Starting phenix.real_space_refine on Fri Jan 17 18:05:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ag4_15415/01_2025/8ag4_15415.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ag4_15415/01_2025/8ag4_15415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ag4_15415/01_2025/8ag4_15415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ag4_15415/01_2025/8ag4_15415.map" model { file = "/net/cci-nas-00/data/ceres_data/8ag4_15415/01_2025/8ag4_15415.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ag4_15415/01_2025/8ag4_15415.cif" } resolution = 2.46 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= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 7118 2.51 5 N 1861 2.21 5 O 2120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 11155 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 4054 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 27, 'TRANS': 474} Chain: "B" Number of atoms: 4302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4302 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 25, 'TRANS': 513} Chain breaks: 2 Chain: "C" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1412 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1387 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 165} Time building chain proxies: 6.58, per 1000 atoms: 0.59 Number of scatterers: 11155 At special positions: 0 Unit cell: (114.395, 119.405, 112.725, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 2120 8.00 N 1861 7.00 C 7118 6.00 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=0, symmetry=0 Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 1.5 seconds 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2642 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 14 sheets defined 33.7% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.582A pdb=" N GLU A 50 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 78 Processing helix chain 'A' and resid 112 through 122 removed outlier: 3.606A pdb=" N ILE A 116 " --> pdb=" O GLY A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 135 Processing helix chain 'A' and resid 142 through 156 Processing helix chain 'A' and resid 179 through 197 Processing helix chain 'A' and resid 238 through 251 removed outlier: 3.770A pdb=" N THR A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 337 Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 377 through 393 removed outlier: 3.681A pdb=" N LEU A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 480 through 495 Processing helix chain 'A' and resid 510 through 519 Processing helix chain 'A' and resid 520 through 530 Processing helix chain 'B' and resid 29 through 49 Processing helix chain 'B' and resid 87 through 97 Processing helix chain 'B' and resid 106 through 122 Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 198 through 216 Processing helix chain 'B' and resid 217 through 222 Processing helix chain 'B' and resid 227 through 231 removed outlier: 3.657A pdb=" N LEU B 231 " --> pdb=" O PHE B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 227 through 231' Processing helix chain 'B' and resid 234 through 238 Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 324 through 326 No H-bonds generated for 'chain 'B' and resid 324 through 326' Processing helix chain 'B' and resid 349 through 351 No H-bonds generated for 'chain 'B' and resid 349 through 351' Processing helix chain 'B' and resid 352 through 356 removed outlier: 3.597A pdb=" N PHE B 355 " --> pdb=" O GLN B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 447 through 461 Processing helix chain 'B' and resid 466 through 470 removed outlier: 3.758A pdb=" N LYS B 469 " --> pdb=" O LYS B 466 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR B 470 " --> pdb=" O ASP B 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 466 through 470' Processing helix chain 'B' and resid 478 through 482 removed outlier: 3.538A pdb=" N LYS B 481 " --> pdb=" O PRO B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 500 removed outlier: 4.160A pdb=" N GLN B 488 " --> pdb=" O ASN B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 516 removed outlier: 3.504A pdb=" N TRP B 513 " --> pdb=" O GLN B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 537 removed outlier: 4.069A pdb=" N THR B 523 " --> pdb=" O PRO B 519 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS B 525 " --> pdb=" O GLU B 521 " (cutoff:3.500A) Proline residue: B 529 - end of helix removed outlier: 3.720A pdb=" N THR B 535 " --> pdb=" O SER B 531 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 536 " --> pdb=" O LYS B 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 229 Processing helix chain 'C' and resid 234 through 243 Processing helix chain 'C' and resid 246 through 251 removed outlier: 4.372A pdb=" N GLU C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 298 removed outlier: 3.790A pdb=" N LYS C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 229 removed outlier: 3.548A pdb=" N LYS D 227 " --> pdb=" O GLY D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 243 Processing helix chain 'D' and resid 281 through 299 Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 109 removed outlier: 6.643A pdb=" N VAL A 85 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLU A 107 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LEU A 83 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 260 through 262 removed outlier: 7.928A pdb=" N VAL A 394 " --> pdb=" O PRO A 415 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ARG A 399 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU A 347 " --> pdb=" O ARG A 399 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N THR A 401 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU A 345 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LYS A 260 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N LEU A 347 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LYS A 262 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N GLY A 349 " --> pdb=" O LYS A 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 300 through 304 Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 329 Processing sheet with id=AA5, first strand: chain 'A' and resid 375 through 376 Processing sheet with id=AA6, first strand: chain 'A' and resid 419 through 420 Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 84 removed outlier: 6.186A pdb=" N LEU B 56 " --> pdb=" O HIS B 80 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N HIS B 82 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ILE B 54 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ARG B 130 