Starting phenix.real_space_refine on Sun May 11 19:03:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cfn_30345/05_2025/7cfn_30345.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cfn_30345/05_2025/7cfn_30345.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cfn_30345/05_2025/7cfn_30345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cfn_30345/05_2025/7cfn_30345.map" model { file = "/net/cci-nas-00/data/ceres_data/7cfn_30345/05_2025/7cfn_30345.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cfn_30345/05_2025/7cfn_30345.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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 46 5.16 5 C 5158 2.51 5 N 1416 2.21 5 O 1492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8112 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1930 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 232, 1914 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 232, 1914 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 1932 Chain: "B" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2587 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2076 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 274, 2070 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 252} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 274, 2070 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 252} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2121 Chain: "R" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 111 Unusual residues: {'CLR': 1, 'FX0': 2, 'PLM': 1} Classifications: {'undetermined': 4, 'water': 1} Link IDs: {None: 4} Time building chain proxies: 6.94, per 1000 atoms: 0.86 Number of scatterers: 8112 At special positions: 0 Unit cell: (79.092, 115.596, 119.652, 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 46 16.00 O 1492 8.00 N 1416 7.00 C 5158 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, 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=2.02 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 155 " 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=0, symmetry=0 Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 1.4 seconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1926 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 10 sheets defined 42.9% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.571A pdb=" N ARG A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.553A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.569A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.501A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.276A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.753A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.704A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.621A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 6 through 23 removed outlier: 4.037A pdb=" N ALA G 10 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.754A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.748A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 19 through 42 removed outlier: 3.987A pdb=" N ALA R 31 " --> pdb=" O LEU R 27 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASP R 42 " --> pdb=" O GLY R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 47 removed outlier: 3.900A pdb=" N ARG R 46 " --> pdb=" O ASP R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 67 removed outlier: 3.581A pdb=" N CYS R 52 " --> pdb=" O PRO R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 75 removed outlier: 3.903A pdb=" N TRP R 75 " --> pdb=" O PRO R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 116 removed outlier: 4.151A pdb=" N LEU R 87 " --> pdb=" O TRP R 83 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL R 88 " --> pdb=" O SER R 84 " (cutoff:3.500A) Proline residue: R 92 - end of helix Processing helix chain 'R' and resid 123 through 140 removed outlier: 3.558A pdb=" N ALA R 127 " --> pdb=" O SER R 123 " (cutoff:3.500A) Proline residue: R 135 - end of helix Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 156 through 161 Processing helix chain 'R' and resid 162 through 173 Processing helix chain 'R' and resid 175 through 207 removed outlier: 4.365A pdb=" N ALA R 181 " --> pdb=" O ALA R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 