Starting phenix.real_space_refine on Sat Aug 3 03:25:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gfz_29989/08_2024/8gfz_29989.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gfz_29989/08_2024/8gfz_29989.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gfz_29989/08_2024/8gfz_29989.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gfz_29989/08_2024/8gfz_29989.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gfz_29989/08_2024/8gfz_29989.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gfz_29989/08_2024/8gfz_29989.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= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 45 5.16 5 C 4311 2.51 5 N 1154 2.21 5 O 1231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 330": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "R GLU 225": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6744 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1763 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 12, 'ARG:plan': 6, 'PHE:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 107 Chain: "B" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2433 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 5, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 87 Chain: "G" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 349 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2147 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 7, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 20 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 5} Link IDs: {None: 5} Time building chain proxies: 4.65, per 1000 atoms: 0.69 Number of scatterers: 6744 At special positions: 0 Unit cell: (85.0346, 132.758, 98.0501, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 P 3 15.00 O 1231 8.00 N 1154 7.00 C 4311 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.2 seconds 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1688 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 8 sheets defined 47.4% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.570A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 232 through 238 removed outlier: 3.527A pdb=" N ILE A 235 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.696A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.604A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.649A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.605A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 24 removed outlier: 3.528A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.623A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.648A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'R' and resid 37 through 61 Processing helix chain 'R' and resid 66 through 97 removed outlier: 4.083A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 104 through 137 removed outlier: 3.598A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL R 126 " --> pdb=" O GLU R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 164 Processing helix chain 'R' and resid 165 through 171 removed outlier: 3.606A pdb=" N ILE R 169 " --> pdb=" O SER R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 238 removed outlier: 3.785A pdb=" N SER R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N VAL R 210 " --> pdb=" O VAL R 206 " (cutoff:3.500A) Proline residue: R 211 - end of helix removed outlier: 3.560A pdb=" N ARG R 221 " --> pdb=" O PHE R 217 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS R 235 " --> pdb=" O GLN R 231 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU R 237 " --> pdb=" O ILE R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 299 removed outlier: 3.705A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.082A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 318 removed outlier: 3.813A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) Processing helix chain 'R' and resid 321 through 327 Processing helix chain 'R' and resid 329 through 339 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.519A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.629A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.646A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.544A 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: 3.905A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.095A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.798A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.887A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.649A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.976A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 346 hydrogen bonds defined for protein. 