Starting phenix.real_space_refine on Tue Jan 21 07:31:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uhb_42268/01_2025/8uhb_42268_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uhb_42268/01_2025/8uhb_42268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uhb_42268/01_2025/8uhb_42268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uhb_42268/01_2025/8uhb_42268.map" model { file = "/net/cci-nas-00/data/ceres_data/8uhb_42268/01_2025/8uhb_42268_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uhb_42268/01_2025/8uhb_42268_trim.cif" } resolution = 3.35 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= 0.038 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 S 65 5.16 5 C 5346 2.51 5 N 1453 2.21 5 O 1553 1.98 5 H 8144 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 16561 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 4754 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 11, 'TRANS': 304} Chain breaks: 1 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 5106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5106 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 3890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3890 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 2 Chain: "G" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 884 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 1911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1911 Classifications: {'peptide': 128} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'WV8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.98, per 1000 atoms: 0.48 Number of scatterers: 16561 At special positions: 0 Unit cell: (85.52, 100.486, 136.832, 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 65 16.00 O 1553 8.00 N 1453 7.00 C 5346 6.00 H 8144 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 5 " - pdb=" SG CYS A 178 " distance=2.03 Simple disulfide: pdb=" SG CYS A 13 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 182 " distance=2.03 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=2.03 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: 4.08 Conformation dependent library (CDL) restraints added in 1.4 seconds 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2026 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 12 sheets defined 39.9% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 19 through 51 removed outlier: 3.835A pdb=" N ILE A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 76 removed outlier: 3.918A pdb=" N ILE A 62 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 64 " --> pdb=" O TRP A 60 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR A 67 " --> pdb=" O HIS A 63 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 68 " --> pdb=" O SER A 64 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A 69 " --> pdb=" O MET A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 87 removed outlier: 3.556A pdb=" N SER A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG A 83 " --> pdb=" O TYR A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 101 removed outlier: 3.686A pdb=" N LYS A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 126 Processing helix chain 'A' and resid 130 through 135 removed outlier: 3.506A pdb=" N LYS A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 157 Proline residue: A 151 - end of helix Processing helix chain 'A' and resid 169 through 178 removed outlier: 3.954A pdb=" N CYS A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 199 through 228 removed outlier: 4.152A pdb=" N ARG A 212 " --> pdb=" O CYS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 278 removed outlier: 4.272A pdb=" N LYS A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Proline residue: A 266 - end of helix removed outlier: 3.725A pdb=" N ASP A 274 " --> pdb=" O CYS A 270 " (cutoff:3.500A) Proline residue: A 275 - end of helix Processing helix chain 'A' and resid 282 through 305 removed outlier: 3.693A pdb=" N ASN A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) Proline residue: A 301 - end of helix Processing