Starting phenix.real_space_refine on Sat Aug 23 14:26:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ndy_0443/08_2025/6ndy_0443.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ndy_0443/08_2025/6ndy_0443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ndy_0443/08_2025/6ndy_0443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ndy_0443/08_2025/6ndy_0443.map" model { file = "/net/cci-nas-00/data/ceres_data/6ndy_0443/08_2025/6ndy_0443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ndy_0443/08_2025/6ndy_0443.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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: 8 Type Number sf(0) Gaussians P 10 5.49 5 Mg 4 5.21 5 S 45 5.16 5 Be 3 3.05 5 C 7846 2.51 5 N 2143 2.21 5 O 2471 1.98 5 F 9 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12531 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2427 Classifications: {'peptide': 314} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 297} Chain breaks: 1 Chain: "B" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2491 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 305} Chain breaks: 1 Chain: "C" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2491 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 305} Chain breaks: 1 Chain: "D" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2491 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 305} Chain breaks: 1 Chain: "E" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2360 Classifications: {'peptide': 304} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 287} Chain breaks: 1 Chain: "G" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 80 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "G" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.88, per 1000 atoms: 0.31 Number of scatterers: 12531 At special positions: 0 Unit cell: (79.57, 141.7, 156.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 45 16.00 P 10 15.00 Mg 4 11.99 F 9 9.00 O 2471 8.00 N 2143 7.00 C 7846 6.00 Be 3 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 674.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2966 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 11 sheets defined 50.2% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 116 through 122 removed outlier: 3.783A pdb=" N LEU A 119 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER A 120 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER A 121 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 122 " --> pdb=" O LEU A 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 122' Processing helix chain 'A' and resid 138 through 155 Proline residue: A 152 - end of helix Processing helix chain 'A' and resid 178 through 189 Processing helix chain 'A' and resid 208 through 224 removed outlier: 4.004A pdb=" N VAL A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 245 through 260 removed outlier: 4.709A pdb=" N ARG A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 290 Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 335 through 356 Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 403 through 413 Processing helix chain 'A' and resid 418 through 433 removed outlier: 3.891A pdb=" N LEU A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 150 through 155 Processing helix chain 'B' and resid 178 through 190 Processing helix chain 'B' and resid 208 through 224 removed outlier: 4.313A pdb=" N VAL B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 261 Processing helix chain 'B' and resid 283 through 290 Processing helix chain 'B' and resid 300 through 313 removed outlier: 3.584A pdb=" N GLY B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 331 Processing helix chain 'B' and resid 335 through 356 Proline residue: B 350 - end of helix Processing helix chain 'B' and resid 402 through 413 removed outlier: 3.998A pdb=" N PHE B 406 " --> pdb=" O THR B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 433 Processing helix chain 'C' and resid 113 through 120 Processing helix chain 'C' and resid 138 through 155 Proline residue: C 152 - end of helix Processing helix chain 'C' and resid 178 through 190 Processing helix chain 'C' and resid 209 through 224 removed outlier: 3.608A pdb=" N LEU C 213 " --> pdb=" O GLU C 209 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 214 " --> pdb=" O SER C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 261 removed outlier: 4.056A pdb=" N ASN C 261 " --> pdb=" O LEU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 290 Processing helix chain 'C' and resid 300 through 313 Processing helix chain 'C' and resid 320 through 331 Processing helix chain 'C' and resid 335 through 356 Proline residue: C 350 - end of helix Processing helix chain 'C' and resid 402 through 413 removed outlier: 3.967A pdb=" N PHE