Starting phenix.real_space_refine on Sat Aug 23 08:03:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7raz_24390/08_2025/7raz_24390.cif Found real_map, /net/cci-nas-00/data/ceres_data/7raz_24390/08_2025/7raz_24390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7raz_24390/08_2025/7raz_24390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7raz_24390/08_2025/7raz_24390.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7raz_24390/08_2025/7raz_24390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7raz_24390/08_2025/7raz_24390.map" } resolution = 3.4 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: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 28 5.16 5 C 6699 2.51 5 N 1799 2.21 5 O 1939 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 10472 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1464 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain: "B" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1464 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain: "C" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1464 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain: "D" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1464 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain: "E" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1464 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain: "F" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1464 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain: "G" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1464 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 2.77, per 1000 atoms: 0.26 Number of scatterers: 10472 At special positions: 0 Unit cell: (98.44, 97.37, 116.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 7 15.00 O 1939 8.00 N 1799 7.00 C 6699 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 343.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2436 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 9 sheets defined 42.0% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 94 through 128 removed outlier: 4.956A pdb=" N GLY A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N SER A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 173 Processing helix chain 'A' and resid 197 through 212 removed outlier: 3.852A pdb=" N VAL A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 265 Processing helix chain 'B' and resid 94 through 128 removed outlier: 4.723A pdb=" N GLY B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N SER B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 173 Processing helix chain 'B' and resid 197 through 212 removed outlier: 3.878A pdb=" N VAL B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 265 Processing helix chain 'C' and resid 92 through 128 removed outlier: 4.118A pdb=" N VAL C 96 " --> pdb=" O GLN C 92 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE C 97 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N GLY C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N SER C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 173 Processing helix chain 'C' and resid 197 through 212 removed outlier: 3.884A pdb=" N VAL C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 265 Processing helix chain 'D' and resid 92 through 128 removed outlier: 4.073A pdb=" N VAL D 96 " --> pdb=" O GLN D 92 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLY D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N SER D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 173 Processing helix chain 'D' and resid 197 through 212 removed outlier: 3.792A pdb=" N VAL D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 265 Processing helix chain 'E' and resid 94 through 128 removed outlier: 4.973A pdb=" N GLY E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N SER E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 173 Processing helix chain 'E' and resid 197 through 212 removed outlier: 3.854A pdb=" N VAL E 201 " --> pdb=" O ASP E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 265 Processing helix chain 'F' and resid 92 through 128 removed outlier: 4.174A pdb=" N VAL F 96 " --> pdb=" O GLN F 92 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE F 97 " --> pdb=" O THR F 93 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N SER F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 173 Processing helix chain 'F' and resid 197 through 212 removed outlier: 3.876A pdb=" N VAL F 201 " --> pdb=" O ASP F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 265 Processing helix chain 'G' and resid 94 through 128 removed outlier: 4.956A pdb=" N GLY G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N SER G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 173 Processing helix chain 'G' and resid 197 through 212 removed outlier: 3.882A pdb=" N VAL G 201 " --> pdb=" O ASP G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 265 Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 138 removed outlier: 7.121A pdb=" N THR A 154 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL A 148 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N SER A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 162 " --> pdb=" O ASN G 177 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N THR G 154 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N VAL G 148 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N SER G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE G 162 " --> pdb=" O ASN F 177 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE F 175 " --> pdb=" O VAL G 164 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N THR F 154 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL F 148 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N SER F 152 " --> pdb=" O VAL F 148 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE F 162 " --> pdb=" O ASN E 177 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE E 175 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL E 145 " --> pdb=" O ARG E 156 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ARG E 156 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE D 175 " --> pdb=" O VAL E 164 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR D 154 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N VAL D 148 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N SER D 152 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE D 162 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N THR C 154 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VAL C 148 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N SER C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE C 162 " --> pdb=" O ASN B 177 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 175 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N THR B 154 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N VAL B 148 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N SER B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE B 162 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 175 " --> pdb=" O VAL B 164 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 192 removed outlier: 6.225A pdb=" N VAL A 236 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU A 225 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ARG A 238 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL A 223 " --> pdb=" O ARG A 238 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 274 through 277 removed outlier: 6.113A pdb=" N ASP A 274 " --> pdb=" O MET B 273 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL B 275 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASN A 276 " --> pdb=" O VAL B 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 192 removed outlier: 6.067A pdb=" N VAL B 236 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LEU B 225 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ARG B 238 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N VAL B 223 " --> pdb=" O ARG B 238 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N TRP B 240 " --> pdb=" O MET B 221 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N MET B 221 " --> pdb=" O TRP B 240 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 183 through 192 removed outlier: 5.734A pdb=" N VAL C 236 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LEU C 225 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ARG C 238 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL C 223 " --> pdb=" O ARG C 238 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N TRP C 240 " --> pdb=" O MET C 221 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N MET C 221 " --> pdb=" O TRP C 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 183 through 192 removed outlier: 6.038A pdb=" N VAL D 236 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU D 225 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ARG D 238 " --> pdb=" O VAL D 223 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N VAL D 223 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N TRP D 240 " --> pdb=" O MET D 221 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N MET D 221 " --> pdb=" O TRP D 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 183 through 192 removed outlier: 6.005A pdb=" N VAL E 236 " --> pdb=" O LEU E 225 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU E 225 " --> pdb=" O VAL E 236 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ARG E 238 " --> pdb=" O VAL E 223 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL E 223 " --> pdb=" O ARG E 238 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N TRP E 240 " --> pdb=" O MET E 221 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N MET E 221 " --> pdb=" O TRP E 240 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 183 through 192 removed outlier: 5.775A pdb=" N VAL F 236 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LEU F 225 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ARG F 238 " --> pdb=" O VAL F 223 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N VAL F 223 " --> pdb=" O ARG F 238 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N TRP F 240 " --> pdb=" O MET F 221 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N MET F 221 " --> pdb=" O TRP F 240 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 183 through 192 removed outlier: 6.152A pdb=" N VAL G 236 " --> pdb=" O LEU G 225 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LEU G 225 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ARG G 238 " --> pdb=" O VAL G 223 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N VAL G 223 " --> pdb=" O ARG G 238 " (cutoff:3.500A) 611 hydrogen bonds defined for protein. 