Starting phenix.real_space_refine on Sun May 3 00:15:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mzf_48755/05_2026/9mzf_48755.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mzf_48755/05_2026/9mzf_48755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mzf_48755/05_2026/9mzf_48755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mzf_48755/05_2026/9mzf_48755.map" model { file = "/net/cci-nas-00/data/ceres_data/9mzf_48755/05_2026/9mzf_48755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mzf_48755/05_2026/9mzf_48755.cif" } resolution = 2.5 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= 0.003 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 56 5.16 5 C 5874 2.51 5 N 1593 2.21 5 O 1715 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9238 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 238 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 3059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3059 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 14, 'TRANS': 359} Chain breaks: 3 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1926 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Chain: "P" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "R" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Time building chain proxies: 2.28, per 1000 atoms: 0.25 Number of scatterers: 9238 At special positions: 0 Unit cell: (91.3, 100.43, 170.15, 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 56 16.00 O 1715 8.00 N 1593 7.00 C 5874 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 340.9 milliseconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2180 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 14 sheets defined 45.6% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.511A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 2 through 29 Processing helix chain 'R' and resid 31 through 53 removed outlier: 3.935A pdb=" N THR R 51 " --> pdb=" O GLN R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 93 removed outlier: 4.027A pdb=" N SER R 93 " --> pdb=" O PRO R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 123 through 127 removed outlier: 3.793A pdb=" N GLU R 127 " --> pdb=" O SER R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 169 removed outlier: 3.642A pdb=" N ILE R 161 " --> pdb=" O SER R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 173 Processing helix chain 'R' and resid 174 through 204 Processing helix chain 'R' and resid 215 through 222 Processing helix chain 'R' and resid 223 through 256 removed outlier: 3.813A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE R 230 " --> pdb=" O CYS R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 292 removed outlier: 3.933A pdb=" N VAL R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) Proline residue: R 277 - end of helix removed outlier: 4.091A pdb=" N PHE R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 302 through 337 removed outlier: 3.613A pdb=" N TRP R 306 " --> pdb=" O ASN R 302 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE R 308 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 345 through 361 removed outlier: 4.070A pdb=" N LEU R 349 " --> pdb=" O ILE R 345 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ALA R 350 " --> pdb=" O LYS R 346 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS R 351 " --> pdb=" O CYS R 347 " (cutoff:3.500A) Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 367 Processing helix chain 'R' and resid 377 through 403 removed outlier: 4.033A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 422 removed outlier: 3.542A pdb=" N ARG R 421 " --> pdb=" O TRP R 417 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU R 422 " --> pdb=" O GLU R 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 40 Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.691A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.793A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.131A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 