C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 433 Processing helix chain 'D' and resid 113 through 120 Processing helix chain 'D' and resid 121 through 123 No H-bonds generated for 'chain 'D' and resid 121 through 123' Processing helix chain 'D' and resid 131 through 135 removed outlier: 3.569A pdb=" N VAL D 135 " --> pdb=" O TRP D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 155 Proline residue: D 152 - end of helix Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 198 through 203 removed outlier: 3.736A pdb=" N LEU D 202 " --> pdb=" O SER D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 224 removed outlier: 3.659A pdb=" N ASN D 224 " --> pdb=" O MET D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 245 through 261 removed outlier: 4.202A pdb=" N ASN D 261 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 282 Processing helix chain 'D' and resid 283 through 290 Processing helix chain 'D' and resid 300 through 312 Processing helix chain 'D' and resid 320 through 331 Processing helix chain 'D' and resid 335 through 356 Proline residue: D 350 - end of helix Processing helix chain 'D' and resid 402 through 413 removed outlier: 3.944A pdb=" N PHE D 406 " --> pdb=" O THR D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 433 Processing helix chain 'E' and resid 138 through 155 Proline residue: E 152 - end of helix Processing helix chain 'E' and resid 178 through 190 Processing helix chain 'E' and resid 199 through 203 removed outlier: 3.755A pdb=" N VAL E 203 " --> pdb=" O SER E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 224 removed outlier: 3.592A pdb=" N ASN E 224 " --> pdb=" O MET E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 238 removed outlier: 3.718A pdb=" N THR E 238 " --> pdb=" O VAL E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 261 Processing helix chain 'E' and resid 283 through 290 Processing helix chain 'E' and resid 300 through 313 removed outlier: 4.147A pdb=" N GLY E 313 " --> pdb=" O GLU E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 331 Processing helix chain 'E' and resid 335 through 356 Proline residue: E 350 - end of helix removed outlier: 3.557A pdb=" N GLN E 355 " --> pdb=" O ILE E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 413 removed outlier: 3.966A pdb=" N PHE E 406 " --> pdb=" O THR E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 432 removed outlier: 3.643A pdb=" N LEU E 423 " --> pdb=" O GLU E 419 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 275 through 276 removed outlier: 8.619A pdb=" N THR A 276 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU A 171 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU A 170 " --> pdb=" O ILE A 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 Processing sheet with id=AA3, first strand: chain 'A' and resid 360 through 363 removed outlier: 4.037A pdb=" N LYS A 372 " --> pdb=" O VAL A 363 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 193 through 197 removed outlier: 6.363A pdb=" N THR B 193 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N PHE B 230 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N PHE B 195 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASP B 232 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL B 197 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B 275 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU B 170 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 360 through 362 Processing sheet with id=AA6, first strand: chain 'C' and resid 193 through 197 removed outlier: 3.503A pdb=" N ILE C 228 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP C 232 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 275 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N GLY C 168 " --> pdb=" O ARG C 292 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE C 294 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU C 170 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG C 293 " --> pdb=" O GLN C 434 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 373 through 375 Processing sheet with id=AA8, first strand: chain 'D' and resid 193 through 197 removed outlier: 6.447A pdb=" N THR D 193 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N PHE D 230 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE D 195 " --> pdb=" O PHE D 230 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASP D 232 " --> pdb=" O PHE D 195 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL D 197 " --> pdb=" O ASP D 232 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LEU D 273 " --> pdb=" O SER D 227 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE D 229 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ALA D 275 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE D 231 " --> pdb=" O ALA D 275 