1008 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: 1.72 Time building geometry restraints manager: 2.84 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: 1737 1.33 - 1.45: 1331 1.45 - 1.57: 3747 1.57 - 1.69: 5 1.69 - 1.81: 62 Bond restraints: 6882 Sorted by residual: bond pdb=" CA GLU R 237 " pdb=" C GLU R 237 " ideal model delta sigma weight residual 1.524 1.486 0.039 1.43e-02 4.89e+03 7.26e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.449 -0.052 2.00e-02 2.50e+03 6.75e+00 bond pdb=" CA GLU R 237 " pdb=" CB GLU R 237 " ideal model delta sigma weight residual 1.531 1.496 0.035 1.34e-02 5.57e+03 6.71e+00 bond pdb=" N LYS R 235 " pdb=" CA LYS R 235 " ideal model delta sigma weight residual 1.459 1.429 0.030 1.21e-02 6.83e+03 6.27e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.570 -0.047 2.00e-02 2.50e+03 5.49e+00 ... (remaining 6877 not shown) Histogram of bond angle deviations from ideal: 100.30 - 107.04: 148 107.04 - 113.78: 3901 113.78 - 120.51: 2634 120.51 - 127.25: 2628 127.25 - 133.99: 77 Bond angle restraints: 9388 Sorted by residual: angle pdb=" N SER R 236 " pdb=" CA SER R 236 " pdb=" C SER R 236 " ideal model delta sigma weight residual 111.28 120.47 -9.19 1.09e+00 8.42e-01 7.11e+01 angle pdb=" N ASP R 234 " pdb=" CA ASP R 234 " pdb=" C ASP R 234 " ideal model delta sigma weight residual 111.82 117.66 -5.84 1.16e+00 7.43e-01 2.53e+01 angle pdb=" O ILE R 233 " pdb=" C ILE R 233 " pdb=" N ASP R 234 " ideal model delta sigma weight residual 121.87 117.29 4.58 9.70e-01 1.06e+00 2.23e+01 angle pdb=" CA ILE R 233 " pdb=" C ILE R 233 " pdb=" N ASP R 234 " ideal model delta sigma weight residual 117.15 121.88 -4.73 1.14e+00 7.69e-01 1.72e+01 angle pdb=" N SER R 236 " pdb=" CA SER R 236 " pdb=" CB SER R 236 " ideal model delta sigma weight residual 110.12 105.99 4.13 1.47e+00 4.63e-01 7.89e+00 ... (remaining 9383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.07: 3895 28.07 - 56.14: 108 56.14 - 84.22: 9 84.22 - 112.29: 0 112.29 - 140.36: 3 Dihedral angle restraints: 4015 sinusoidal: 1417 harmonic: 2598 Sorted by residual: dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -35.77 140.36 1 2.00e+01 2.50e-03 4.25e+01 dihedral pdb=" O3A GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PB GTP A 401 " pdb=" PG GTP A 401 " ideal model delta sinusoidal sigma weight residual 303.79 175.06 128.74 1 2.00e+01 2.50e-03 3.90e+01 dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 -57.70 126.97 1 2.00e+01 2.50e-03 3.84e+01 ... (remaining 4012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 797 0.041 - 0.082: 244 0.082 - 0.123: 61 0.123 - 0.164: 3 0.164 - 0.205: 1 Chirality restraints: 1106 Sorted by residual: chirality pdb=" CA SER R 236 " pdb=" N SER R 236 " pdb=" C SER R 236 " pdb=" CB SER R 236 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" CA ILE A 244 " pdb=" N ILE A 244 " pdb=" C ILE A 244 " pdb=" CB ILE A 244 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 1103 not shown) Planarity restraints: 1177 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 205 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C ILE R 205 " -0.028 2.00e-02 2.50e+03 pdb=" O ILE R 205 " 0.010 2.00e-02 2.50e+03 pdb=" N VAL R 206 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.82e+00 pdb=" N PRO A 332 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR R 281 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.79e+00 pdb=" C THR R 281 " 0.023 2.00e-02 2.50e+03 pdb=" O THR R 281 " -0.009 2.00e-02 2.50e+03 pdb=" N PHE R 282 " -0.008 2.00e-02 2.50e+03 ... (remaining 1174 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 510 2.74 - 3.28: 6307 3.28 - 3.82: 10683 3.82 - 4.36: 12368 4.36 - 4.90: 22591 Nonbonded interactions: 52459 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.201 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.236 3.040 nonbonded pdb=" OD1 ASP R 113 " pdb=" OH TYR R 316 " model vdw 2.279 3.040 nonbonded pdb=" OD2 ASP R 113 " pdb=" OAM G1I R 501 " model vdw 2.309 3.040 nonbonded pdb=" O TYR R 132 " pdb=" OG1 THR R 136 " model vdw 2.309 3.040 ... (remaining 52454 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: 1.650 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.890 Find NCS groups