353 removed outlier: 4.214A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.178A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.893A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.284A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.706A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.845A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.645A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.885A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.537A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 58 through 60 removed outlier: 5.465A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 65 through 66 removed outlier: 3.557A pdb=" N THR R 65 " --> pdb=" O TRP R 72 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 83 through 84 removed outlier: 3.562A pdb=" N VAL R 83 " --> pdb=" O VAL R 100 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 104 through 105 removed outlier: 3.919A pdb=" N LEU R 109 " --> pdb=" O THR R 105 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 112 through 114 removed outlier: 3.618A pdb=" N ASP R 114 " --> pdb=" O LEU R 118 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.340A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) 487 hydrogen bonds defined for protein. 1377 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: 1.19 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2994 1.34 - 1.46: 2290 1.46 - 1.58: 4070 1.58 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 9430 Sorted by residual: bond pdb=" N ASN P 28 " pdb=" CA ASN P 28 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.28e-02 6.10e+03 5.25e+00 bond pdb=" N MET P 27 " pdb=" CA MET P 27 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.33e-02 5.65e+03 5.18e+00 bond pdb=" N VAL R 30 " pdb=" CA VAL R 30 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N ASP A 11 " pdb=" CA ASP A 11 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" N THR G 6 " pdb=" CA THR G 6 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.90e+00 ... (remaining 9425 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 12148 1.10 - 2.19: 511 2.19 - 3.29: 85 3.29 - 4.38: 28 4.38 - 5.48: 7 Bond angle restraints: 12779 Sorted by residual: angle pdb=" N ALA B 203 " pdb=" CA ALA B 203 " pdb=" C ALA B 203 " ideal model delta sigma weight residual 110.06 115.52 -5.46 1.43e+00 4.89e-01 1.46e+01 angle pdb=" N GLU P 21 " pdb=" CA GLU P 21 " pdb=" CB GLU P 21 " ideal model delta sigma weight residual 110.22 115.70 -5.48 1.54e+00 4.22e-01 1.26e+01 angle pdb=" N ARG R 299 " pdb=" CA ARG R 299 " pdb=" C ARG R 299 " ideal model delta sigma weight residual 109.40 114.43 -5.03 1.63e+00 3.76e-01 9.52e+00 angle pdb=" N MET P 27 " pdb=" CA MET P 27 " pdb=" C MET P 27 " ideal model delta sigma weight residual 112.89 109.45 3.44 1.24e+00 6.50e-01 7.70e+00 angle pdb=" C ILE R 147 " pdb=" N TYR R 148 " pdb=" CA TYR R 148 " ideal model delta sigma weight residual 121.14 116.41 4.73 1.75e+00 3.27e-01 7.29e+00 ... (remaining 12774 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 5137 16.99 - 33.99: 363 33.99 - 50.98: 45 50.98 - 67.98: 19 67.98 - 84.97: 16 Dihedral angle restraints: 5580 sinusoidal: 2209 harmonic: 3371 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 154.43 -61.43 1 1.00e+01 1.00e-02 5.01e+01 dihedral pdb=" CA PHE R 66 " pdb=" C PHE R 66 " pdb=" N ASP R 67 " pdb=" CA ASP R 67 " ideal model delta harmonic sigma weight residual 180.00 157.19 22.81 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 158.54 21.46 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 5577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 926 0.032 - 0.063: 323 0.063 - 0.095: 97 0.095 - 0.126: 50 0.126 - 0.158: 10 Chirality restraints: 1406 Sorted by residual: chirality pdb=" CA GLU P 21 " pdb=" N GLU P 21 " pdb=" C GLU P 21 " pdb=" CB GLU P 21 