helix chain 'A' and resid 308 through 319 Processing helix chain 'A' and resid 327 through 331 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.761A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.677A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 38 Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 269 through 279 removed outlier: 3.526A pdb=" N ASP C 274 " --> pdb=" O LEU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 303 Processing helix chain 'C' and resid 334 through 353 removed outlier: 4.249A pdb=" N LYS C 338 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG C 342 " --> pdb=" O LYS C 338 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU C 344 " --> pdb=" O PHE C 340 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N PHE C 345 " --> pdb=" O ILE C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 391 removed outlier: 3.951A pdb=" N VAL C 375 " --> pdb=" O ASN C 371 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP C 381 " --> pdb=" O ASN C 377 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C 383 " --> pdb=" O CYS C 379 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.532A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.673A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.986A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.984A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.617A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.715A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.809A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.471A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 40 through 41 Processing sheet with id=AA9, first strand: chain 'C' and resid 208 through 209 Processing sheet with id=AB1, first strand: chain 'C' and resid 246 through 249 removed outlier: 7.020A pdb=" N VAL C 287 " --> pdb=" O TYR C 360 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N HIS C 362 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU C 289 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.502A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 390 hydrogen bonds defined for protein. 1113 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: 6.58 Time building geometry restraints manager: 4.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8118 1.03 - 1.23: 141 1.23 - 1.43: 3560 1.43 - 1.62: 4828 1.62 - 1.82: 94 Bond restraints: 16741 Sorted by residual: bond pdb=" C8 WV8 A 401 " pdb=" N9 WV8 A 401 " ideal model delta sigma weight residual 1.359 1.326 0.033 2.00e-02 2.50e+03 2.74e+00 bond pdb=" C MET A 77 " pdb=" O MET A 77 " ideal model delta sigma weight residual 1.244 1.231 0.013 1.00e-02 1.00e+04 1.60e+00 bond pdb=" CB TRP B 99 " pdb=" CG TRP B 99 " ideal model delta sigma weight residual 1.498 1.468 0.030 3.10e-02 1.04e+03 9.30e-01 bond pdb=" C VAL A 250 " pdb=" O VAL A 250 " ideal model delta sigma weight residual 1.237 1.226 0.011 1.12e-02 7.97e+03 9.28e-01 bond pdb=" C8 WV8 A 401 " pdb=" O7 WV8 A 401 " ideal model delta sigma weight residual 1.361 1.344 0.017 2.00e-02 2.50e+03 6.90e-01 ... (remaining 16736 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 27324 1.01 - 2.02: 2542 2.02 - 3.03: 149 3.03 - 4.04: 44 4.04 - 5.05: 14 Bond angle restraints: 30073 Sorted by residual: angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.20 109.67 3.53 9.60e-01 1.09e+00 1.35e+01 angle pdb=" N ILE C 372 " pdb=" CA ILE C 372 " pdb=" C ILE C 372 " ideal model delta sigma weight residual 112.35 107.30 5.05 1.41e+00 5.03e-01 1.28e+01 angle pdb=" N ILE C 235 " pdb=" CA ILE C 235 " pdb=" C ILE C 235 " ideal model delta sigma weight residual 113.07 108.53 4.54 1.37e+00 5.33e-01 1.10e+01 angle pdb=" N ASP C 310 " pdb=" CA ASP C 310 " pdb=" C ASP C 310 " ideal model delta sigma weight residual 114.04 110.13 3.91 1.24e+00 6.50e-01 9.93e+00 angle pdb=" N VAL A 46 " pdb=" CA VAL A 46 " pdb=" C VAL A 46 " ideal model delta sigma weight residual 111.45 108.65 2.80 9.30e-01 1.16e+00 9.06e+00 ... (remaining 30068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 7184 17.66 - 35.32: 599 35.32 - 52.98: 