from input model: 0.060 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: 0.000 Load rotamer database and sin/cos tables:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 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 0.052 6882 Z= 0.189 Angle : 0.500 9.190 9388 Z= 0.287 Chirality : 0.041 0.205 1106 Planarity : 0.003 0.034 1177 Dihedral : 13.528 140.362 2324 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.72 (0.28), residues: 873 helix: 1.44 (0.27), residues: 381 sheet: 0.47 (0.41), residues: 165 loop : -0.60 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 99 HIS 0.005 0.001 HIS B 183 PHE 0.014 0.001 PHE B 234 TYR 0.008 0.001 TYR A 339 ARG 0.003 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.820 Fit side-chains REVERT: A 386 MET cc_start: 0.8572 (ttm) cc_final: 0.8269 (ttp) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 1.2666 time to fit residues: 130.5992 Evaluate side-chains 81 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 0.0770 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS R 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6882 Z= 0.160 Angle : 0.487 5.552 9388 Z= 0.262 Chirality : 0.041 0.131 1106 Planarity : 0.003 0.027 1177 Dihedral : 8.624 140.355 979 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.20 % Allowed : 7.51 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.28), residues: 873 helix: 1.78 (0.27), residues: 391 sheet: 0.56 (0.39), residues: 171 loop : -0.57 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 99 HIS 0.004 0.001 HIS B 183 PHE 0.013 0.001 PHE A 212 TYR 0.009 0.001 TYR A 339 ARG 0.002 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.746 Fit side-chains REVERT: R 231 GLN cc_start: 0.8158 (tm-30) cc_final: 0.7593 (tt0) REVERT: R 239 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7869 (ptt180) outliers start: 8 outliers final: 2 residues processed: 94 average time/residue: 1.2753 time to fit residues: 125.9379 Evaluate side-chains 88 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain R residue 239 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 66 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** R 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6882 Z= 0.166 Angle : 0.474 5.459 9388 Z= 0.253 Chirality : 0.041 0.130 1106 Planarity : 0.003 0.030 1177 Dihedral : 8.323 139.701 979 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.90 % Allowed : 10.51 % Favored : 88.59 % 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: 1.22 (0.29), residues: 873 helix: 1.97 (0.27), residues: 390 sheet: 0.67 (0.40), residues: 166 loop : -0.56 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 297 HIS 0.005 0.001 HIS A 220 PHE 0.013 0.001 PHE A 212 TYR 0.008 0.001 TYR A 339 ARG 0.002 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 0.719 Fit side-chains REVERT: R 79 ASP cc_start: 0.8429 (m-30) cc_final: 0.8088 (m-30) REVERT: R 231 GLN cc_start: 0.8060 (tm-30) cc_final: 0.7781 (tm-30) outliers start: 6 outliers final: 3 residues processed: 93 average time/residue: 1.1692 time to fit residues: 114.7556 Evaluate side-chains 83 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 80 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 136 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.9990 chunk 60 optimal weight: 0.0170 chunk 41 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 overall best weight: 0.6418 ------------------------------------------------------------------------------- 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** R 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6882 Z= 0.147 Angle : 0.455 5.510 9388 Z= 0.244 Chirality : 0.040 0.130 1106 Planarity : 0.003 0.031 1177 Dihedral : 8.137 138.691 979 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.35 % Allowed : 12.31 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.29), residues: 873 helix: 2.10 (0.27), residues: 390 sheet: 0.72 (0.40), residues: 171 loop : -0.52 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 99 HIS 0.006 0.001 HIS A 220 PHE 0.013 0.001 PHE A 212 TYR 0.008 0.001 TYR A 339 ARG 0.002 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 0.728 Fit side-chains REVERT: B 303 ASP cc_start: 0.8354 (p0) cc_final: 0.8099 (p0) REVERT: R 79 ASP cc_start: 0.8419 (m-30) cc_final: 0.8066 (m-30) REVERT: R 228 ARG cc_start: 0.7835 (ttp80) cc_final: 0.7188 (ttm110) REVERT: R 231 GLN cc_start: 0.7932 (tm-30) cc_final: 0.7645 (tm-30) outliers start: 9 outliers final: 4 residues processed: 85 average time/residue: 1.3161 time to fit residues: 117.4655 Evaluate side-chains 79 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 146 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 63 optimal weight: 0.0870 chunk 35 optimal weight: 0.2980 chunk 72 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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** R 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6882 Z= 0.134 Angle : 0.445 5.559 9388 Z= 0.238 Chirality : 0.040 0.129 1106 Planarity : 0.003 0.030 1177 Dihedral : 7.908 136.127 979 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.35 % Allowed : 12.91 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.29), residues: 873 helix: 2.20 (0.27), residues: 390 sheet: 0.84 (0.40), residues: 169 loop : -0.54 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 99 HIS 0.006 0.001 HIS A 220 PHE 0.013 0.001 PHE A 212 TYR 0.007 0.001 TYR A 339 ARG 0.002 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 0.672 Fit side-chains REVERT: A 25 LYS cc_start: 0.7748 (tttt) cc_final: 0.7515 (ttmm) REVERT: A 386 MET cc_start: 0.8648 (ttm) cc_final: 0.8205 (ttp) REVERT: B 303 ASP cc_start: 0.8369 (p0) cc_final: 0.8091 (p0) REVERT: R 79 ASP cc_start: 0.8325 (m-30) cc_final: 0.7964 (m-30) REVERT: R 231 GLN cc_start: 0.7895 (tm-30) cc_final: 0.7617 (tm-30) outliers start: 9 outliers final: 3 residues processed: 87 average time/residue: 1.3353 time to fit residues: 122.3534 Evaluate side-chains 81 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 2.9990 chunk 16 optimal weight: 0.0030 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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** R 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6882 Z= 0.133 Angle : 0.444 5.521 9388 Z= 0.238 Chirality : 0.040 0.129 1106 Planarity : 0.003 0.030 1177 Dihedral : 7.680 129.207 979 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.50 % Allowed : 13.06 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.29), residues: 873 helix: 2.26 (0.27), residues: 390 sheet: 0.85 (0.40), residues: 168 loop : -0.54 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 99 HIS 0.007 0.001 HIS A 220 PHE 0.014 0.001 PHE A 212 TYR 0.007 0.001 TYR A 339 ARG 0.004 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 0.743 Fit side-chains REVERT: A 25 LYS cc_start: 0.7684 (tttt) cc_final: 0.7465 (ttmm) REVERT: A 386 MET cc_start: 0.8642 (ttm) cc_final: 0.8199 (ttp) REVERT: B 303 ASP cc_start: 0.8341 (p0) cc_final: 0.8052 (p0) REVERT: R 79 ASP cc_start: 0.8314 (m-30) cc_final: 0.7940 (m-30) REVERT: R 228 ARG cc_start: 0.7845 (ttp80) cc_final: 0.7196 (ttm110) REVERT: R 231 GLN cc_start: 0.7862 (tm-30) cc_final: 0.7620 (tm-30) outliers start: 10 outliers final: 7 residues processed: 87 average time/residue: 1.2607 time to fit residues: 115.4244 Evaluate side-chains 86 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 302 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 0.0980 chunk 52 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** R 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6882 Z= 0.144 Angle : 0.455 5.549 9388 Z= 0.243 Chirality : 0.041 0.260 1106 Planarity : 0.003 0.030 1177 Dihedral : 7.556 126.021 979 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.95 % Allowed : 13.36 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.29), residues: 873 helix: 2.29 (0.27), residues: 390 sheet: 0.84 (0.40), residues: 168 loop : -0.53 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 99 HIS 0.007 0.001 HIS A 220 PHE 0.014 0.001 PHE A 212 TYR 0.007 0.001 TYR A 339 ARG 0.004 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.731 Fit side-chains REVERT: A 25 LYS cc_start: 0.7653 (tttt) cc_final: 0.7440 (ttmm) REVERT: A 221 MET cc_start: 0.8121 (ttp) cc_final: 0.7773 (ttp) REVERT: A 386 MET cc_start: 0.8669 (ttm) cc_final: 0.8228 (ttp) REVERT: B 303 ASP cc_start: 0.8380 (p0) cc_final: 0.8079 (p0) REVERT: R 79 ASP cc_start: 0.8326 (m-30) cc_final: 0.7965 (m-30) REVERT: R 156 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7925 (ttp) REVERT: R 231 GLN cc_start: 0.7878 (tm-30) cc_final: 0.7609 (tm-30) outliers start: 13 outliers final: 7 residues processed: 85 average time/residue: 1.2422 time to fit residues: 111.2952 Evaluate side-chains 83 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 75 