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.23e-01 chirality pdb=" CA VAL R 30 " pdb=" N VAL R 30 " pdb=" C VAL R 30 " pdb=" CB VAL R 30 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.65e-01 chirality pdb=" CA GLU R 387 " pdb=" N GLU R 387 " pdb=" C GLU R 387 " pdb=" CB GLU R 387 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.34e-01 ... (remaining 1403 not shown) Planarity restraints: 1625 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL R 282 " -0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO R 283 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO R 283 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 283 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR P 10 " -0.011 2.00e-02 2.50e+03 9.14e-03 1.67e+00 pdb=" CG TYR P 10 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR P 10 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR P 10 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR P 10 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR P 10 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR P 10 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR P 10 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 276 " -0.020 5.00e-02 4.00e+02 2.95e-02 1.40e+00 pdb=" N PRO R 277 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO R 277 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 277 " -0.017 5.00e-02 4.00e+02 ... (remaining 1622 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1456 2.76 - 3.29: 9288 3.29 - 3.83: 15478 3.83 - 4.36: 19185 4.36 - 4.90: 32140 Nonbonded interactions: 77547 Sorted by model distance: nonbonded pdb=" O TRP R 33 " pdb=" OE1 GLN R 37 " model vdw 2.224 3.040 nonbonded pdb=" O GLN P 17 " pdb=" OE1 GLU P 21 " model vdw 2.257 3.040 nonbonded pdb=" O LYS R 383 " pdb=" OE1 GLU R 387 " model vdw 2.281 3.040 nonbonded pdb=" O ARG A 374 " pdb=" OD1 ASP A 378 " model vdw 2.375 3.040 nonbonded pdb=" OD2 ASP N 106 " pdb=" OD1 ASN A 279 " model vdw 2.436 3.040 ... (remaining 77542 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 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: 1.480 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.290 Find NCS groups from input model: 0.040 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:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 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 : 0.003 0.183 9437 Z= 0.236 Angle : 0.548 5.477 12791 Z= 0.326 Chirality : 0.040 0.158 1406 Planarity : 0.003 0.040 1625 Dihedral : 12.627 84.974 3382 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.10 % Allowed : 0.10 % Favored : 99.80 % 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 are not related in a simple way. whole: 0.89 (0.25), residues: 1134 helix: 1.70 (0.25), residues: 445 sheet: -0.40 (0.35), residues: 221 loop : 0.14 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.022 0.001 TYR P 10 PHE 0.015 0.001 PHE R 143 TRP 0.016 0.001 TRP R 417 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9430) covalent geometry : angle 0.54713 (12779) SS BOND : bond 0.00236 ( 6) SS BOND : angle 1.08199 ( 12) hydrogen bonds : bond 0.18028 ( 487) hydrogen bonds : angle 6.98555 ( 1377) Misc. bond : bond 0.18319 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 0.372 Fit side-chains REVERT: B 186 ASP cc_start: 0.7043 (m-30) cc_final: 0.6740 (m-30) REVERT: B 212 ASP cc_start: 0.6603 (t0) cc_final: 0.6257 (t0) REVERT: B 303 ASP cc_start: 0.7809 (m-30) cc_final: 0.7568 (m-30) REVERT: B 323 ASP cc_start: 0.4527 (p0) cc_final: 0.4113 (p0) REVERT: B 325 MET cc_start: 0.6830 (mmm) cc_final: 0.6221 (mpt) REVERT: N 21 SER cc_start: 0.7789 (m) cc_final: 0.7589 (m) REVERT: N 46 GLU cc_start: 0.8025 (pt0) cc_final: 0.7812 (pt0) REVERT: N 87 LYS cc_start: 0.6799 (ptpp) cc_final: 0.6549 (mttm) REVERT: P 9 ASP cc_start: 0.7021 (m-30) cc_final: 0.6571 (m-30) REVERT: P 10 TYR cc_start: 0.7075 (t80) cc_final: 0.6727 (t80) REVERT: P 12 LYS