135 52.98 - 70.64: 21 70.64 - 88.30: 9 Dihedral angle restraints: 7948 sinusoidal: 4200 harmonic: 3748 Sorted by residual: dihedral pdb=" CB CYS A 5 " pdb=" SG CYS A 5 " pdb=" SG CYS A 178 " pdb=" CB CYS A 178 " ideal model delta sinusoidal sigma weight residual 93.00 175.02 -82.02 1 1.00e+01 1.00e-02 8.27e+01 dihedral pdb=" CB CYS A 96 " pdb=" SG CYS A 96 " pdb=" SG CYS A 182 " pdb=" CB CYS A 182 " ideal model delta sinusoidal sigma weight residual -86.00 -154.02 68.02 1 1.00e+01 1.00e-02 6.01e+01 dihedral pdb=" CA ILE C 341 " pdb=" C ILE C 341 " pdb=" N ARG C 342 " pdb=" CA ARG C 342 " ideal model delta harmonic sigma weight residual 180.00 155.50 24.50 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 7945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 787 0.032 - 0.064: 371 0.064 - 0.096: 94 0.096 - 0.128: 44 0.128 - 0.160: 8 Chirality restraints: 1304 Sorted by residual: chirality pdb=" CA ILE C 341 " pdb=" N ILE C 341 " pdb=" C ILE C 341 " pdb=" CB ILE C 341 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CB VAL A 46 " pdb=" CA VAL A 46 " pdb=" CG1 VAL A 46 " pdb=" CG2 VAL A 46 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA ILE C 244 " pdb=" N ILE C 244 " pdb=" C ILE C 244 " pdb=" CB ILE C 244 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 1301 not shown) Planarity restraints: 2509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5 WV8 A 401 " 0.048 2.00e-02 2.50e+03 3.77e-02 1.78e+01 pdb=" C8 WV8 A 401 " -0.013 2.00e-02 2.50e+03 pdb=" N10 WV8 A 401 " -0.051 2.00e-02 2.50e+03 pdb=" N9 WV8 A 401 " 0.039 2.00e-02 2.50e+03 pdb=" O7 WV8 A 401 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 234 " 0.020 2.00e-02 2.50e+03 1.16e-02 4.04e+00 pdb=" CG PHE B 234 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE B 234 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE B 234 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 234 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 234 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 234 " 0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE B 234 " -0.005 2.00e-02 2.50e+03 pdb=" HD2 PHE B 234 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE B 234 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE B 234 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE B 234 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 281 " 0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO A 282 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 282 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 282 " 0.026 5.00e-02 4.00e+02 ... (remaining 2506 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.06: 262 2.06 - 2.69: 26322 2.69 - 3.33: 47799 3.33 - 3.96: 61919 3.96 - 4.60: 97889 Nonbonded interactions: 234191 Sorted by model distance: nonbonded pdb=" HE2 HIS C 362 " pdb=" OD2 ASP C 378 " model vdw 1.420 2.450 nonbonded pdb=" OD1 ASP C 331 " pdb=" H VAL C 334 " model vdw 1.525 2.450 nonbonded pdb=" OD1 ASP B 228 " pdb=" HH TYR N 117 " model vdw 1.564 2.450 nonbonded pdb=" O ARG B 68 " pdb=" HG SER B 84 " model vdw 1.606 2.450 nonbonded pdb="HH12 ARG N 67 " pdb=" OD2 ASP N 90 " model vdw 1.630 2.450 ... (remaining 234186 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: 0.920 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: 0.280 Extract box with map and model: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 37.130 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8597 Z= 0.239 Angle : 0.619 5.054 11643 Z= 0.367 Chirality : 0.041 0.160 1304 Planarity : 0.003 0.048 1482 Dihedral : 14.115 88.305 3086 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: -1.42 (0.26), residues: 1059 helix: 0.13 (0.28), residues: 385 sheet: -1.84 (0.33), residues: 218 loop : -1.30 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.035 0.001 PHE B 234 TYR 0.013 0.001 TYR C 311 ARG 0.009 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.6142 time to fit residues: 141.4942 Evaluate side-chains 116 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 81 optimal weight: 0.0870 chunk 31 