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 372 through 375 removed outlier: 4.222A pdb=" N LYS D 372 " --> pdb=" O VAL D 363 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL D 363 " --> pdb=" O LYS D 372 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 193 through 195 removed outlier: 6.672A pdb=" N THR E 193 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N PHE E 230 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE E 195 " --> pdb=" O PHE E 230 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASP E 232 " --> pdb=" O PHE E 195 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N SER E 227 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LEU E 273 " --> pdb=" O SER E 227 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE E 229 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA E 275 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE E 231 " --> pdb=" O ALA E 275 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 372 through 375 removed outlier: 4.255A pdb=" N LYS E 372 " --> pdb=" O VAL E 363 " (cutoff:3.500A) 553 hydrogen bonds defined for protein. 1614 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.06 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4106 1.34 - 1.46: 2151 1.46 - 1.58: 6385 1.58 - 1.69: 15 1.69 - 1.81: 80 Bond restraints: 12737 Sorted by residual: bond pdb=" C4 ADP C 501 " pdb=" C5 ADP C 501 " ideal model delta sigma weight residual 1.490 1.386 0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C4 ADP B 501 " pdb=" C5 ADP B 501 " ideal model delta sigma weight residual 1.490 1.387 0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" C4 ADP A 501 " pdb=" C5 ADP A 501 " ideal model delta sigma weight residual 1.490 1.388 0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" C5 ADP C 501 " pdb=" C6 ADP C 501 " ideal model delta sigma weight residual 1.490 1.403 0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C5 ADP A 501 " pdb=" C6 ADP A 501 " ideal model delta sigma weight residual 1.490 1.404 0.086 2.00e-02 2.50e+03 1.85e+01 ... (remaining 12732 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 16962 2.99 - 5.98: 190 5.98 - 8.96: 54 8.96 - 11.95: 14 11.95 - 14.94: 3 Bond angle restraints: 17223 Sorted by residual: angle pdb=" C ASN E 265 " pdb=" N ASP E 266 " pdb=" CA ASP E 266 " ideal model delta sigma weight residual 122.46 130.35 -7.89 1.41e+00 5.03e-01 3.13e+01 angle pdb=" C GLY B 239 " pdb=" N THR B 240 " pdb=" CA THR B 240 " ideal model delta sigma weight residual 121.54 131.26 -9.72 1.91e+00 2.74e-01 2.59e+01 angle pdb=" O1B ADP A 501 " pdb=" PB ADP A 501 " pdb=" O3B ADP A 501 " ideal model delta sigma weight residual 119.90 104.96 14.94 3.00e+00 1.11e-01 2.48e+01 angle pdb=" O2B ADP B 501 " pdb=" PB ADP B 501 " pdb=" O3B ADP B 501 " ideal model delta sigma weight residual 119.90 104.96 14.94 3.00e+00 1.11e-01 2.48e+01 angle pdb=" O2B ADP C 501 " pdb=" PB ADP C 501 " pdb=" O3B ADP C 501 " ideal model delta sigma weight residual 119.90 105.52 14.38 3.00e+00 1.11e-01 2.30e+01 ... (remaining 17218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.41: 7581 32.41 - 64.82: 196 64.82 - 97.23: 14 97.23 - 129.63: 3 129.63 - 162.04: 2 Dihedral angle restraints: 7796 sinusoidal: 3213 harmonic: 4583 Sorted by residual: dihedral pdb=" C5' ADP E 501 " pdb=" O5' ADP E 501 " pdb=" PA ADP E 501 " pdb=" O2A ADP E 501 " ideal model delta sinusoidal sigma weight residual -60.00 102.04 -162.04 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" O2A ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PA ADP D 501 " pdb=" PB ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 73.34 -133.34 1 2.00e+01 2.50e-03 4.05e+01 dihedral pdb=" C5' ADP A 501 " pdb=" O5' ADP A 501 " pdb=" PA ADP A 501 " pdb=" O2A ADP A 501 " ideal model delta sinusoidal sigma weight residual 300.00 178.17 121.83 1 2.00e+01 2.50e-03 3.67e+01 ... (remaining 7793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1612 0.056 - 0.113: 272 0.113 - 0.169: 62 0.169 - 0.225: 9 0.225 - 0.282: 2 Chirality restraints: 1957 Sorted by residual: chirality pdb=" CB ILE A 278 " pdb=" CA ILE A 278 " pdb=" CG1 ILE A 278 " pdb=" CG2 ILE A 278 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB ILE C 278 " pdb=" CA ILE C 278 " pdb=" CG1 ILE C 278 " pdb=" CG2 ILE C 278 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB ILE A 228 " pdb=" CA ILE A 228 " pdb=" CG1 ILE A 228 " pdb=" CG2 ILE A 228 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1954 not shown) Planarity restraints: 2206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 147 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.52e+00 pdb=" C GLU C 147 " -0.041 2.00e-02 2.50e+03 pdb=" O GLU C 147 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA C 148 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN C 349 " -0.038 5.00e-02 4.00e+02 5.60e-02 5.03e+00 pdb=" N PRO C 350 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 350 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 350 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 374 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO D 375 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 375 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 375 " 0.030 5.00e-02 4.00e+02 ... (remaining 2203 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 166 2.61 - 3.18: 9937 3.18 - 3.75: 19375 3.75 - 4.33: 25287 4.33 - 4.90: 43033 Nonbonded interactions: 97798 Sorted by model distance: nonbonded pdb=" OG SER A 180 " pdb="MG MG A 503 " model vdw 2.037 2.170 nonbonded pdb=" OG SER C 180 " pdb="MG MG C 503 " model vdw 2.038 2.170 nonbonded pdb=" F1 BEF C 502 " pdb="MG MG C 503 " model vdw 2.038 2.120 nonbonded pdb=" OG SER B 180 " pdb="MG MG B 503 " model vdw 2.038 2.170 nonbonded pdb=" O2B ADP A 501 " pdb="MG MG A 503 " model vdw 2.038 2.170 ... (remaining 97793 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 126 through 433) selection = (chain 'B' and resid 126 through 433) selection = (chain 'C' and resid 126 through 433) selection = (chain 'D' and resid 126 through 433) selection = (chain 'E' and resid 126 through 433) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.630 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5424 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 : 0.012 0.709 12740 Z= 1.112 Angle : 0.892 14.941 17223 Z= 0.451 Chirality : 0.048 0.282 1957 Planarity : 0.006 0.056 2206 Dihedral : 14.707 162.042 4830 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.78 (0.16), residues: 1574 helix: -2.38 (0.12), residues: 751 sheet: -2.34 (0.39), residues: 160 loop : -2.54 (0.21), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 251 TYR 0.008 0.001 TYR C 181 PHE 0.011 0.001 PHE A 308 TRP 0.010 0.001 TRP E 280 HIS 0.001 0.000 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.00467 (12737) covalent geometry : angle 0.89200 (17223) hydrogen bonds : bond 0.09906 ( 553) hydrogen bonds : angle 6.39954 ( 1614) Misc. bond : bond 0.70646 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 423 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLN cc_start: 0.6605 (mt0) cc_final: 0.6377 (tt0) REVERT: A 343 VAL cc_start: 0.7244 (t) cc_final: 0.6738 (t) REVERT: A 351 ILE cc_start: 0.6725 (mp) cc_final: 0.6225 (mm) REVERT: B 162 ASN cc_start: 0.6193 (m110) cc_final: 0.5773 (t0) REVERT: B 431 ASP cc_start: 0.6700 (m-30) cc_final: 0.6482 (m-30) REVERT: C 289 ARG cc_start: 0.4564 (mmt90) cc_final: 0.4098 (mpt180) REVERT: C 373 LEU cc_start: 0.7974 (mp) cc_final: 0.7662 (tp) REVERT: D 355 GLN cc_start: 0.6696 (mt0) cc_final: 0.6203 (tt0) REVERT: D 425 GLN cc_start: 0.5833 (mm-40) cc_final: 0.5476 (mt0) REVERT: E 157 HIS cc_start: 0.5602 (p90) cc_final: 0.5377 (p-80) REVERT: E 233 GLU cc_start: 0.7046 (mp0) cc_final: 0.6579 (mp0) outliers start: 0 outliers final: 0 residues processed: 423 average time/residue: 0.1282 time to fit residues: 74.0963 Evaluate side-chains 207 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.2980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.0870 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 355 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 ASN C 281 GLN C 311 ASN C 437 ASN D 265 ASN ** D 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.117467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.093594 restraints weight = 29495.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.094592 restraints weight = 22174.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.095509 restraints weight = 17221.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.095663 restraints weight = 13490.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.096075 restraints weight = 12774.554| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12740 Z= 0.149 Angle : 0.703 10.562 17223 Z= 0.340 Chirality : 0.043 0.214 1957 Planarity : 0.005 0.047 2206 Dihedral : 9.330 160.624 1756 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.29 % Allowed : 14.05 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.23 (0.19), residues: 1574 helix: -0.76 (0.17), residues: 799 sheet: -1.66 (0.41), residues: 160 loop : -2.29 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 325 TYR 0.014 0.002 TYR C 181 PHE 0.016 0.002 PHE D 432 TRP 0.019 0.002 TRP C 280 HIS 0.004 0.001 HIS C 359 Details of bonding type rmsd covalent geometry : bond 0.00330 (12737) covalent geometry : angle 0.70271 (17223) hydrogen bonds : bond 0.03323 ( 553) hydrogen bonds : angle 5.22556 ( 1614) Misc. bond : bond 0.00062 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 235 time to evaluate : 0.488 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: A 348 MET cc_start: 0.7514 (tpp) cc_final: 0.6841 (tpp) REVERT: B 308 PHE cc_start: 0.6566 (OUTLIER) cc_final: 0.6045 (t80) REVERT: B 330 MET cc_start: 0.8726 (mmt) cc_final: 0.8457 (mmm) REVERT: C 113 LYS cc_start: 0.6235 (pttm) cc_final: 0.5892 (mtmm) REVERT: C 259 GLN cc_start: 0.5888 (mm-40) cc_final: 0.3701 (mt0) REVERT: C 277 ASN cc_start: 0.5573 (m-40) cc_final: 0.5348 (m-40) REVERT: D 425 GLN cc_start: 0.6510 (mm-40) cc_final: 0.6112 (mt0) REVERT: E 233 GLU cc_start: 0.7091 (mp0) cc_final: 0.6637 (mp0) REVERT: E 386 MET cc_start: 0.5032 (OUTLIER) cc_final: 0.4739 (mtm) outliers start: 31 outliers final: 17 residues processed: 252 average time/residue: 0.0915 time to fit residues: 34.9793 Evaluate side-chains 201 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain G residue 6 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 17 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 155 optimal weight: 30.0000 chunk 16 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN B 355 GLN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 GLN D 359 HIS ** E 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.116373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.092190 restraints weight = 30213.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.092306 restraints weight = 21499.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.093133 restraints weight = 18899.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.093489 restraints weight = 16164.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.093564 restraints weight = 14314.287| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.9138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 12740 Z= 0.273 Angle : 0.909 9.209 17223 Z= 0.453 Chirality : 0.052 0.233 1957 Planarity : 0.006 0.076 2206 Dihedral : 9.184 134.441 1756 Min Nonbonded Distance : 1.690 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.55 % Allowed : 17.31 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.99 (0.20), residues: 1574 helix: -0.72 (0.18), residues: 768 sheet: -1.42 (0.43), residues: 148 loop : -1.94 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 304 TYR 0.029 0.004 TYR D 324 PHE 0.028 0.003 PHE C 432 TRP 0.033 0.003 TRP D 280 HIS 0.004 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00629 (12737) covalent geometry : angle 0.90893 (17223) hydrogen bonds : bond 0.05210 ( 553) hydrogen bonds : angle 5.91937 ( 1614) Misc. bond : bond 0.00132 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 178 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LYS cc_start: 0.6662 (mtpp) cc_final: 0.6456 (mtpp) REVERT: C 252 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8360 (tp) REVERT: D 123 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.8181 (mt) REVERT: D 260 MET cc_start: 0.6236 (mtp) cc_final: 0.5899 (mtm) REVERT: D 421 ASP cc_start: 0.7809 (t0) cc_final: 0.7338 (t0) REVERT: D 425 GLN cc_start: 0.8357 (mm-40) cc_final: 0.7968 (mm-40) outliers start: 48 outliers final: 21 residues processed: 214 average time/residue: 0.1148 time to fit residues: 35.6534 Evaluate side-chains 143 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain E residue 276 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 59 optimal weight: 0.6980 chunk 90 optimal weight: 8.9990 chunk 102 optimal weight: 0.3980 chunk 103 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 124 optimal weight: 20.0000 chunk 156 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 GLN E 281 GLN E 427 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.115474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.091389 restraints weight = 29404.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.090639 restraints weight = 23997.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.090896 restraints weight = 19338.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.091332 restraints weight = 18092.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.091465 restraints weight = 16994.489| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.9504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12740 Z= 0.131 Angle : 0.680 8.572 17223 Z= 0.329 Chirality : 0.045 0.340 1957 Planarity : 0.004 0.037 2206 Dihedral : 8.411 124.811 1756 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.29 % Allowed : 19.23 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.21), residues: 1574 helix: -0.02 (0.18), residues: 757 sheet: -1.52 (0.41), residues: 157 loop : -1.43 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 430 TYR 0.009 0.001 TYR A 181 PHE 0.019 0.002 PHE C 432 TRP 0.013 0.001 TRP C 388 HIS 0.002 0.000 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00288 (12737) covalent geometry : angle 0.67981 (17223) hydrogen bonds : bond 0.03307 ( 553) hydrogen