Starting phenix.real_space_refine on Sun Aug 4 13:59:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0m_32244/08_2024/7w0m_32244.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0m_32244/08_2024/7w0m_32244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0m_32244/08_2024/7w0m_32244.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0m_32244/08_2024/7w0m_32244.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0m_32244/08_2024/7w0m_32244.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0m_32244/08_2024/7w0m_32244.cif" } resolution = 3.71 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= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2101 atoms to isotropic. 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 67 5.16 5 C 5690 2.51 5 N 1509 2.21 5 O 1663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 234": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8929 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1758 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 418 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "R" Number of atoms: 2321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2321 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 11, 'TRANS': 278} Chain: "S" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1794 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Chain: "R" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'8EH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.19, per 1000 atoms: 0.58 Number of scatterers: 8929 At special positions: 0 Unit cell: (92.65, 119.85, 131.75, 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 67 16.00 O 1663 8.00 N 1509 7.00 C 5690 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 181 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.66 Conformation dependent library (CDL) restraints added in 1.6 seconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 15 sheets defined 36.1% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.695A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.037A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 271 through 279 removed outlier: 3.503A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.883A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.878A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA B 21 " --> pdb=" O GLN B 17 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ARG B 22 " --> pdb=" O ILE B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.835A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 39 through 55 removed outlier: 3.562A pdb=" N GLN C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN C 55 " --> pdb=" O LYS C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 74 removed outlier: 3.561A pdb=" N LEU C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 55 Processing helix chain 'R' and resid 64 through 81 removed outlier: 4.494A pdb=" N THR R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 91 removed outlier: 4.020A pdb=" N TRP R 85 " --> pdb=" O THR R 81 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR R 89 " --> pdb=" O TRP R 85 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TYR R 90 " --> pdb=" O ALA R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 132 removed outlier: 3.979A pdb=" N LYS R 103 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 148 through 162 removed outlier: 4.604A pdb=" N TRP R 154 " --> pdb=" O THR R 150 " (cutoff:3.500A) Processing helix chain 'R' and resid 162 through 167 removed outlier: 3.963A pdb=" N VAL R 166 " --> pdb=" O MET R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 231 removed outlier: 4.080A pdb=" N ALA R 196 " --> pdb=" O SER R 192 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N THR R 207 " --> pdb=" O VAL R 203 " (cutoff:3.500A) Proline residue: R 213 - end of helix Processing helix chain 'R' and resid 238 through 276 removed outlier: 4.087A pdb=" N LYS R 242 " --> pdb=" O GLU R 238 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL R 254 " --> pdb=" O ILE R 250 " (cutoff:3.500A) Proline residue: R 263 - end of helix removed outlier: 4.014A pdb=" N LEU R 276 " --> pdb=" O MET R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 291 removed outlier: 4.361A pdb=" N LEU R 285 " --> pdb=" O CYS R 281 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE R 286 " --> pdb=" O ASP R 282 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 304 removed outlier: 4.244A pdb=" N ILE R 297 " --> pdb=" O TYR R 293 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER R 302 " --> pdb=" O SER R 298 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 311 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 52 through 56 removed outlier: 3.781A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35 removed outlier: 6.164A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 removed outlier: 3.577A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.071A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.837A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP B 83 " --> pdb=" O ASN B 88 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.039A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.820A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP B 169 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.910A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.539A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.163A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 168 through 171 removed outlier: 3.736A pdb=" N GLN R 180 " --> pdb=" O GLY R 171 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 5 through 7 removed outlier: 3.818A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU S 81 " --> pdb=" O LEU S 20 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR S 78 " --> pdb=" O ASP S 73 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP S 73 " --> pdb=" O THR S 78 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER S 71 " --> pdb=" O PHE S 80 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR S 69 " --> pdb=" O GLN S 82 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 49 through 51 removed outlier: 3.842A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TRP S 36 " --> pdb=" O ALA S 49 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 147 Processing sheet with id=AB5, first strand: chain 'S' and resid 156 through 160 Processing sheet with id=AB6, first strand: chain 'S' and resid 186 through 187 352 hydrogen bonds defined for protein. 1014 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: 2.32 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2854 1.35 - 1.47: 2370 1.47 - 1.60: 3801 1.60 - 1.72: 1 1.72 - 1.85: 98 Bond restraints: 9124 Sorted by residual: bond pdb=" C30 8EH R 401 " pdb=" C31 8EH R 401 " ideal model delta sigma weight residual 1.472 1.569 -0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" C30 8EH R 401 " pdb=" N29 8EH R 401 " ideal model delta sigma weight residual 1.313 1.399 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C10 8EH R 401 " pdb=" N11 8EH R 401 " ideal model delta sigma weight residual 1.421 1.500 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C12 8EH R 401 " pdb=" N28 8EH R 401 " ideal model delta sigma weight residual 1.307 1.386 -0.079 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C30 8EH R 401 " pdb=" N11 8EH R 401 " ideal model delta sigma weight residual 1.375 1.446 -0.071 2.00e-02 2.50e+03 1.27e+01 ... (remaining 9119 not shown) Histogram of bond angle deviations from ideal: 99.12 - 106.10: 150 106.10 - 113.09: 4900 113.09 - 120.07: 3241 120.07 - 127.05: 3975 127.05 - 134.04: 99 Bond angle restraints: 12365 Sorted by residual: angle pdb=" C LEU R 167 " pdb=" N ARG R 168 " pdb=" CA ARG R 168 " ideal model delta sigma weight residual 120.75 128.01 -7.26 1.51e+00 4.39e-01 2.31e+01 angle pdb=" CA VAL R 166 " pdb=" CB VAL R 166 " pdb=" CG2 VAL R 166 " ideal model delta sigma weight residual 110.40 117.90 -7.50 1.70e+00 3.46e-01 1.94e+01 angle pdb=" O15 8EH R 401 " pdb=" S14 8EH R 401 " pdb=" O16 8EH R 401 " ideal model delta sigma weight residual 119.97 107.69 12.28 3.00e+00 1.11e-01 1.68e+01 angle pdb=" N VAL R 148 " pdb=" CA VAL R 148 " pdb=" C VAL R 148 " ideal model delta sigma weight residual 112.96 108.95 4.01 1.00e+00 1.00e+00 1.61e+01 angle pdb=" CA GLU S 234 " pdb=" C GLU S 234 " pdb=" O GLU S 234 " ideal model delta sigma weight residual 121.16 116.83 4.33 1.12e+00 7.97e-01 1.50e+01 ... (remaining 12360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 4863 17.87 - 35.74: 444 35.74 - 53.61: 62 53.61 - 71.48: 15 71.48 - 89.35: 12 Dihedral angle restraints: 5396 sinusoidal: 2108 harmonic: 3288 Sorted by residual: dihedral pdb=" CB CYS R 102 " pdb=" SG CYS R 102 " pdb=" SG CYS R 181 " pdb=" CB CYS R 181 " ideal model delta sinusoidal sigma weight residual 93.00 171.61 -78.61 1 1.00e+01 1.00e-02 7.70e+01 dihedral pdb=" CA TYR S 94 " pdb=" C TYR S 94 " pdb=" N TYR S 95 " pdb=" CA TYR S 95 " ideal model delta harmonic sigma weight residual 180.00 154.31 25.69 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA THR B 164 " pdb=" C THR B 164 " pdb=" N THR B 165 " pdb=" CA THR B 165 " ideal model delta harmonic sigma weight residual 180.00 -158.94 -21.06 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 5393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1257 0.072 - 0.144: 128 0.144 - 0.217: 4 0.217 - 0.289: 2 0.289 - 0.361: 3 Chirality restraints: 1394 Sorted by residual: chirality pdb=" C19 8EH R 401 " pdb=" C17 8EH R 401 " pdb=" C21 8EH R 401 " pdb=" O20 8EH R 401 " both_signs ideal model delta sigma weight residual False -2.43 -2.79 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CA LEU S 233 " pdb=" N LEU S 233 " pdb=" C LEU S 233 " pdb=" CB LEU S 233 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CB VAL R 166 " pdb=" CA VAL R 166 " pdb=" CG1 VAL R 166 " pdb=" CG2 VAL R 166 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 1391 not shown) Planarity restraints: 1555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL S 147 " 0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO S 148 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO S 148 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO S 148 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP R 313 " -0.040 5.00e-02 4.00e+02 5.93e-02 5.62e+00 pdb=" N PRO R 314 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO R 314 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 314 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP R 95 " 0.032 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO R 96 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO R 96 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 96 " 0.027 5.00e-02 4.00e+02 ... (remaining 1552 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1558 2.76 - 3.30: 8547 3.30 - 3.83: 13975 3.83 - 4.37: 15727 4.37 - 4.90: 27291 Nonbonded interactions: 67098 Sorted by model distance: nonbonded pdb=" OG SER B 97 " pdb=" OD2 ASP B 118 " model vdw 2.230 3.040 nonbonded pdb=" NE ARG R 91 " pdb=" O ASP R 94 " model vdw 2.269 3.120 nonbonded pdb=" OE1 GLN B 176 " pdb=" OG1 THR B 179 " model vdw 2.270 3.040 nonbonded pdb=" O THR A 327 " pdb=" N LYS A 330 " model vdw 2.272 3.120 nonbonded pdb=" ND2 ASN R 46 " pdb=" O ALA R 72 " model vdw 2.277 3.120 ... (remaining 67093 