236 removed outlier: 3.797A pdb=" N ALA R 217 " --> pdb=" O ALA R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 252 removed outlier: 3.785A pdb=" N TYR R 240 " --> pdb=" O CYS R 236 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL R 241 " --> pdb=" O TRP R 237 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU R 252 " --> pdb=" O VAL R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 257 through 275 removed outlier: 4.498A pdb=" N THR R 261 " --> pdb=" O LEU R 257 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU R 262 " --> pdb=" O GLY R 258 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER R 264 " --> pdb=" O GLY R 260 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER R 272 " --> pdb=" O LEU R 268 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA R 273 " --> pdb=" O GLY R 269 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA R 274 " --> pdb=" O SER R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 282 Processing helix chain 'R' and resid 284 through 289 removed outlier: 3.842A pdb=" N THR R 288 " --> pdb=" O ASP R 284 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.864A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.649A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.895A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.665A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.773A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.661A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.711A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.611A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.062A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.733A pdb=" N LEU N 81 " --> pdb=" O LEU N 20 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.757A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP N 50 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1111 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: 2.09 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1954 1.33 - 1.45: 1779 1.45 - 1.58: 4492 1.58 - 1.70: 1 1.70 - 1.82: 63 Bond restraints: 8289 Sorted by residual: bond pdb=" C27 FX0 R 401 " pdb=" O04 FX0 R 401 " ideal model delta sigma weight residual 1.251 1.359 -0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" C27 FX0 R 403 " pdb=" O04 FX0 R 403 " ideal model delta sigma weight residual 1.251 1.358 -0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C ALA R 289 " pdb=" N PRO R 290 " ideal model delta sigma weight residual 1.334 1.429 -0.095 2.34e-02 1.83e+03 1.65e+01 bond pdb=" C HIS A 387 " pdb=" O HIS A 387 " ideal model delta sigma weight residual 1.237 1.206 0.031 1.17e-02 7.31e+03 6.94e+00 bond pdb=" C LEU A 388 " pdb=" O LEU A 388 " ideal model delta sigma weight residual 1.237 1.208 0.029 1.17e-02 7.31e+03 6.09e+00 ... (remaining 8284 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 10627 1.95 - 3.91: 525 3.91 - 5.86: 81 5.86 - 7.82: 30 7.82 - 9.77: 10 Bond angle restraints: 11273 Sorted by residual: angle pdb=" N VAL R 170 " pdb=" CA VAL R 170 " pdb=" C VAL R 170 " ideal model delta sigma weight residual 110.72 115.97 -5.25 1.01e+00 9.80e-01 2.71e+01 angle pdb=" N LEU R 90 " pdb=" CA LEU R 90 " pdb=" C LEU R 90 " ideal model delta sigma weight residual 111.69 117.96 -6.27 1.23e+00 6.61e-01 2.60e+01 angle pdb=" N GLU A 392 " pdb=" CA GLU A 392 " pdb=" C GLU A 392 " ideal model delta sigma weight residual 110.80 118.87 -8.07 2.13e+00 2.20e-01 1.43e+01 angle pdb=" C ASP B 66 " pdb=" N SER B 67 " pdb=" CA SER B 67 " ideal model delta sigma weight residual 123.47 129.26 -5.79 1.53e+00 4.27e-01 1.43e+01 angle pdb=" CA ALA R 91 " pdb=" C ALA R 91 " pdb=" N PRO R 92 " ideal model delta sigma weight residual 120.93 117.35 3.58 1.06e+00 8.90e-01 1.14e+01 ... (remaining 11268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.71: 4796 14.71 - 29.42: 238 29.42 - 44.13: 75 44.13 - 58.83: 16 58.83 - 73.54: 10 Dihedral angle restraints: 5135 sinusoidal: 2146 harmonic: 2989 Sorted by residual: dihedral pdb=" CA ASP A 331 " pdb=" C ASP A 331 " pdb=" N PRO A 332 " pdb=" CA PRO A 332 " ideal model delta harmonic sigma weight residual -180.00 -153.57 -26.43 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA ASP B 195 " pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta harmonic sigma weight residual -180.00 -156.36 -23.64 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 156.84 23.16 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 5132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1031 0.077 - 0.154: 215 0.154 - 0.231: 28 0.231 - 0.308: 6 0.308 - 0.385: 2 Chirality restraints: 1282 Sorted by residual: chirality pdb=" CA GLU A 392 " pdb=" N GLU A 392 " pdb=" C GLU A 392 " pdb=" CB GLU A 392 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA LEU R 90 " pdb=" N LEU R 90 " pdb=" C LEU R 90 " pdb=" CB LEU R 90 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CB VAL A 241 " pdb=" CA VAL A 241 " pdb=" CG1 VAL A 241 " pdb=" CG2 VAL A 241 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 1279 not shown) Planarity restraints: 1433 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS N 87 " -0.049 5.00e-02 4.00e+02 7.42e-02 8.81e+00 pdb=" N PRO N 88 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO N 88 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO N 88 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA R 289 " -0.042 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO R 290 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO R 290 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO R 290 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 281 " -0.024 2.00e-02 2.50e+03 1.60e-02 6.36e+00 pdb=" CG TRP A 281 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP A 281 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 281 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 281 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 281 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 281 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 281 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 281 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 281 " -0.011 2.00e-02 2.50e+03 ... (remaining 1430 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 48 2.56 - 3.15: 6006 3.15 - 3.73: 12132 3.73 - 4.32: 16769 4.32 - 4.90: 28921 Nonbonded interactions: 63876 Sorted by model distance: nonbonded pdb=" CD2 LEU A 394 " pdb=" OXT LEU A 394 " model vdw 1.979 3.460 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.240 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.291 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.296 3.040 nonbonded pdb=" O ARG B 22 " pdb=" NE2 GLN B 259 " model vdw 2.337 3.120 ... (remaining 63871 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.400 Find NCS groups from input model: 0.070 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:11.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 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 : 0.008 0.108 8292 Z= 0.332 Angle : 1.039 9.772 11279 Z= 0.543 Chirality : 0.064 0.385 1282 Planarity : 0.007 0.074 1433 Dihedral : 10.747 73.543 3200 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.12 % Allowed : 3.31 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.77 (0.22), residues: 1020 helix: -1.41 (0.21), residues: 398 sheet: -1.88 (0.31), residues: 236 loop : -2.04 (0.26), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP A 281 HIS 0.013 0.003 HIS A 41 PHE 0.026 0.003 PHE B 151 TYR 0.021 0.003 TYR A 339 ARG 0.013 0.001 ARG A 342 Details of bonding type rmsd hydrogen bonds : bond 0.19234 ( 386) hydrogen bonds : angle 6.97273 ( 1111) SS BOND : bond 0.00535 ( 3) SS BOND : angle 0.89410 ( 6) covalent geometry : bond 0.00752 ( 8289) covalent geometry : angle 1.03880 (11273) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: A 33 ASP cc_start: 0.7813 (m-30) cc_final: 0.7568 (m-30) REVERT: A 35 GLN cc_start: 0.7176 (mt0) cc_final: 0.6666 (mp10) REVERT: A 40 THR cc_start: 0.8881 (t) cc_final: 0.8556 (m) REVERT: A 60 MET cc_start: 0.4235 (ptt) cc_final: 0.3659 (pmt) REVERT: A 284 ASP cc_start: 0.8170 (m-30) cc_final: 0.7847 (m-30) REVERT: B 155 ASN cc_start: 0.7960 (t0) cc_final: 0.7641 (t0) REVERT: B 186 ASP cc_start: 0.7886 (p0) cc_final: 0.7593 (p0) REVERT: B 323 ASP cc_start: 0.7911 (m-30) cc_final: 0.7587 (m-30) REVERT: G 21 MET cc_start: 0.7013 (ttt) cc_final: 0.6603 (ttm) REVERT: R 116 ARG cc_start: 0.8070 (mtt-85) cc_final: 0.7848 (mtt-85) REVERT: R 204 ARG cc_start: 0.6992 (ttt90) cc_final: 