cc_start: 0.6634 (mttt) cc_final: 0.6378 (mttp) REVERT: R 40 ARG cc_start: 0.5343 (mtm-85) cc_final: 0.4872 (mtm180) REVERT: R 138 GLU cc_start: 0.6189 (tt0) cc_final: 0.5362 (tm-30) REVERT: R 201 LEU cc_start: 0.7159 (tp) cc_final: 0.6942 (tp) REVERT: R 367 PHE cc_start: 0.6480 (m-80) cc_final: 0.6019 (m-80) REVERT: R 407 ASN cc_start: 0.6723 (t0) cc_final: 0.6508 (t0) REVERT: A 17 LYS cc_start: 0.5518 (tttt) cc_final: 0.5289 (pttm) REVERT: A 28 LYS cc_start: 0.6102 (tttp) cc_final: 0.5325 (mmtp) REVERT: A 50 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6297 (mt-10) REVERT: A 216 LYS cc_start: 0.7932 (mttm) cc_final: 0.7596 (mmpt) REVERT: A 265 ARG cc_start: 0.7227 (mtp85) cc_final: 0.6382 (tpt90) REVERT: A 307 LYS cc_start: 0.7480 (mttm) cc_final: 0.6845 (mptm) REVERT: A 358 TYR cc_start: 0.6935 (m-80) cc_final: 0.6635 (m-80) REVERT: A 370 GLU cc_start: 0.7052 (pm20) cc_final: 0.6482 (tp30) REVERT: A 372 ILE cc_start: 0.6966 (mt) cc_final: 0.6734 (mp) outliers start: 1 outliers final: 0 residues processed: 202 average time/residue: 0.6799 time to fit residues: 145.0671 Evaluate side-chains 119 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN N 3 GLN N 84 ASN ** P 1 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 177 ASN R 182 ASN R 240 ASN R 300 ASN R 394 GLN A 387 HIS A 390 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.185877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.132215 restraints weight = 9600.343| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.77 r_work: 0.3271 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 9437 Z= 0.181 Angle : 0.630 7.757 12791 Z= 0.342 Chirality : 0.046 0.167 1406 Planarity : 0.004 0.037 1625 Dihedral : 4.979 22.453 1263 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.62 % Allowed : 6.98 % Favored : 91.40 % 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 are not related in a simple way. whole: 1.24 (0.25), residues: 1134 helix: 2.20 (0.23), residues: 454 sheet: -0.15 (0.34), residues: 218 loop : 0.02 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 380 TYR 0.033 0.002 TYR R 148 PHE 0.019 0.002 PHE R 143 TRP 0.025 0.002 TRP R 91 HIS 0.021 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 9430) covalent geometry : angle 0.62960 (12779) SS BOND : bond 0.00205 ( 6) SS BOND : angle 1.15409 ( 12) hydrogen bonds : bond 0.04838 ( 487) hydrogen bonds : angle 4.96485 ( 1377) Misc. bond : bond 0.00123 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.363 Fit side-chains REVERT: B 42 ARG cc_start: 0.7246 (mmp-170) cc_final: 0.6623 (tpt170) REVERT: B 46 ARG cc_start: 0.8306 (mmm160) cc_final: 0.7890 (mmp80) REVERT: B 96 ARG cc_start: 0.7833 (ttm-80) cc_final: 0.7533 (mtt180) REVERT: B 217 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8019 (ppp) REVERT: B 325 MET cc_start: 0.8575 (mmm) cc_final: 0.8100 (mpt) REVERT: P 9 ASP cc_start: 0.7885 (m-30) cc_final: 0.7594 (m-30) REVERT: P 10 TYR cc_start: 0.8128 (t80) cc_final: 0.7751 (t80) REVERT: P 12 LYS cc_start: 0.7983 (mttt) cc_final: 0.7697 (mttp) REVERT: P 16 GLU cc_start: 0.7005 (tt0) cc_final: 0.6366 (tm-30) REVERT: R 139 GLU cc_start: 0.6589 (mt-10) cc_final: 0.6283 (mm-30) REVERT: R 262 GLU cc_start: 0.5774 (OUTLIER) cc_final: 0.5474 (tp30) REVERT: R 286 ILE cc_start: 0.5724 (OUTLIER) cc_final: 0.5393 (mt) REVERT: R 407 ASN cc_start: 0.7745 (t0) cc_final: 0.7497 (t0) REVERT: A 28 LYS cc_start: 0.7683 (tttp) cc_final: 0.7068 (mmtp) REVERT: A 35 GLN cc_start: 0.7780 (tm-30) cc_final: 0.7109 (mm110) REVERT: A 38 ARG cc_start: 0.8587 (mmt180) cc_final: 0.8359 (mpt180) REVERT: A 50 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7029 (mt-10) REVERT: A 211 LYS cc_start: 0.8375 (mmtm) cc_final: 0.8017 (mptp) REVERT: A 325 THR cc_start: 0.7976 (p) cc_final: 0.7672 (t) REVERT: A 370 GLU cc_start: 0.7903 (pm20) cc_final: 0.7650 (mm-30) outliers start: 16 outliers final: 3 residues processed: 144 average time/residue: 