bonds : angle 5.22306 ( 1614) Misc. bond : bond 0.00043 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 MET cc_start: 0.8045 (mpp) cc_final: 0.7822 (mpp) REVERT: B 386 MET cc_start: 0.3948 (ppp) cc_final: 0.2344 (ptt) REVERT: C 113 LYS cc_start: 0.6362 (pttm) cc_final: 0.6070 (mtmm) REVERT: C 260 MET cc_start: 0.8190 (ttm) cc_final: 0.7766 (mtt) REVERT: C 437 ASN cc_start: 0.6806 (t0) cc_final: 0.6427 (m110) REVERT: E 388 TRP cc_start: 0.6841 (p90) cc_final: 0.6379 (p-90) outliers start: 31 outliers final: 14 residues processed: 174 average time/residue: 0.1045 time to fit residues: 27.2807 Evaluate side-chains 131 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain G residue 6 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 108 optimal weight: 0.2980 chunk 22 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 147 optimal weight: 6.9990 chunk 5 optimal weight: 0.3980 chunk 127 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 1 optimal weight: 0.0370 chunk 43 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 overall best weight: 0.5462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN ** E 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.114846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.090142 restraints weight = 29704.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.089842 restraints weight = 23593.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.090215 restraints weight = 19466.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.090610 restraints weight = 17334.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.090750 restraints weight = 16354.434| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.9713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12740 Z= 0.119 Angle : 0.638 10.486 17223 Z= 0.307 Chirality : 0.044 0.380 1957 Planarity : 0.004 0.039 2206 Dihedral : 7.940 129.112 1756 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.14 % Allowed : 19.38 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.22), residues: 1574 helix: 0.25 (0.19), residues: 760 sheet: -1.48 (0.40), residues: 162 loop : -1.23 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 325 TYR 0.007 0.001 TYR B 295 PHE 0.013 0.001 PHE D 432 TRP 0.010 0.001 TRP C 388 HIS 0.003 0.001 HIS D 359 Details of bonding type rmsd covalent geometry : bond 0.00260 (12737) covalent geometry : angle 0.63803 (17223) hydrogen bonds : bond 0.03110 ( 553) hydrogen bonds : angle 5.09007 ( 1614) Misc. bond : bond 0.00031 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 MET cc_start: 0.5742 (ppp) cc_final: 0.5403 (ppp) REVERT: B 386 MET cc_start: 0.3444 (ppp) cc_final: 0.1974 (ptt) REVERT: C 113 LYS cc_start: 0.6319 (pttm) cc_final: 0.6004 (mtmm) REVERT: C 260 MET cc_start: 0.8259 (ttm) cc_final: 0.7841 (mtt) REVERT: C 437 ASN cc_start: 0.6792 (t0) cc_final: 0.6532 (m110) REVERT: E 388 TRP cc_start: 0.6663 (p90) cc_final: 0.6284 (p-90) outliers start: 29 outliers final: 21 residues processed: 147 average time/residue: 0.0956 time to fit residues: 21.7722 Evaluate side-chains 131 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain G residue 6 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 4 optimal weight: 0.3980 chunk 153 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 261 ASN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 GLN ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.110877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.084596 restraints weight = 29174.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.084868 restraints weight = 18294.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.085408 restraints weight = 15513.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.085760 restraints weight = 13802.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.085978 restraints weight = 12124.003| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 1.0277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12740 Z= 0.142 Angle : 0.655 9.290 17223 Z= 0.316 Chirality : 0.045 0.404 1957 Planarity : 0.004 0.044 2206 Dihedral : 7.783 133.691 1756 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.51 % Allowed : 19.38 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.22), residues: 1574 helix: 0.42 (0.19), residues: 769 sheet: -1.31 (0.41), residues: 165 loop : -1.01 (0.27), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 325 TYR 0.009 0.001 TYR B 295 PHE 0.012 0.001 PHE C 360 TRP 0.010 0.001 TRP C 388 HIS 0.004 0.001 HIS D 359 Details of bonding type rmsd covalent geometry : bond 0.00318 (12737) covalent geometry : angle 0.65525 (17223) hydrogen bonds : bond 0.03160 ( 553) hydrogen bonds : angle 5.13751 ( 1614) Misc. bond : bond 0.00040 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 0.385 Fit side-chains REVERT: B 386 MET cc_start: 