1782 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.60 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1736 1.31 - 1.43: 2611 1.43 - 1.56: 6195 1.56 - 1.68: 14 1.68 - 1.81: 56 Bond restraints: 10612 Sorted by residual: bond pdb=" C8 PTY C 301 " pdb=" O7 PTY C 301 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C8 PTY B 301 " pdb=" O7 PTY B 301 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C8 PTY D 301 " pdb=" O7 PTY D 301 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C8 PTY F 301 " pdb=" O7 PTY F 301 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C8 PTY A 301 " pdb=" O7 PTY A 301 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 10607 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 14127 3.37 - 6.74: 174 6.74 - 10.11: 8 10.11 - 13.48: 6 13.48 - 16.85: 7 Bond angle restraints: 14322 Sorted by residual: angle pdb=" O11 PTY D 301 " pdb=" P1 PTY D 301 " pdb=" O14 PTY D 301 " ideal model delta sigma weight residual 92.90 109.75 -16.85 3.00e+00 1.11e-01 3.16e+01 angle pdb=" O11 PTY F 301 " pdb=" P1 PTY F 301 " pdb=" O14 PTY F 301 " ideal model delta sigma weight residual 92.90 109.71 -16.81 3.00e+00 1.11e-01 3.14e+01 angle pdb=" O11 PTY E 301 " pdb=" P1 PTY E 301 " pdb=" O14 PTY E 301 " ideal model delta sigma weight residual 92.90 109.61 -16.71 3.00e+00 1.11e-01 3.10e+01 angle pdb=" O11 PTY C 301 " pdb=" P1 PTY C 301 " pdb=" O14 PTY C 301 " ideal model delta sigma weight residual 92.90 109.52 -16.62 3.00e+00 1.11e-01 3.07e+01 angle pdb=" O11 PTY G 301 " pdb=" P1 PTY G 301 " pdb=" O14 PTY G 301 " ideal model delta sigma weight residual 92.90 109.35 -16.45 3.00e+00 1.11e-01 3.01e+01 ... (remaining 14317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.06: 6148 26.06 - 52.11: 220 52.11 - 78.17: 22 78.17 - 104.23: 11 104.23 - 130.28: 4 Dihedral angle restraints: 6405 sinusoidal: 2618 harmonic: 3787 Sorted by residual: dihedral pdb=" CA MET A 126 " pdb=" C MET A 126 " pdb=" N PHE A 127 " pdb=" CA PHE A 127 " ideal model delta harmonic sigma weight residual 180.00 158.97 21.03 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" C3 PTY C 301 " pdb=" O11 PTY C 301 " pdb=" P1 PTY C 301 " pdb=" O12 PTY C 301 " ideal model delta sinusoidal sigma weight residual -59.77 70.51 -130.28 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" CA MET D 126 " pdb=" C MET D 126 " pdb=" N PHE D 127 " pdb=" CA PHE D 127 " ideal model delta harmonic sigma weight residual 180.00 160.50 19.50 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 6402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1066 0.035 - 0.071: 395 0.071 - 0.106: 158 0.106 - 0.142: 43 0.142 - 0.177: 4 Chirality restraints: 1666 Sorted by residual: chirality pdb=" CA ILE A 176 " pdb=" N ILE A 176 " pdb=" C ILE A 176 " pdb=" CB ILE A 176 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CA MET A 126 " pdb=" N MET A 126 " pdb=" C MET A 126 " pdb=" CB MET A 126 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CA ILE E 176 " pdb=" N ILE E 176 " pdb=" C ILE E 176 " pdb=" CB ILE E 176 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.10e-01 ... (remaining 1663 not shown) Planarity restraints: 1827 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 127 " 0.012 2.00e-02 2.50e+03 1.34e-02 3.13e+00 pdb=" CG PHE B 127 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE B 127 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE B 127 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE B 127 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 127 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 127 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 127 " 0.011 2.00e-02 2.50e+03 1.29e-02 2.92e+00 pdb=" CG PHE C 127 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE C 127 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE C 127 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 127 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C 127 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 127 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 127 " 0.011 2.00e-02 2.50e+03 1.26e-02 2.78e+00 pdb=" CG PHE G 127 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE G 127 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE G 127 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE G 127 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE G 127 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE G 127 " 0.001 2.00e-02 2.50e+03 ... (remaining 1824 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1018 2.74 - 3.28: 11144 3.28 - 3.82: 17876 3.82 - 4.36: 19872 4.36 - 4.90: 34337 Nonbonded interactions: 84247 Sorted by model distance: nonbonded pdb=" O VAL A 192 " pdb=" OG SER A 232 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR F 194 " pdb=" O GLY F 229 " model vdw 2.205 3.040 nonbonded pdb=" ND2 ASN B 276 " pdb=" OD1 ASP C 274 " model vdw 2.214 3.120 nonbonded pdb=" OE2 GLU F 227 " pdb=" ND2 ASN F 234 " model vdw 2.247 3.120 nonbonded pdb=" OE2 GLU B 227 " pdb=" ND2 ASN B 234 " model vdw 2.251 3.120 ... (remaining 84242 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: 0.01 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.130 Find NCS groups from input model: 0.210 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: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 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 : 0.004 0.069 10612 Z= 0.203 Angle : 0.871 16.852 14322 Z= 0.378 Chirality : 0.044 0.177 1666 Planarity : 0.003 0.022 1827 Dihedral : 13.679 130.284 3969 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: 1.13 (0.23), residues: 1316 helix: 2.05 (0.23), residues: 546 sheet: 0.55 (0.31), residues: 259 loop : -0.56 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 238 TYR 0.007 0.001 TYR F 135 PHE 0.030 0.002 PHE B 127 TRP 0.002 0.001 TRP E 240 Details of bonding type rmsd covalent geometry : bond 0.00430 (10612) covalent geometry : angle 0.87051 (14322) hydrogen bonds : bond 0.09035 ( 611) hydrogen bonds : angle 4.34058 ( 1782) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.387 Fit side-chains REVERT: A 149 GLN cc_start: 0.9336 (mm-40) cc_final: 0.8944 (mm-40) REVERT: A 227 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8568 (tm-30) REVERT: A 273 MET cc_start: 0.8276 (tmm) cc_final: 0.7996 (tmm) REVERT: B 181 GLU cc_start: 0.8686 (tp30) cc_final: 0.8162 (tp30) REVERT: C 149 GLN cc_start: 0.9300 (mm-40) cc_final: 0.9009 (mm-40) REVERT: C 155 MET cc_start: 0.8507 (ptm) cc_final: 0.8176 (tmm) REVERT: C 227 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8007 (tm-30) REVERT: D 151 PHE cc_start: 0.8274 (p90) cc_final: 0.8061 (p90) REVERT: D 227 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8473 (tm-30) REVERT: F 149 GLN cc_start: 0.9309 (mm-40) cc_final: 0.9011 (mm-40) REVERT: G 227 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8583 (tm-30) REVERT: G 273 MET cc_start: 0.8361 (tmm) cc_final: 0.7890 (tmm) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.0832 time to fit residues: 17.5084 Evaluate side-chains 117 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 112 GLN G 112 GLN G 167 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.055725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.043739 restraints weight = 51981.723| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 4.05 r_work: 0.2620 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10612 Z= 0.158 Angle : 0.617 9.849 14322 Z= 0.304 Chirality : 0.044 0.185 1666 Planarity : 0.003 0.022 1827 Dihedral : 11.736 143.147 1610 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.08 % Allowed : 8.68 % Favored : 90.24 % 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: 0.93 (0.22), residues: 1316 helix: 1.64 (0.21), residues: 560 sheet: 0.59 (0.29), residues: 273 loop : -0.55 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 131 TYR 0.012 0.001 TYR A 194 PHE 0.026 0.001 PHE G 151 TRP 0.001 0.000 TRP E 251 Details of bonding type rmsd covalent geometry : bond 0.00355 (10612) covalent geometry : angle 0.61707 (14322) hydrogen bonds : bond 0.03916 ( 611) hydrogen bonds : angle 4.07496 ( 1782) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 149 GLN cc_start: 0.9421 (mm-40) cc_final: 0.9026 (mm-40) REVERT: A 227 GLU cc_start: 0.9265 (tm-30) cc_final: 0.8834 (tm-30) REVERT: A 273 MET cc_start: 0.9002 (tmm) cc_final: 0.8590 (tmm) REVERT: B 112 GLN cc_start: 0.8890 (tm-30) cc_final: 0.8635 (tp-100) REVERT: B 181 GLU cc_start: 0.8915 (tp30) cc_final: 0.8387 (tp30) REVERT: C 149 GLN cc_start: 0.9391 (mm-40) cc_final: 0.9099 (mm-40) REVERT: D 227 GLU cc_start: 0.9243 (tm-30) cc_final: 0.8667 (tm-30) REVERT: F 149 GLN cc_start: 0.9346 (mm-40) cc_final: 0.9035 (mm-40) REVERT: G 273 MET cc_start: 0.8967 (tmm) cc_final: 0.8610 (tmm) outliers start: 12 outliers final: 7 residues processed: 130 average time/residue: 0.0909 time to fit residues: 17.3807 Evaluate side-chains 120 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 171 ILE 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: 57.898 > 50: distance: 2 - 18: 23.337 distance: 6 - 23: 15.406 distance: 11 - 31: 19.826 distance: 14 - 18: 23.581 distance: 18 - 19: 34.697 distance: 19 - 20: 14.554 distance: 19 - 22: 35.036 distance: 20 - 21: 6.471 distance: 20 - 23: 26.306 distance: 23 - 24: 11.122 distance: 24 - 25: 18.252 distance: 24 - 27: 12.170 distance: 25 - 26: 19.592 distance: 25 - 31: 3.488 distance: 26 - 50: 17.280 distance: 27 - 28: 11.436 distance: 28 - 29: 18.588 distance: 28 - 30: 9.744 distance: 31 - 32: 7.265 distance: 32 - 33: 26.993 distance: 32 - 35: 7.620 distance: 33 - 34: 16.686 distance: 33 - 40: 9.130 distance: 34 - 58: 20.513 distance: 35 - 36: 16.120 distance: 36 - 37: 3.505 distance: 37 - 38: 11.935 distance: 37 - 39: 17.114 distance: 40 - 41: 8.510 distance: 41 - 42: 11.664 distance: 42 - 43: 20.537 distance: 42 - 44: 3.614 distance: 43 - 64: 15.634 distance: 44 - 45: 10.813 distance: 45 - 46: 6.161 distance: 45 - 48: 5.324 distance: 46 - 47: 16.225 distance: 46 - 50: 11.060 distance: 47 - 72: 47.967 distance: 48 - 49: 22.913 distance: 50 - 51: 37.165 distance: 51 - 52: 45.713 distance: 51 - 54: 25.420 distance: 52 - 53: 13.886 distance: 52 - 58: 23.931 distance: 53 - 80: 52.494 distance: 54 - 55: 12.614 distance: 55 - 56: 30.337 distance: 55 - 57: 23.648 distance: 58 - 59: 18.426 distance: 59 - 60: 26.354 distance: 59 - 62: 18.006 distance: 60 - 61: 10.015 distance: 60 - 64: 31.741 distance: 61 - 85: 23.453 distance: 62 - 63: 15.871 distance: 64 - 65: 21.507 distance: 65 - 68: 13.188 distance: 66 - 67: 10.113 distance: 66 - 72: 9.796 distance: 67 - 90: 23.493 distance: 68 - 69: 15.789 distance: 69 - 70: 5.781 distance: 69 - 71: 3.572 distance: 72 - 73: 10.311 distance: 73 - 74: 6.572 distance: 73 - 76: 11.829 distance: 74 - 75: 11.933 distance: 74 - 80: 14.878 distance: 75 - 94: 20.671 distance: 76 - 77: 19.898 distance: 77 - 78: 22.684 distance: 77 - 79: 36.993 distance: 80 - 81: 4.535 distance: 81 - 82: 9.705 distance: 81 - 84: 4.297 distance: 82 - 83: 7.190 distance: 82 - 85: 24.817 distance: 83 - 100: 29.902