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.600 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 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 0.100 9124 Z= 0.296 Angle : 0.761 12.279 12365 Z= 0.405 Chirality : 0.047 0.361 1394 Planarity : 0.005 0.076 1555 Dihedral : 14.112 89.348 3275 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.90 (0.25), residues: 1118 helix: 0.51 (0.29), residues: 352 sheet: -1.72 (0.32), residues: 256 loop : -2.30 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.027 0.001 PHE S 27 TYR 0.022 0.002 TYR S 235 ARG 0.005 0.000 ARG R 315 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7512 (tm-30) REVERT: A 191 PHE cc_start: 0.8395 (t80) cc_final: 0.8183 (t80) REVERT: A 193 ASP cc_start: 0.7955 (m-30) cc_final: 0.7741 (m-30) REVERT: A 245 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7718 (mm-30) REVERT: A 271 LYS cc_start: 0.8171 (tptp) cc_final: 0.7911 (tptt) REVERT: A 344 ILE cc_start: 0.7883 (tt) cc_final: 0.7677 (tt) REVERT: A 348 LEU cc_start: 0.7514 (tp) cc_final: 0.7254 (tt) REVERT: B 25 CYS cc_start: 0.8399 (m) cc_final: 0.7912 (t) REVERT: B 61 MET cc_start: 0.6892 (tmm) cc_final: 0.6578 (tmm) REVERT: B 124 TYR cc_start: 0.8294 (m-80) cc_final: 0.7711 (m-80) REVERT: B 197 ARG cc_start: 0.7869 (mtp85) cc_final: 0.7578 (mtp85) REVERT: B 199 PHE cc_start: 0.8189 (p90) cc_final: 0.7933 (p90) REVERT: B 212 ASP cc_start: 0.7593 (t0) cc_final: 0.7318 (t70) REVERT: B 220 GLN cc_start: 0.7811 (mt0) cc_final: 0.7520 (mt0) REVERT: B 233 CYS cc_start: 0.7497 (t) cc_final: 0.7115 (t) REVERT: B 247 ASP cc_start: 0.7413 (t0) cc_final: 0.7060 (t0) REVERT: B 314 ARG cc_start: 0.7502 (ptp-170) cc_final: 0.7216 (ptm160) REVERT: R 97 PHE cc_start: 0.7240 (m-10) cc_final: 0.7018 (m-10) REVERT: R 162 MET cc_start: 0.5536 (mmp) cc_final: 0.5175 (mmp) REVERT: R 165 MET cc_start: 0.7280 (tpt) cc_final: 0.6920 (tpt) REVERT: R 166 VAL cc_start: 0.7767 (t) cc_final: 0.7111 (t) REVERT: R 183 MET cc_start: 0.4866 (tmm) cc_final: 0.4437 (tmm) REVERT: R 268 LYS cc_start: 0.8837 (mttt) cc_final: 0.8499 (mttt) REVERT: R 284 ASP cc_start: 0.8074 (t0) cc_final: 0.7810 (t0) REVERT: R 301 ASN cc_start: 0.7790 (t0) cc_final: 0.7429 (t0) REVERT: S 34 MET cc_start: 0.7776 (mmm) cc_final: 0.7165 (mmm) REVERT: S 85 SER cc_start: 0.7950 (p) cc_final: 0.7679 (m) REVERT: S 89 GLU cc_start: 0.7756 (tp30) cc_final: 0.7500 (tp30) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.2195 time to fit residues: 91.1584 Evaluate side-chains 279 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.0870 chunk 84 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 0.2980 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN B 175 GLN B 259 GLN ** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9124 Z= 0.195 Angle : 0.641 8.640 12365 Z= 0.327 Chirality : 0.043 0.223 1394 Planarity : 0.004 0.048 1555 Dihedral : 8.631 73.840 1261 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.03 % Allowed : 12.58 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.71 (0.25), residues: 1118 helix: 0.68 (0.29), residues: 352 sheet: -1.41 (0.32), residues: 255 loop : -2.32 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 261 HIS 0.004 0.001 HIS A 213 PHE 0.013 0.001 PHE R 291 TYR 0.030 0.002 TYR S 235 ARG 0.003 0.000 ARG R 315 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 278 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7558 (tm-30) REVERT: A 26 ASP cc_start: 0.7921 (t0) cc_final: 0.7477 (t0) REVERT: A 191 PHE cc_start: 0.8422 (t80) cc_final: 0.8218 (t80) REVERT: A 193 ASP cc_start: 0.7965 (m-30) cc_final: 0.7747 (m-30) REVERT: A 205 ARG cc_start: 0.7233 (mmp80) cc_final: 0.6863 (mmp80) REVERT: A 216 GLU cc_start: 0.7813 (tp30) cc_final: 0.7554 (tp30) REVERT: A 245 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7719 (mm-30) REVERT: A 344 ILE cc_start: 0.7883 (tt) cc_final: 0.7667 (tt) REVERT: A 348 LEU cc_start: 0.7532 (tp) cc_final: 0.7313 (tp) REVERT: B 25 CYS cc_start: 0.8269 (m) cc_final: 0.7920 (t) REVERT: B 59 TYR cc_start: 0.8424 (m-80) cc_final: 0.7966 (m-80) REVERT: B 61 MET cc_start: 0.7013 (tmm) cc_final: 0.6503 (tmm) REVERT: B 102 THR cc_start: 0.8436 (t) cc_final: 0.8061 (m) REVERT: B 197 ARG cc_start: 0.7817 (mtp85) cc_final: 0.7541 (mtp85) REVERT: B 212 ASP cc_start: 0.7646 (t0) cc_final: 0.7302 (t70) REVERT: B 220 GLN cc_start: 0.7697 (mt0) cc_final: 0.7437 (mt0) REVERT: B 233 CYS cc_start: 0.7585 (t) cc_final: 0.7140 (t) REVERT: R 36 MET cc_start: 0.6675 (mmp) cc_final: 0.6449 (mmp) REVERT: R 71 LEU cc_start: 0.7436 (tp) cc_final: 0.6804 (mm) REVERT: R 97 PHE cc_start: 0.7199 (m-10) cc_final: 0.6928 (m-10) REVERT: R 162 MET cc_start: 0.5197 (mmp) cc_final: 0.4828 (mmp) REVERT: R 183 MET cc_start: 0.5007 (tmm) cc_final: 0.4378 (tmm) REVERT: R 268 LYS cc_start: 0.8911 (mttt) cc_final: 0.8503 (mttt) REVERT: R 284 ASP cc_start: 0.8024 (t0) cc_final: 0.7767 (t0) REVERT: S 34 MET cc_start: 0.7721 (mmm) cc_final: 0.6931 (mmm) REVERT: S 85 SER cc_start: 0.7953 (p) cc_final: 0.7711 (m) REVERT: S 230 MET cc_start: 0.7875 (ttp) cc_final: 0.7610 (ttt) outliers start: 10 outliers final: 4 residues processed: 280 average time/residue: 0.2040 time to fit residues: 78.0221 Evaluate side-chains 276 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 272 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 192 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.8092 > 50: distance: 5 - 11: 8.216 distance: 11 - 12: 5.285 distance: 12 - 13: 4.375 distance: 12 - 15: 19.192 distance: 13 - 14: 8.002 distance: 13 - 21: 14.085 distance: 15 - 16: 20.309 distance: 16 - 17: 22.581 distance: 16 - 18: 15.549 distance: 17 - 19: 9.844 distance: 18 - 20: 6.967 distance: 19 - 20: 5.888 distance: 21 - 22: 13.570 distance: 22 - 23: 10.795 distance: 22 - 25: 6.314 distance: 23 - 24: 20.088 distance: 23 - 35: 13.705 distance: 25 - 26: 7.702 distance: 26 - 27: 19.296 distance: 26 - 28: 5.947 distance: 27 - 29: 9.945 distance: 28 - 30: 6.529 distance: 28 - 31: 6.775 distance: 29 - 30: 8.905 distance: 30 - 32: 6.634 distance: 31 - 33: 7.544 distance: 33 - 34: 9.637 distance: 35 - 36: 18.830 distance: 36 - 37: 10.393 distance: 37 - 38: 11.512 distance: 37 - 39: 13.329 distance: 39 - 40: 4.899 distance: 40 - 41: 10.416 distance: 40 - 43: 20.574 distance: 41 - 42: 4.011 distance: 41 - 46: 15.603 distance: 43 - 44: 23.362 distance: 43 - 45: 28.025 distance: 46 - 47: 13.162 distance: 47 - 48: 8.291 distance: 47 - 50: 25.286 distance: 48 - 49: 7.195 distance: 48 - 54: 8.164 distance: 50 - 51: 16.741 distance: 51 - 52: 8.598 distance: 51 - 53: 13.555 distance: 54 - 55: 5.456 distance: 55 - 56: 14.870 distance: 55 - 58: 7.214 distance: 56 - 57: 17.474 distance: 56 - 60: 34.076 distance: 58 - 59: 39.350 distance: 60 - 61: 15.893 distance: 61 - 62: 34.616 distance: 61 - 64: 39.784 distance: 62 - 63: 6.100 distance: 62 - 71: 7.927 distance: 64 - 65: 23.527 distance: 65 - 66: 14.094 distance: 66 - 67: 11.624 distance: 67 - 68: 6.703 distance: 68 - 69: 5.869 distance: 68 - 70: 15.746 distance: 71 - 72: 21.990 distance: 72 - 73: 18.353 distance: 72 - 75: 8.390 distance: 73 - 74: 12.428 distance: 73 - 79: 6.715 distance: 75 - 76: 7.440 distance: 76 - 77: 16.028 distance: 76 - 78: 37.112 distance: 80 - 81: 5.483 distance: 80 - 83: 13.987 distance: 81 - 82: 15.334 distance: 81 - 87: 6.016 distance: 83 - 84: 15.367 distance: 84 - 85: 15.330 distance: 84 - 86: 18.961 distance: 87 - 88: 3.560 distance: 88 - 89: 11.002 distance: 88 - 91: 17.616 distance: 89 - 90: 8.644 distance: 89 - 94: 8.610 distance: 91 - 92: 8.980 distance: 91 - 93: 28.607