0.4028 (ppp) cc_final: 0.2782 (ptt) REVERT: C 113 LYS cc_start: 0.6249 (pttm) cc_final: 0.5853 (mtmm) REVERT: C 260 MET cc_start: 0.8587 (ttm) cc_final: 0.8154 (mtt) REVERT: C 437 ASN cc_start: 0.7224 (t0) cc_final: 0.6777 (m110) REVERT: E 388 TRP cc_start: 0.6602 (p90) cc_final: 0.6258 (p-90) outliers start: 34 outliers final: 19 residues processed: 147 average time/residue: 0.0887 time to fit residues: 20.2595 Evaluate side-chains 125 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain G residue 6 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 53 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 68 optimal weight: 0.1980 chunk 129 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 HIS ** E 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.109019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.082572 restraints weight = 29213.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.082788 restraints weight = 19014.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.083773 restraints weight = 15243.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.084083 restraints weight = 12959.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.084229 restraints weight = 11690.627| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 1.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12740 Z= 0.154 Angle : 0.682 12.563 17223 Z= 0.326 Chirality : 0.045 0.366 1957 Planarity : 0.004 0.039 2206 Dihedral : 7.847 131.746 1756 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.44 % Allowed : 20.56 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.22), residues: 1574 helix: 0.49 (0.19), residues: 770 sheet: -1.26 (0.42), residues: 159 loop : -0.99 (0.26), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 287 TYR 0.010 0.001 TYR B 295 PHE 0.015 0.001 PHE C 195 TRP 0.012 0.001 TRP E 280 HIS 0.003 0.001 HIS D 359 Details of bonding type rmsd covalent geometry : bond 0.00354 (12737) covalent geometry : angle 0.68156 (17223) hydrogen bonds : bond 0.03301 ( 553) hydrogen bonds : angle 5.14123 ( 1614) Misc. bond : bond 0.00045 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.367 Fit side-chains REVERT: C 260 MET cc_start: 0.8732 (ttm) cc_final: 0.8185 (mtt) REVERT: C 437 ASN cc_start: 0.7483 (t0) cc_final: 0.6801 (m110) REVERT: E 348 MET cc_start: 0.7352 (ppp) cc_final: 0.7141 (mmt) REVERT: E 388 TRP cc_start: 0.6620 (p90) cc_final: 0.6103 (p-90) outliers start: 33 outliers final: 21 residues processed: 140 average time/residue: 0.0962 time to fit residues: 20.9424 Evaluate side-chains 121 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 129 ASN Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain G residue 6 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 83 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 2 optimal weight: 0.8980 chunk 57 optimal weight: 0.0980 chunk 118 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 GLN ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 HIS E 191 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.109692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.083371 restraints weight = 29444.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.082920 restraints weight = 21175.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.083745 restraints weight = 17513.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.084544 restraints weight = 14927.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.084713 restraints weight = 13112.581| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 1.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12740 Z= 0.127 Angle : 0.671 13.609 17223 Z= 0.319 Chirality : 0.044 0.380 1957 Planarity : 0.004 0.042 2206 Dihedral : 7.694 134.032 1756 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.70 % Allowed : 21.38 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.22), residues: 1574 helix: 0.65 (0.19), residues: 771 sheet: -1.11 (0.42), residues: 159 loop : -0.93 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 414 TYR 0.013 0.001 TYR C 181 PHE 0.019 0.001 PHE C 432 TRP 0.021 0.001 TRP D 388 HIS 0.004 0.001 HIS D 359 Details of bonding type rmsd covalent geometry : bond 0.00284 (12737) covalent geometry : angle 0.67086 (17223) hydrogen bonds : bond 0.03042 ( 553) hydrogen bonds : angle 5.02771 ( 1614) Misc. bond : bond 0.00032 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.543 Fit side-chains REVERT: C 260 MET cc_start: 0.8699 (ttm) cc_final: 0.8169 (mtt) REVERT: C 437 ASN cc_start: 0.7445 (t0) cc_final: 0.6823 (m110) REVERT: E 388 TRP cc_start: 0.6612 (p90) cc_final: 0.6241 (p-90) REVERT: E 401 LEU cc_start: 0.6090 (pt) cc_final: 0.5796 (tt) outliers start: 23 outliers final: 16 residues processed: 125 average time/residue: 0.0864 time to fit residues: 17.5427 Evaluate side-chains 119 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain G residue 6 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 120 optimal weight: 0.0370 chunk 80 optimal weight: 0.6980 chunk 71 optimal weight: 0.0030 chunk 137 optimal weight: 0.0870 chunk 87 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.2846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.111345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.085702 restraints weight = 29570.