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 55 HIS B 16 ASN B 155 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.073726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.057485 restraints weight = 86124.405| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 4.32 r_work: 0.2913 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8597 Z= 0.177 Angle : 0.563 5.568 11643 Z= 0.307 Chirality : 0.040 0.136 1304 Planarity : 0.004 0.048 1482 Dihedral : 5.484 38.398 1183 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.33 % Allowed : 8.03 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.23 (0.26), residues: 1059 helix: 0.33 (0.27), residues: 400 sheet: -1.65 (0.33), residues: 222 loop : -1.31 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.006 0.001 HIS C 362 PHE 0.018 0.001 PHE C 212 TYR 0.010 0.001 TYR B 59 ARG 0.004 0.000 ARG C 283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 124 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.9059 (tmm) cc_final: 0.8859 (tmm) REVERT: C 268 GLU cc_start: 0.8596 (pt0) cc_final: 0.8395 (pt0) REVERT: C 279 ASN cc_start: 0.9730 (t0) cc_final: 0.9276 (t0) REVERT: G 21 MET cc_start: 0.9388 (ttt) cc_final: 0.9169 (ttm) REVERT: N 34 MET cc_start: 0.8789 (mmm) cc_final: 0.8416 (tpp) outliers start: 3 outliers final: 3 residues processed: 126 average time/residue: 0.5293 time to fit residues: 89.2103 Evaluate side-chains 116 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 379 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 1 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 176 GLN ** C 371 ASN ** 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 = 0.3388 r_free = 0.3388 target = 0.070242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.054726 restraints weight = 87420.538| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 4.18 r_work: 0.2843 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 8597 Z= 0.338 Angle : 0.582 5.805 11643 Z= 0.321 Chirality : 0.041 0.131 1304 Planarity : 0.004 0.040 1482 Dihedral : 5.215 33.950 1183 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.89 % Allowed : 8.92 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.95 (0.27), residues: 1059 helix: 0.55 (0.27), residues: 400 sheet: -1.44 (0.33), residues: 225 loop : -1.19 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.006 0.001 HIS C 362 PHE 0.019 0.001 PHE B 234 TYR 0.011 0.001 TYR C 358 ARG 0.004 0.001 ARG N 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.9091 (tmm) cc_final: 0.8874 (tmm) REVERT: B 322 ASP cc_start: 0.9063 (m-30) cc_final: 0.8783 (t0) REVERT: C 279 ASN cc_start: 0.9729 (t0) cc_final: 0.9254 (t0) REVERT: G 21 MET cc_start: 0.9399 (ttt) cc_final: 0.9135 (ttm) REVERT: N 34 MET cc_start: 0.8731 (mmm) cc_final: 0.8407 (mmm) outliers start: 8 outliers final: 5 residues processed: 117 average time/residue: 0.5210 time to fit residues: 81.2659 Evaluate side-chains 106 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain G residue 41 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 29 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.070143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.054681 restraints weight = 87060.761| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 4.15 r_work: 0.2850 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8597 Z= 0.243 Angle : 0.537 5.542 11643 Z= 0.293 Chirality : 0.040 0.136 1304 Planarity : 0.003 0.039 1482 Dihedral : 5.063 33.290 1183 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.78 % Allowed : 9.59 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.70 (0.27), residues: 1059 helix: 0.82 (0.27), residues: 402 sheet: -1.25 (0.34), residues: 215 loop : -1.19 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS C 362 PHE 0.018 0.001 PHE C 222 TYR 0.008 0.001 TYR A 200 ARG 0.003 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.9046 (tmm) cc_final: 0.8834 (tmm) REVERT: B 61 MET cc_start: 0.9327 (ppp) cc_final: 0.9085 (ppp) REVERT: B 230 ASN cc_start: 0.9420 (m-40) cc_final: 0.9053 (m110) REVERT: B 322 ASP cc_start: 0.9059 (m-30) cc_final: 0.8806 (t0) REVERT: C 15 GLU cc_start: 0.9483 (OUTLIER) cc_final: 0.9244 (tm-30) REVERT: G 21 MET cc_start: 0.9428 (ttt) cc_final: 0.9177 (ttm) REVERT: G 47 GLU cc_start: 0.8779 (mp0) cc_final: 0.8412 (mp0) REVERT: N 34 MET cc_start: 0.8764 (mmm) cc_final: 0.8348 (tpp) outliers start: 7 outliers final: 4 residues processed: 117 average time/residue: 0.5388 time to fit residues: 84.0358 Evaluate side-chains 111 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.070342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.054525 restraints weight = 88211.774| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 4.18 r_work: 0.2863 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8597 Z= 0.179 Angle : 0.517 5.193 11643 Z= 0.279 Chirality : 0.039 0.134 1304 Planarity : 0.003 0.037 1482 Dihedral : 4.845 34.081 1183 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.78 % Allowed : 10.70 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.46 (0.27), residues: 1059 helix: 1.12 (0.27), residues: 399 sheet: -1.08 (0.35), residues: 213 loop : -1.17 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS C 362 PHE 0.023 0.001 PHE C 222 TYR 0.008 0.001 TYR C 358 ARG 0.002 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9549 (mtm) cc_final: 0.9297 (mtm) REVERT: A 81 MET cc_start: 0.9645 (OUTLIER) cc_final: 0.9365 (ttm) REVERT: A 158 MET cc_start: 0.9007 (tmm) cc_final: 0.8792 (tmm) REVERT: B 61 MET cc_start: 0.9322 (ppp) cc_final: 0.8974 (ppp) REVERT: B 138 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8525 (mm-30) REVERT: B 230 ASN cc_start: 0.9439 (m-40) cc_final: 0.9139 (m110) REVERT: B 322 ASP cc_start: 0.9033 (m-30) cc_final: 0.8769 (t0) REVERT: C 15 GLU cc_start: 0.9484 (OUTLIER) cc_final: 0.9260 (tm-30) REVERT: G 21 MET cc_start: 0.9442 (ttt) cc_final: 0.9191 (ttm) REVERT: G 47 GLU cc_start: 0.8819 (mp0) cc_final: 0.8436 (mp0) REVERT: N 34 MET cc_start: 0.8794 (mmm) cc_final: 0.8331 (tpp) outliers start: 7 outliers final: 5 residues processed: 120 average time/residue: 0.5360 time to fit residues: 86.8766 Evaluate side-chains 113 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 44 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.069542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.053994 restraints weight = 87969.525| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 4.08 r_work: 0.2900 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 8597 Z= 0.320 Angle : 0.553 5.296 11643 Z= 0.303 Chirality : 0.040 0.136 1304 Planarity : 0.003 0.036 1482 Dihedral : 4.872 33.626 1183 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.11 % Allowed : 11.37 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.36 (0.27), residues: 1059 helix: 1.24 (0.27), residues: 402 sheet: -1.03 (0.35), residues: 210 loop : -1.16 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS C 220 PHE 0.025 0.001 PHE C 222 TYR 0.013 0.001 TYR A 200 ARG 0.002 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue ILE 11 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue VAL 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue SER 19 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue ILE 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue TYR 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue MET 273 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue SER 328 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue LYS 332 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASP cc_start: 0.9334 (m-30) cc_final: 0.9067 (t0) REVERT: A 158 MET cc_start: 0.9014 (tmm) cc_final: 0.8812 (tmm) REVERT: B 262 MET cc_start: 0.8853 (ttm) cc_final: 0.8610 (ttm) REVERT: B 322 ASP cc_start: 0.9008 (m-30) cc_final: 0.8791 (t0) REVERT: G 21 MET cc_start: 0.9383 (ttt) cc_final: 0.9118 (ttm) REVERT: N 34 MET cc_start: 0.8804 (mmm) cc_final: 0.8351 (tpp) REVERT: N 77 ASN cc_start: 0.9316 (m-40) cc_final: 0.8902 (p0) outliers start: 10 outliers final: 8 residues processed: 111 average time/residue: 0.5043 time to fit residues: 75.1555 Evaluate side-chains 107 