0.6508 (ttm110) REVERT: R 254 ARG cc_start: 0.7701 (ptm-80) cc_final: 0.6945 (ptt180) REVERT: R 268 LEU cc_start: 0.8111 (tt) cc_final: 0.7754 (tp) outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 1.1862 time to fit residues: 217.2656 Evaluate side-chains 110 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 58 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 213 GLN A 371 ASN B 44 GLN B 237 ASN B 259 GLN B 295 ASN B 340 ASN R 93 ASN ** R 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.154583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.117515 restraints weight = 23555.729| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 5.24 r_work: 0.2992 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8292 Z= 0.145 Angle : 0.657 11.980 11279 Z= 0.318 Chirality : 0.044 0.283 1282 Planarity : 0.005 0.049 1433 Dihedral : 6.089 51.201 1378 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.20 % Allowed : 11.95 % Favored : 84.85 % 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: -0.92 (0.25), residues: 1020 helix: 0.68 (0.25), residues: 404 sheet: -1.29 (0.33), residues: 227 loop : -1.47 (0.28), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 149 HIS 0.004 0.001 HIS A 220 PHE 0.011 0.001 PHE A 212 TYR 0.020 0.001 TYR R 251 ARG 0.006 0.001 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.04950 ( 386) hydrogen bonds : angle 4.76705 ( 1111) SS BOND : bond 0.00393 ( 3) SS BOND : angle 0.85559 ( 6) covalent geometry : bond 0.00330 ( 8289) covalent geometry : angle 0.65709 (11273) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: A 26 ILE cc_start: 0.7465 (mm) cc_final: 0.7206 (mt) REVERT: A 35 GLN cc_start: 0.7147 (mt0) cc_final: 0.6580 (mp10) REVERT: A 40 THR cc_start: 0.8686 (t) cc_final: 0.8357 (m) REVERT: A 284 ASP cc_start: 0.8727 (m-30) cc_final: 0.8154 (m-30) REVERT: A 356 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7080 (ttt180) REVERT: A 392 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7998 (mt-10) REVERT: B 155 ASN cc_start: 0.7895 (t0) cc_final: 0.7575 (t0) REVERT: B 254 ASP cc_start: 0.8670 (t0) cc_final: 0.8262 (t0) REVERT: B 268 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7846 (m110) REVERT: B 323 ASP cc_start: 0.7727 (m-30) cc_final: 0.7337 (m-30) REVERT: G 21 MET cc_start: 0.7198 (ttt) cc_final: 0.6964 (ttm) REVERT: N 50 ASP cc_start: 0.8513 (p0) cc_final: 0.8303 (p0) REVERT: R 33 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7146 (mp) REVERT: R 251 TYR cc_start: 0.8477 (t80) cc_final: 0.8173 (t80) REVERT: R 254 ARG cc_start: 0.7634 (ptm-80) cc_final: 0.6850 (ptt180) REVERT: R 268 LEU cc_start: 0.8084 (tt) cc_final: 0.7718 (tp) outliers start: 27 outliers final: 7 residues processed: 143 average time/residue: 1.1301 time to fit residues: 172.4423 Evaluate side-chains 119 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 123 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 0 optimal weight: 20.0000 chunk 62 optimal weight: 0.1980 chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 237 ASN ** R 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.155687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.118203 restraints weight = 23499.474| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 5.21 r_work: 0.3000 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8292 Z= 0.120 Angle : 0.601 9.948 11279 Z= 0.289 Chirality : 0.042 0.278 1282 Planarity : 0.004 0.043 1433 Dihedral : 5.503 56.353 1378 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.37 % Allowed : 15.62 % Favored : 82.01 % 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: -0.16 (0.26), residues: 1020 helix: 1.52 (0.26), residues: 399 sheet: -1.08 (0.33), residues: 231 loop : -1.14 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 149 HIS 0.003 0.001 HIS A 220 PHE 0.012 0.001 PHE A 212 TYR 0.018 0.001 TYR R 251 ARG 0.007 0.001 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.04075 ( 386) hydrogen bonds : angle 4.33347 ( 1111) SS BOND : bond 0.00186 ( 3) SS BOND : angle 0.92033 ( 6) covalent geometry : bond 0.00269 ( 8289) covalent geometry : angle 0.60092 (11273) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: A 26 ILE cc_start: 0.7421 (mm) cc_final: 0.7189 (mt) REVERT: A 35 GLN cc_start: 0.7085 (mt0) cc_final: 