0.7076 time to fit residues: 107.8351 Evaluate side-chains 119 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 247 GLU Chi-restraints excluded: chain R residue 262 GLU Chi-restraints excluded: chain R residue 286 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 75 optimal weight: 0.0980 chunk 60 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 73 optimal weight: 0.0970 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 1 HIS A 213 GLN A 279 ASN A 292 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.179853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.122968 restraints weight = 9347.199| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.49 r_work: 0.3200 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9437 Z= 0.202 Angle : 0.619 8.433 12791 Z= 0.338 Chirality : 0.046 0.170 1406 Planarity : 0.004 0.034 1625 Dihedral : 5.117 22.849 1263 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.63 % Allowed : 8.70 % Favored : 88.66 % 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 are not related in a simple way. whole: 1.26 (0.25), residues: 1134 helix: 2.17 (0.23), residues: 459 sheet: 0.12 (0.34), residues: 221 loop : -0.10 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 228 TYR 0.030 0.002 TYR R 148 PHE 0.017 0.002 PHE R 230 TRP 0.019 0.002 TRP A 234 HIS 0.012 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 9430) covalent geometry : angle 0.61862 (12779) SS BOND : bond 0.00413 ( 6) SS BOND : angle 0.82936 ( 12) hydrogen bonds : bond 0.05487 ( 487) hydrogen bonds : angle 4.88612 ( 1377) Misc. bond : bond 0.00076 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.409 Fit side-chains REVERT: B 42 ARG cc_start: 0.7526 (mmp-170) cc_final: 0.7064 (tpt170) REVERT: B 46 ARG cc_start: 0.8375 (mmm160) cc_final: 0.7943 (mmp80) REVERT: B 96 ARG cc_start: 0.8273 (ttm-80) cc_final: 0.7816 (mtt180) REVERT: B 137 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7790 (mtt-85) REVERT: B 177 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8319 (p) REVERT: B 214 ARG cc_start: 0.7863 (mtt90) cc_final: 0.7420 (mtt-85) REVERT: N 5 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7630 (mp10) REVERT: N 82 GLN cc_start: 0.8442 (tp40) cc_final: 0.8165 (tp-100) REVERT: N 105 ARG cc_start: 0.6949 (ttp-110) cc_final: 0.6608 (ptm160) REVERT: N 106 ASP cc_start: 0.8760 (p0) cc_final: 0.8547 (p0) REVERT: P 16 GLU cc_start: 0.7064 (tt0) cc_final: 0.6452 (tm-30) REVERT: R 139 GLU cc_start: 0.6619 (mt-10) cc_final: 0.6382 (mm-30) REVERT: R 262 GLU cc_start: 0.5666 (OUTLIER) cc_final: 0.5459 (tp30) REVERT: R 286 ILE cc_start: 0.5969 (mp) cc_final: 0.5622 (mt) REVERT: R 407 ASN cc_start: 0.7721 (t0) cc_final: 0.7419 (t0) REVERT: A 35 GLN cc_start: 0.7976 (tm-30) cc_final: 0.7506 (mp10) REVERT: A 38 ARG cc_start: 0.8601 (mmt180) cc_final: 0.8370 (mpt180) REVERT: A 50 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7007 (mt-10) REVERT: A 216 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7847 (mtpt) REVERT: A 265 ARG cc_start: 0.8266 (mtp85) cc_final: 0.7904 (mtm180) REVERT: A 325 THR cc_start: 0.8025 (p) cc_final: 0.7735 (t) REVERT: A 370 GLU cc_start: 0.7975 (pm20) cc_final: 0.7710 (mm-30) outliers start: 26 outliers final: 6 residues processed: 133 average time/residue: 0.7285 time to fit residues: 102.3537 Evaluate side-chains 119 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain R residue 247 GLU Chi-restraints excluded: chain R residue 262 GLU Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 319 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 86 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 105 optimal weight: 9.