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain R residue 302 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 0.0020 chunk 53 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 41 optimal weight: 0.3980 chunk 7 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 chunk 81 optimal weight: 0.0980 chunk 74 optimal weight: 0.6980 overall best weight: 0.2988 ------------------------------------------------------------------------------- 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** R 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6882 Z= 0.106 Angle : 0.427 5.449 9388 Z= 0.228 Chirality : 0.040 0.140 1106 Planarity : 0.003 0.026 1177 Dihedral : 7.166 118.337 979 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.80 % Allowed : 13.66 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.29), residues: 873 helix: 2.40 (0.27), residues: 390 sheet: 0.74 (0.41), residues: 165 loop : -0.54 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 99 HIS 0.006 0.001 HIS A 220 PHE 0.015 0.001 PHE A 212 TYR 0.006 0.001 TYR A 339 ARG 0.005 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 0.768 Fit side-chains REVERT: A 268 GLU cc_start: 0.7563 (tp30) cc_final: 0.6975 (tt0) REVERT: A 386 MET cc_start: 0.8632 (ttm) cc_final: 0.8201 (ttp) REVERT: B 303 ASP cc_start: 0.8322 (p0) cc_final: 0.8052 (p0) REVERT: R 79 ASP cc_start: 0.8184 (m-30) cc_final: 0.7868 (m-30) REVERT: R 156 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7897 (ttp) REVERT: R 228 ARG cc_start: 0.7806 (ttp80) cc_final: 0.7150 (ttm110) outliers start: 12 outliers final: 8 residues processed: 86 average time/residue: 1.1745 time to fit residues: 106.6653 Evaluate side-chains 87 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.691 > 50: distance: 33 - 50: 7.900 distance: 42 - 68: 19.355 distance: 48 - 50: 7.090 distance: 49 - 75: 22.980 distance: 50 - 51: 4.114 distance: 51 - 52: 8.888 distance: 51 - 54: 9.656 distance: 52 - 53: 10.549 distance: 52 - 57: 12.004 distance: 53 - 83: 20.269 distance: 54 - 55: 17.327 distance: 54 - 56: 14.631 distance: 57 - 58: 16.704 distance: 58 - 59: 10.941 distance: 58 - 61: 15.905 distance: 59 - 60: 4.062 distance: 59 - 68: 10.358 distance: 60 - 89: 26.115 distance: 61 - 62: 7.633 distance: 62 - 63: 11.986 distance: 62 - 64: 16.265 distance: 63 - 65: 10.967 distance: 64 - 66: 7.408 distance: 65 - 67: 22.218 distance: 66 - 67: 19.891 distance: 68 - 69: 8.459 distance: 69 - 70: 8.253 distance: 69 - 72: 18.865 distance: 70 - 71: 15.518 distance: 70 - 75: 6.281 distance: 71 - 103: 47.708 distance: 72 - 73: 14.503 distance: 72 - 74: 9.625 distance: 75 - 76: 3.135 distance: 76 - 77: 6.377 distance: 76 - 79: 24.105 distance: 77 - 78: 19.205 distance: 77 - 83: 4.770 distance: 79 - 80: 11.447 distance: 80 - 81: 26.139 distance: 80 - 82: 5.283 distance: 83 - 84: 21.948 distance: 84 - 85: 16.495 distance: 84 - 87: 19.495 distance: 85 - 86: 11.071 distance: 85 - 89: 16.494 distance: 87 - 88: 10.180 distance: 89 - 90: 33.405 distance: 90 - 91: 13.557 distance: 90 - 93: 6.411 distance: 91 - 92: 23.901 distance: 91 - 103: 20.202 distance: 93 - 94: 22.487 distance: 94 - 95: 13.022 distance: 94 - 96: 18.891 distance: 95 - 97: 17.172 distance: 96 - 98: 11.135 distance: 96 - 99: 15.202 distance: 97 - 98: 23.256 distance: 98 - 100: 23.904 distance: 99 - 101: 6.347 distance: 100 - 102: 8.481 distance: 101 - 102: 10.505 distance: 103 - 104: 5.850 distance: 104 - 105: 19.224 distance: 104 - 107: 25.899 distance: 105 - 106: 36.230 distance: 105 - 111: 29.733 distance: 106 - 140: 30.946 distance: 107 - 108: 4.491 distance: 108 - 109: 44.843 distance: 108 - 110: 11.981 distance: 111 - 112: 7.082 distance: 111 - 117: 33.063 distance: 112 - 113: 10.845 distance: 112 - 115: 15.902 distance: 113 - 114: 11.953 distance: 113 - 118: 13.792 distance: 114 - 148: 28.654 distance: 115 - 116: 15.881 distance: 116 - 117: 12.381 distance: 118 - 119: 10.120 distance: 119 - 120: 4.576 distance: 119 - 122: 14.318 distance: 120 - 121: 3.755 distance: 120 - 129: 6.854 distance: 121 - 155: 9.126 distance: 122 - 123: 12.127 distance: 123 - 124: 8.326 distance: 123 - 125: 13.552 distance: 124 - 126: 22.332 distance: 125 - 127: 26.671 distance: 127 - 128: 16.478 distance: 130 - 131: 5.822 distance: 130 - 133: 3.428 distance: 131 - 140: 4.599 distance: 134 - 135: 8.510 distance: 134 - 136: 8.302 distance: 135 - 137: 11.961 distance: 136 - 138: 13.772 distance: 137 - 139: 13.962 distance: 138 - 139: 17.854