0.6498 (mp10) REVERT: A 40 THR cc_start: 0.8556 (t) cc_final: 0.8237 (m) REVERT: A 209 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7457 (tm-30) REVERT: A 309 GLU cc_start: 0.7711 (mp0) cc_final: 0.7486 (mp0) REVERT: A 392 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7935 (mt-10) REVERT: B 19 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6577 (tpp80) REVERT: B 155 ASN cc_start: 0.7843 (t0) cc_final: 0.7518 (t0) REVERT: B 186 ASP cc_start: 0.8229 (p0) cc_final: 0.7777 (p0) REVERT: B 254 ASP cc_start: 0.8608 (t0) cc_final: 0.8177 (t0) REVERT: B 262 MET cc_start: 0.8516 (ttm) cc_final: 0.8200 (ttp) REVERT: B 323 ASP cc_start: 0.7554 (m-30) cc_final: 0.7176 (m-30) REVERT: N 7 SER cc_start: 0.7813 (p) cc_final: 0.7502 (m) REVERT: R 254 ARG cc_start: 0.7417 (ptm-80) cc_final: 0.6737 (ptt180) REVERT: R 268 LEU cc_start: 0.8004 (tt) cc_final: 0.7678 (tp) outliers start: 20 outliers final: 7 residues processed: 133 average time/residue: 0.9919 time to fit residues: 141.8581 Evaluate side-chains 123 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain R residue 123 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 36 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 19 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.153074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.114664 restraints weight = 18782.061| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 4.13 r_work: 0.2997 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8292 Z= 0.152 Angle : 0.630 9.773 11279 Z= 0.299 Chirality : 0.043 0.302 1282 Planarity : 0.004 0.049 1433 Dihedral : 5.492 59.650 1378 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.08 % Allowed : 15.62 % Favored : 81.30 % 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: 0.14 (0.26), residues: 1020 helix: 1.71 (0.26), residues: 406 sheet: -0.81 (0.33), residues: 229 loop : -1.03 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP R 149 HIS 0.005 0.001 HIS A 220 PHE 0.015 0.002 PHE N 108 TYR 0.018 0.001 TYR R 251 ARG 0.012 0.001 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.04182 ( 386) hydrogen bonds : angle 4.27132 ( 1111) SS BOND : bond 0.00312 ( 3) SS BOND : angle 1.00303 ( 6) covalent geometry : bond 0.00360 ( 8289) covalent geometry : angle 0.62973 (11273) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: A 26 ILE cc_start: 0.7540 (mm) cc_final: 0.7293 (mt) REVERT: A 35 GLN cc_start: 0.7322 (mt0) cc_final: 0.6650 (mp10) REVERT: A 40 THR cc_start: 0.8698 (t) cc_final: 0.8390 (m) REVERT: A 209 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7493 (tm-30) REVERT: A 309 GLU cc_start: 0.7664 (mp0) cc_final: 0.7460 (mp0) REVERT: A 392 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7942 (mt-10) REVERT: B 19 ARG cc_start: 0.6999 (OUTLIER) cc_final: 0.6720 (tpp80) REVERT: B 67 SER cc_start: 0.8485 (t) cc_final: 0.8262 (t) REVERT: B 155 ASN cc_start: 0.7892 (t0) cc_final: 0.7565 (t0) REVERT: B 186 ASP cc_start: 0.8240 (p0) cc_final: 0.7824 (p0) REVERT: B 254 ASP cc_start: 0.8573 (t0) cc_final: 0.8176 (t0) REVERT: B 262 MET cc_start: 0.8507 (ttm) cc_final: 0.8128 (ttp) REVERT: B 323 ASP cc_start: 0.7609 (m-30) cc_final: 0.7199 (m-30) REVERT: N 7 SER cc_start: 0.7902 (p) cc_final: 0.7584 (m) REVERT: R 158 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8459 (mp10) REVERT: R 254 ARG cc_start: 0.7347 (ptm-80) cc_final: 0.6851 (ptt180) REVERT: R 268 LEU cc_start: 0.8050 (tt) cc_final: 0.7691 (tp) outliers start: 26 outliers final: 9 residues processed: 129 average time/residue: 1.0722 time to fit residues: 148.5254 Evaluate side-chains 126 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 157 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 62 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 16 optimal weight: 30.0000 chunk 85 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN ** R 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.149510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.111365 restraints weight = 20400.655| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 4.56 r_work: 0.2947 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8292 Z= 0.194 Angle : 0.651 10.015 11279 Z= 0.313 Chirality : 0.045 0.289 1282 Planarity : 0.004 0.038 1433 Dihedral : 5.633 