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.085536 restraints weight = 19096.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.086765 restraints weight = 15445.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.087353 restraints weight = 13065.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.087399 restraints weight = 12154.457| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 1.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12740 Z= 0.110 Angle : 0.658 12.260 17223 Z= 0.312 Chirality : 0.043 0.330 1957 Planarity : 0.004 0.042 2206 Dihedral : 7.418 131.181 1756 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.55 % Allowed : 21.23 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.22), residues: 1574 helix: 0.66 (0.19), residues: 789 sheet: -0.82 (0.42), residues: 162 loop : -0.81 (0.27), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 414 TYR 0.010 0.001 TYR C 181 PHE 0.017 0.001 PHE C 432 TRP 0.019 0.001 TRP D 388 HIS 0.005 0.001 HIS D 359 Details of bonding type rmsd covalent geometry : bond 0.00235 (12737) covalent geometry : angle 0.65801 (17223) hydrogen bonds : bond 0.02785 ( 553) hydrogen bonds : angle 4.90978 ( 1614) Misc. bond : bond 0.00017 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.550 Fit side-chains REVERT: A 257 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8024 (mm) REVERT: A 281 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7790 (pt0) REVERT: A 349 GLN cc_start: 0.8480 (tp40) cc_final: 0.8052 (tm-30) REVERT: C 260 MET cc_start: 0.8721 (ttm) cc_final: 0.8183 (mtt) REVERT: C 437 ASN cc_start: 0.7298 (t0) cc_final: 0.6717 (m110) REVERT: E 388 TRP cc_start: 0.6498 (p90) cc_final: 0.6252 (p-90) outliers start: 21 outliers final: 12 residues processed: 130 average time/residue: 0.0898 time to fit residues: 18.9946 Evaluate side-chains 120 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain G residue 6 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.6904 > 50: distance: 60 - 85: 22.533 distance: 67 - 90: 4.388 distance: 78 - 101: 4.684 distance: 81 - 85: 21.280 distance: 85 - 86: 13.052 distance: 86 - 87: 19.173 distance: 86 - 89: 27.225 distance: 87 - 88: 18.047 distance: 87 - 90: 20.781 distance: 90 - 91: 7.665 distance: 91 - 92: 11.828 distance: 91 - 94: 11.574 distance: 92 - 93: 12.230 distance: 92 - 101: 17.275 distance: 94 - 95: 28.485 distance: 95 - 96: 13.096 distance: 96 - 97: 17.856 distance: 97 - 98: 12.954 distance: 98 - 99: 18.815 distance: 98 - 100: 13.591 distance: 101 - 102: 13.659 distance: 102 - 103: 17.434 distance: 102 - 105: 30.074 distance: 103 - 104: 11.588 distance: 103 - 110: 34.229 distance: 105 - 106: 40.529 distance: 106 - 107: 13.470 distance: 107 - 108: 17.144 distance: 107 - 109: 8.128 distance: 110 - 111: 26.306 distance: 111 - 112: 24.531 distance: 111 - 114: 14.483 distance: 112 - 113: 12.112 distance: 112 - 118: 22.292 distance: 114 - 115: 25.829 distance: 115 - 116: 29.547 distance: 115 - 117: 38.625 distance: 118 - 119: 33.800 distance: 119 - 120: 7.471 distance: 119 - 122: 34.710 distance: 120 - 121: 43.024 distance: 120 - 127: 22.461 distance: 122 - 123: 45.229 distance: 123 - 124: 22.984 distance: 124 - 125: 32.649 distance: 125 - 126: 8.390 distance: 127 - 128: 18.412 distance: 127 - 133: 36.176 distance: 128 - 129: 40.595 distance: 128 - 131: 41.485 distance: 129 - 130: 47.937 distance: 129 - 134: 56.536 distance: 131 - 132: 17.927 distance: 132 - 133: 23.122 distance: 134 - 135: 20.454 distance: 135 - 136: 22.127 distance: 135 - 138: 42.644 distance: 136 - 137: 28.539 distance: 136 - 140: 17.426 distance: 138 - 139: 23.755 distance: 140 - 141: 14.291 distance: 141 - 142: 12.504 distance: 142 - 143: 17.134 distance: 142 - 148: 12.426 distance: 144 - 145: 24.656 distance: 144 - 146: 12.292 distance: 145 - 147: 24.893 distance: 149 - 150: 8.563 distance: 149 - 152: 9.348 distance: 150 - 151: 20.688 distance: 150 - 156: 5.210 distance: 152 - 153: 15.122 distance: 152 - 154: 24.121 distance: 153 - 155: 12.891 distance: 156 - 157: 10.139 distance: 157 - 158: 9.545 distance: 157 - 160: 4.107 distance: 158 - 159: 25.760 distance: 158 - 167: 6.000 distance: 160 - 161: 15.579 distance: 161 - 162: 4.869 distance: 161 - 163: 8.953 distance: 162 - 164: 12.673 distance: 163 - 165: 19.085 distance: 164 - 166: 12.407 distance: 165 - 166: 13.291