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 3 GLN A 31 GLN A 292 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.178580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.121880 restraints weight = 9441.285| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.49 r_work: 0.3186 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9437 Z= 0.209 Angle : 0.614 6.405 12791 Z= 0.338 Chirality : 0.046 0.172 1406 Planarity : 0.004 0.039 1625 Dihedral : 5.152 23.340 1263 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.53 % Allowed : 11.54 % Favored : 85.93 % 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 are not related in a simple way. whole: 1.10 (0.24), residues: 1134 helix: 1.98 (0.23), residues: 461 sheet: 0.30 (0.34), residues: 214 loop : -0.29 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 228 TYR 0.028 0.002 TYR R 148 PHE 0.017 0.002 PHE B 199 TRP 0.019 0.002 TRP A 234 HIS 0.012 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 9430) covalent geometry : angle 0.61392 (12779) SS BOND : bond 0.00582 ( 6) SS BOND : angle 0.92756 ( 12) hydrogen bonds : bond 0.05316 ( 487) hydrogen bonds : angle 4.79657 ( 1377) Misc. bond : bond 0.00046 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.385 Fit side-chains REVERT: B 42 ARG cc_start: 0.7570 (mmp-170) cc_final: 0.7148 (tpt170) REVERT: B 46 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8026 (mmp80) REVERT: B 96 ARG cc_start: 0.8277 (ttm-80) cc_final: 0.7852 (mtt180) REVERT: B 177 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8313 (p) REVERT: B 214 ARG cc_start: 0.7897 (mtt90) cc_final: 0.7427 (mtt-85) REVERT: N 5 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7711 (mp10) REVERT: N 105 ARG cc_start: 0.7040 (ttp-110) cc_final: 0.6587 (ptm160) REVERT: P 16 GLU cc_start: 0.7142 (tt0) cc_final: 0.6629 (tm-30) REVERT: R 139 GLU cc_start: 0.6727 (mt-10) cc_final: 0.6447 (mm-30) REVERT: R 286 ILE cc_start: 0.5969 (mp) cc_final: 0.5724 (mt) REVERT: R 364 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: R 378 THR cc_start: 0.7329 (m) cc_final: 0.6980 (p) REVERT: R 407 ASN cc_start: 0.7729 (t0) cc_final: 0.7401 (t0) REVERT: A 35 GLN cc_start: 0.8002 (tm-30) cc_final: 0.7561 (mp10) REVERT: A 38 ARG cc_start: 0.8629 (mmt180) cc_final: 0.8407 (mpt180) REVERT: A 50 GLU cc_start: 0.7703 (mm-30) cc_final: 0.6965 (mt-10) REVERT: A 216 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7978 (mmpt) REVERT: A 265 ARG cc_start: 0.8267 (mtp85) cc_final: 0.7911 (mtm180) REVERT: A 325 THR cc_start: 0.8023 (p) cc_final: 0.7725 (t) REVERT: A 370 GLU cc_start: 0.7968 (pm20) cc_final: 0.7700 (mm-30) outliers start: 25 outliers final: 7 residues processed: 127 average time/residue: 0.7329 time to fit residues: 98.3095 Evaluate side-chains 119 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 247 GLU Chi-restraints excluded: chain R residue 262 GLU Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 364 GLU Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 319 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 44 optimal weight: 0.0040 chunk 49 optimal weight: 0.0980 chunk 110 optimal weight: 0.9990 chunk 83 optimal weight: 0.0770 chunk 32 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.4354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 3 GLN A 31 GLN A 213 GLN A 292 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.182904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.127530 restraints weight = 9466.215| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.49 r_work: 0.3274 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9437 Z= 0.107 Angle : 0.487 6.278 12791 Z= 0.268 Chirality : 0.040 0.161 1406 Planarity : 0.003 0.037 1625 Dihedral : 4.575 22.343 1263 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.82 % Allowed : 12.65 % Favored : 85.53 % 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 are not related in a simple way. whole: 1.56 (0.25), residues: 1134 helix: 2.45 (0.23), residues: 467 sheet: 0.60 (0.34), residues: 207 loop : -0.20 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 380 TYR 0.024 0.001 TYR R 148 PHE 0.016 0.001 PHE A 212 TRP 0.016 0.001 TRP A 234 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 