85 - 86: 31.350 distance: 85 - 91: 13.223 distance: 86 - 115: 31.306 distance: 87 - 88: 32.217 distance: 88 - 89: 20.670 distance: 88 - 90: 21.777 distance: 91 - 92: 29.611 distance: 92 - 93: 11.963 distance: 92 - 95: 21.468 distance: 93 - 94: 12.348 distance: 93 - 99: 30.953 distance: 95 - 96: 16.138 distance: 96 - 97: 12.312 distance: 96 - 98: 17.859 distance: 99 - 100: 25.949 distance: 100 - 101: 27.363 distance: 100 - 103: 19.518 distance: 101 - 102: 10.860 distance: 101 - 104: 20.974