59.529 1378 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.96 % Allowed : 16.45 % Favored : 80.59 % 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: 0.19 (0.26), residues: 1020 helix: 1.69 (0.26), residues: 411 sheet: -0.81 (0.33), residues: 231 loop : -0.94 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP R 149 HIS 0.005 0.001 HIS A 220 PHE 0.020 0.002 PHE N 108 TYR 0.017 0.002 TYR R 251 ARG 0.007 0.001 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04547 ( 386) hydrogen bonds : angle 4.30528 ( 1111) SS BOND : bond 0.00195 ( 3) SS BOND : angle 1.10316 ( 6) covalent geometry : bond 0.00470 ( 8289) covalent geometry : angle 0.65028 (11273) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: A 26 ILE cc_start: 0.7456 (mm) cc_final: 0.7188 (mt) REVERT: A 35 GLN cc_start: 0.7312 (mt0) cc_final: 0.6656 (mp10) REVERT: A 309 GLU cc_start: 0.7642 (mp0) cc_final: 0.7441 (mp0) REVERT: B 19 ARG cc_start: 0.6951 (OUTLIER) cc_final: 0.6685 (tpp80) REVERT: B 67 SER cc_start: 0.8485 (t) cc_final: 0.8242 (t) REVERT: B 155 ASN cc_start: 0.7970 (t0) cc_final: 0.7635 (t0) REVERT: B 234 PHE cc_start: 0.9213 (OUTLIER) cc_final: 0.8808 (m-80) REVERT: B 254 ASP cc_start: 0.8590 (t0) cc_final: 0.8169 (t0) REVERT: B 262 MET cc_start: 0.8477 (ttm) cc_final: 0.8035 (ttp) REVERT: B 323 ASP cc_start: 0.7604 (m-30) cc_final: 0.7163 (m-30) REVERT: N 7 SER cc_start: 0.7852 (p) cc_final: 0.7502 (m) REVERT: N 69 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8324 (m) REVERT: N 110 VAL cc_start: 0.8982 (t) cc_final: 0.8440 (m) REVERT: R 158 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8508 (mp10) REVERT: R 254 ARG cc_start: 0.7342 (ptm-80) cc_final: 0.6670 (ptt180) REVERT: R 268 LEU cc_start: 0.8077 (tt) cc_final: 0.7698 (tp) outliers start: 25 outliers final: 7 residues processed: 128 average time/residue: 1.0778 time to fit residues: 147.3247 Evaluate side-chains 121 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 33 LYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 157 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.3902 > 50: distance: 56 - 64: 11.702 distance: 64 - 65: 12.900 distance: 64 - 70: 17.646 distance: 65 - 66: 10.086 distance: 65 - 68: 12.070 distance: 66 - 67: 5.179 distance: 66 - 71: 8.169 distance: 68 - 69: 18.285 distance: 69 - 70: 5.725 distance: 71 - 72: 17.755 distance: 72 - 73: 27.863 distance: 72 - 75: 17.517 distance: 73 - 74: 19.901 distance: 73 - 79: 13.113 distance: 75 - 76: 35.755 distance: 76 - 77: 28.162 distance: 76 - 78: 11.826 distance: 79 - 82: 32.955 distance: 79 - 88: 26.685 distance: 80 - 81: 45.146 distance: 80 - 82: 48.808 distance: 80 - 88: 29.317 distance: 80 - 94: 50.761 distance: 82 - 83: 20.827 distance: 83 - 84: 13.804 distance: 84 - 85: 13.681 distance: 85 - 86: 5.948 distance: 85 - 87: 16.517 distance: 88 - 89: 20.295 distance: 89 - 90: 33.438 distance: 90 - 91: 32.980 distance: 91 - 92: 16.564 distance: 91 - 93: 18.530 distance: 94 - 95: 51.008 distance: 94 - 100: 42.686 distance: 95 - 96: 42.181 distance: 95 - 98: 16.107 distance: 96 - 97: 21.295 distance: 96 - 101: 20.814 distance: 98 - 99: 23.547 distance: 99 - 100: 30.410 distance: 101 - 102: 15.964 distance: 101 - 107: 20.680 distance: 102 - 103: 15.688 distance: 102 - 105: 16.231 distance: 103 - 104: 11.237 distance: 103 - 108: 3.910 distance: 105 - 106: 14.859 distance: 106 - 107: 24.239 distance: 108 - 109: 21.060 distance: 109 - 110: 43.958 distance: 110 - 111: 54.390 distance: 110 - 112: 46.669 distance: 112 - 113: 15.975 distance: 113 - 114: 8.596 distance: 113 - 116: 8.265 distance: 114 - 115: 14.915 distance: 114 - 118: 7.064 distance: 116 - 117: 3.649 distance: 118 - 119: 3.943 distance: 119 - 120: 3.795 distance: 119 - 122: 3.788 distance: 120 - 121: 4.963 distance: 120 - 126: 4.883 distance: 121 - 150: 3.560 distance: 122 - 123: 6.900 distance: 122 - 124: 3.299 distance: 126 - 127: 3.287 distance: 127 - 128: 10.153 distance: 127 - 130: 6.776 distance: 128 - 129: 12.740 distance: 128 - 137: 9.272 distance: 129 - 158: 4.116 distance: 130 - 131: 8.504 distance: 131 - 132: 7.538 distance: 134 - 135: 3.652 distance: 138 - 139: 8.719 distance: 138 - 141: 5.551 distance: 139 - 140: 9.030 distance: 139 - 145: 5.867 distance: 140 - 165: 6.057 distance: 141 - 142: 5.404