9430) covalent geometry : angle 0.48506 (12779) SS BOND : bond 0.00387 ( 6) SS BOND : angle 1.36559 ( 12) hydrogen bonds : bond 0.04158 ( 487) hydrogen bonds : angle 4.42088 ( 1377) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.350 Fit side-chains REVERT: B 42 ARG cc_start: 0.7533 (mmp-170) cc_final: 0.7138 (tpt170) REVERT: B 46 ARG cc_start: 0.8230 (mmm160) cc_final: 0.7903 (mmp80) REVERT: B 59 TYR cc_start: 0.8848 (OUTLIER) cc_final: 0.8329 (t80) REVERT: B 96 ARG cc_start: 0.8159 (ttm-80) cc_final: 0.7800 (mtt180) REVERT: B 214 ARG cc_start: 0.7800 (mtt90) cc_final: 0.7361 (mtt-85) REVERT: N 5 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7648 (mp10) REVERT: P 12 LYS cc_start: 0.8117 (mttm) cc_final: 0.7867 (mttm) REVERT: P 16 GLU cc_start: 0.7037 (tt0) cc_final: 0.6518 (tm-30) REVERT: R 139 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6506 (mt-10) REVERT: R 286 ILE cc_start: 0.5880 (mp) cc_final: 0.5575 (mt) REVERT: R 348 ARG cc_start: 0.6753 (OUTLIER) cc_final: 0.6352 (tpt170) REVERT: R 364 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7469 (mp0) REVERT: R 378 THR cc_start: 0.7316 (m) cc_final: 0.6957 (p) REVERT: R 407 ASN cc_start: 0.7727 (t0) cc_final: 0.7375 (t0) REVERT: A 35 GLN cc_start: 0.7952 (tm-30) cc_final: 0.7504 (mp10) REVERT: A 50 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7018 (mt-10) REVERT: A 265 ARG cc_start: 0.8224 (mtp85) cc_final: 0.7898 (mtm180) REVERT: A 325 THR cc_start: 0.7881 (p) cc_final: 0.7602 (t) REVERT: A 370 GLU cc_start: 0.7984 (pm20) cc_final: 0.7695 (mm-30) outliers start: 18 outliers final: 6 residues processed: 126 average time/residue: 0.7039 time to fit residues: 93.7484 Evaluate side-chains 118 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 247 GLU Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 348 ARG Chi-restraints excluded: chain R residue 364 GLU Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/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-2.1rc2-6044/lib/python3.9/site-packages/iotbx/cli_parser.py", line 995, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.836 > 50: distance: 8 - 10: 10.838 distance: 10 - 11: 17.886 distance: 11 - 12: 13.343 distance: 12 - 13: 10.317 distance: 12 - 14: 9.117 distance: 14 - 15: 10.499 distance: 15 - 16: 16.728 distance: 15 - 18: 13.294 distance: 16 - 17: 5.370 distance: 16 - 22: 6.001 distance: 18 - 19: 5.304 distance: 19 - 20: 18.414 distance: 19 - 21: 14.635 distance: 22 - 23: 6.026 distance: 23 - 24: 18.178 distance: 23 - 26: 12.263 distance: 24 - 25: 23.691 distance: 24 - 29: 29.271 distance: 26 - 27: 11.122 distance: 26 - 28: 11.306 distance: 29 - 30: 12.282 distance: 30 - 31: 16.077 distance: 30 - 33: 10.394 distance: 31 - 32: 14.604 distance: 31 - 38: 10.651 distance: 33 - 34: 10.163 distance: 34 - 35: 7.357 distance: 35 - 36: 12.035 distance: 35 - 37: 10.898 distance: 38 - 39: 10.038 distance: 38 - 44: 8.771 distance: 39 - 40: 14.766 distance: 39 - 42: 26.293 distance: 40 - 41: 25.131 distance: 40 - 45: 32.117 distance: 42 - 43: 13.111 distance: 43 - 44: 22.711 distance: 45 - 46: 8.498 distance: 46 - 47: 30.902 distance: 47 - 48: 11.914 distance: 47 - 49: 35.870 distance: 49 - 50: 17.157 distance: 50 - 51: 13.773 distance: 51 - 52: 19.804 distance: 51 - 53: 5.833 distance: 53 - 54: 8.916 distance: 54 - 57: 13.127 distance: 55 - 56: 9.872 distance: 55 - 59: 14.616 distance: 57 - 58: 17.032 distance: 59 - 60: 7.653 distance: 59 - 109: 11.315 distance: 60 - 63: 14.756 distance: 61 - 62: 10.894 distance: 61 - 67: 7.540 distance: 62 - 106: 17.885 distance: 63 - 64: 8.365 distance: 64 - 65: 24.695 distance: 64 - 66: 6.441 distance: 67 - 68: 4.116 distance: 68 - 69: 9.376 distance: 68 - 71: 9.638 distance: 69 - 70: 23.193 distance: 69 - 78: 12.939 distance: 71 - 72: 9.048 distance: 72 - 73: 11.280 distance: 73 - 74: 8.800 distance: 74 - 75: 10.004 distance: 75 - 76: 8.264 distance: 75 - 77: 10.764