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 390 GLN Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 56.0084 > 50: distance: 248 - 262: 6.145 distance: 262 - 263: 4.927 distance: 262 - 270: 8.304 distance: 263 - 264: 13.351 distance: 263 - 266: 11.727 distance: 263 - 271: 11.597 distance: 264 - 265: 12.974 distance: 264 - 274: 6.694 distance: 266 - 267: 14.463 distance: 266 - 272: 19.058 distance: 266 - 273: 22.825 distance: 267 - 268: 22.138 distance: 267 - 269: 29.621 distance: 274 - 275: 11.241 distance: 274 - 282: 18.469 distance: 275 - 276: 10.390 distance: 275 - 278: 17.293 distance: 275 - 283: 19.567 distance: 276 - 277: 22.619 distance: 276 - 288: 10.725 distance: 278 - 279: 31.083 distance: 278 - 284: 31.770 distance: 278 - 285: 25.369 distance: 279 - 280: 16.873 distance: 279 - 281: 16.633 distance: 281 - 286: 28.948 distance: 281 - 287: 17.486 distance: 288 - 289: 22.192 distance: 288 - 299: 22.522 distance: 289 - 290: 15.763 distance: 289 - 292: 6.710 distance: 289 - 300: 18.087 distance: 290 - 291: 45.373 distance: 290 - 312: 27.788 distance: 292 - 293: 7.416 distance: 292 - 301: 14.656 distance: 292 - 302: 17.717 distance: 293 - 294: 5.683 distance: 293 - 303: 6.894 distance: 293 - 304: 5.774 distance: 294 - 305: 6.590 distance: 294 - 306: 7.308 distance: 295 - 307: 15.532 distance: 296 - 298: 6.611 distance: 297 - 308: 6.026 distance: 297 - 309: 3.503 distance: 298 - 311: 3.125 distance: 312 - 313: 22.964 distance: 312 - 319: 35.663 distance: 313 - 314: 17.778 distance: 313 - 316: 10.723 distance: 313 - 320: 27.043 distance: 314 - 315: 23.043 distance: 314 - 328: 24.026 distance: 316 - 317: 23.523 distance: 316 - 318: 14.115 distance: 316 - 321: 31.256 distance: 317 - 322: 12.168 distance: 317 - 323: 9.117 distance: 317 - 324: 15.572 distance: 318 - 325: 12.168 distance: 318 - 326: 12.576 distance: 318 - 327: 17.000 distance: 328 - 329: 17.436 distance: 328 - 334: 15.924 distance: 329 - 330: 18.295 distance: 329 - 332: 32.088 distance: 329 - 335: 22.702 distance: 330 - 331: 10.399 distance: 332 - 333: 30.369 distance: 332 - 336: 15.470 distance: 332 - 337: 23.721 distance: 333 - 338: 22.952 distance: 339 - 345: 14.551 distance: 339 - 496: 15.582 distance: 340 - 341: 19.848 distance: 340 - 343: 7.624 distance: 340 - 346: 9.743 distance: 341 - 342: 11.213 distance: 341 - 350: 21.663 distance: 342 - 493: 7.519 distance: 343 - 344: 14.528 distance: 343 - 347: 13.654 distance: 343 - 348: 16.512 distance: 344 - 349: 12.816 distance: 350 - 351: 26.277 distance: 350 - 358: 13.669 distance: 351 - 352: 25.729 distance: 351 - 354: 42.839 distance: 351 - 359: 21.737 distance: 352 - 353: 14.988 distance: 352 - 369: 23.844 distance: 354 - 355: 28.011 distance: 354 - 360: 33.385 distance: 354 - 361: 37.587 distance: 355 - 356: 11.873 distance: 355 - 357: 23.170 distance: 355 - 362: 8.011 distance: 356 - 363: 7.348 distance: 356 - 364: 18.970 distance: 356 - 365: 4.689 distance: 357 - 366: 17.746 distance: 357 - 367: 13.888 distance: 357 - 368: 8.731 distance: 369 - 370: 39.586 distance: 369 - 373: 30.518 distance: 369 - 472: 12.526 distance: 370 - 371: 4.910 distance: 370 - 374: 43.045 distance: 370 - 375: 38.784 distance: 371 - 372: 43.102 distance: 371 - 376: 51.616 distance: 372 - 469: 20.748 distance: 376 - 377: 23.238 distance: 376 - 383: 25.981 distance: 377 - 378: 20.519 distance: 377 - 380: 18.817 distance: 377 - 384: 17.740 distance: 378 - 379: 16.188 distance: 378 - 392: 17.815 distance: 380 - 381: 4.959 distance: 380 - 382: 6.294 distance: 380 - 385: 12.784 distance: 381 - 386: 19.500 distance: 381 - 387: 14.975 distance: 381 - 388: 18.846 distance: 382 - 389: 11.085 distance: 382 - 390: 9.068 distance: 382 - 391: 8.781 distance: 392 - 393: 8.809 distance: 392 - 399: 18.121 distance: 393 - 394: 18.049 distance: 393 - 396: 17.542 distance: 393 - 400: 29.695 distance: 394 - 395: 18.512 distance: 394 - 406: 7.382 distance: 396 - 397: 16.745 distance: 396 - 398: 21.789 distance: 396 - 401: 22.827 distance: 397 - 402: 33.896 distance: 398 - 403: 12.962 distance: 398 - 404: 16.308 distance: 398 - 405: 12.627