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N GLN B 162 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE B 132 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE B 164 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE B 134 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N TYR B 225 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE B 163 " --> pdb=" O TYR B 225 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 247 through 252 removed outlier: 6.572A pdb=" N VAL B 361 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N GLN B 360 " --> pdb=" O GLN B 423 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLN B 423 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ALA B 366 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N GLU B 417 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N VAL B 405 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N MET B 389 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL B 390 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE B 345 " --> pdb=" O VAL B 390 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE B 392 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N PHE B 340 " --> pdb=" O PRO B 248 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ARG B 250 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL B 342 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N THR B 252 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N GLY B 344 " --> pdb=" O THR B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 313 through 315 Processing sheet with id=AB1, first strand: chain 'B' and resid 464 through 465 Processing sheet with id=AB2, first strand: chain 'C' and resid 165 through 168 Processing sheet with id=AB3, first strand: chain 'C' and resid 231 through 232 removed outlier: 6.695A pdb=" N GLY C 205 " --> pdb=" O VAL C 217 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 165 through 168 Processing sheet with id=AB5, first strand: chain 'D' and resid 231 through 232 removed outlier: 6.468A pdb=" N GLY D 205 " --> pdb=" O VAL D 217 " (cutoff:3.500A) 471 hydrogen bonds defined for protein. 1287 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: 3.69 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3638 1.34 - 1.46: 1744 1.46 - 1.57: 5908 1.57 - 1.69: 0 1.69 - 1.81: 91 Bond restraints: 11381 Sorted by residual: bond pdb=" C THR B 524 " pdb=" O THR B 524 " ideal model delta sigma weight residual 1.237 1.250 -0.014 1.19e-02 7.06e+03 1.35e+00 bond pdb=" CA ILE B 528 " pdb=" C ILE B 528 " ideal model delta sigma weight residual 1.524 1.535 -0.011 1.05e-02 9.07e+03 1.03e+00 bond pdb=" CA ASN B 66 " pdb=" CB ASN B 66 " ideal model delta sigma weight residual 1.534 1.546 -0.013 1.30e-02 5.92e+03 9.65e-01 bond pdb=" C ASN D 328 " pdb=" N MET D 329 " ideal model delta sigma weight residual 1.331 1.351 -0.020 2.07e-02 2.33e+03 9.26e-01 bond pdb=" CG1 ILE A 116 " pdb=" CD1 ILE A 116 " ideal model delta sigma weight residual 1.513 1.478 0.035 3.90e-02 6.57e+02 7.99e-01 ... (remaining 11376 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 15175 1.80 - 3.60: 173 3.60 - 5.40: 18 5.40 - 7.20: 1 7.20 - 9.00: 1 Bond angle restraints: 15368 Sorted by residual: angle pdb=" N MET B 20 " pdb=" CA MET B 20 " pdb=" C MET B 20 " ideal model delta sigma weight residual 111.81 107.81 4.00 1.44e+00 4.82e-01 7.72e+00 angle pdb=" C GLN B 527 " pdb=" N ILE B 528 " pdb=" CA ILE B 528 " ideal model delta sigma weight residual 122.13 117.09 5.04 1.85e+00 2.92e-01 7.43e+00 angle pdb=" C ASN D 219 " pdb=" N HIS D 220 " pdb=" CA HIS D 220 " ideal model delta sigma weight residual 123.05 126.57 -3.52 1.57e+00 4.06e-01 5.02e+00 angle pdb=" CA LYS A 249 " pdb=" CB LYS A 249 " pdb=" CG LYS A 249 " ideal model delta sigma weight residual 114.10 118.19 -4.09 2.00e+00 2.50e-01 4.18e+00 angle pdb=" C TYR A 217 " pdb=" N ARG A 218 " pdb=" CA ARG A 218 " ideal model delta sigma weight residual 121.54 125.16 -3.62 1.91e+00 2.74e-01 3.59e+00 ... (remaining 15363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 6339 17.54 - 35.09: 492 35.09 - 52.63: 89 52.63 - 70.18: 24 70.18 - 87.72: 12 Dihedral angle restraints: 6956 sinusoidal: 2890 harmonic: 4066 Sorted by residual: dihedral pdb=" CA PHE D 246 " pdb=" C PHE D 246 " pdb=" N SER D 247 " pdb=" CA SER D 247 " ideal model delta harmonic sigma weight residual 180.00 -163.03 -16.97 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA THR D 242 " pdb=" C THR D 242 " pdb=" N ILE D 243 " pdb=" CA ILE D 243 " ideal model delta harmonic sigma weight residual -180.00 -163.19 -16.81 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CG ARG B 260 " pdb=" CD ARG B 260 " pdb=" NE ARG B 260 " pdb=" CZ ARG B 260 " ideal model delta sinusoidal sigma weight residual 180.00 135.49 44.51 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 6953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 938 0.027 - 0.053: 483 0.053 - 0.080: 169 0.080 - 0.107: 95 0.107 - 0.134: 37 Chirality restraints: 1722 Sorted by residual: chirality pdb=" CA ILE C 319 " pdb=" N ILE C 319 " pdb=" C ILE C 319 " pdb=" CB ILE C 319 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA HIS D 220 " pdb=" N HIS D 220 " pdb=" C HIS D 220 " pdb=" CB HIS D 220 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA VAL B 361 " pdb=" N VAL B 361 " pdb=" C VAL B 361 " pdb=" CB VAL B 361 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 1719 not shown) Planarity restraints: 1977 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 282 " 0.039 5.00e-02 4.00e+02 5.95e-02 5.66e+00 pdb=" N PRO A 283 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 103 " -0.011 2.00e-02 2.50e+03 1.02e-02 2.09e+00 pdb=" CG TYR A 103 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 103 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 103 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR A 103 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 103 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 103 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 103 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 369 " 0.024 5.00e-02 4.00e+02 3.59e-02 2.07e+00 pdb=" N PRO A 370 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " 0.020 5.00e-02 4.00e+02 ... (remaining 1974 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 340 2.72 - 3.26: 10367 3.26 - 3.81: 16871 3.81 - 4.35: 22089 4.35 - 4.90: 37223 Nonbonded interactions: 86890 Sorted by model distance: nonbonded pdb=" OH TYR D 169 " pdb=" OD1 ASP D 284 " model vdw 2.170 3.040 nonbonded pdb=" OG1 THR B 19 " pdb=" OG SER B 139 " model vdw 2.209 3.040 nonbonded pdb=" NZ LYS A 461 " pdb=" OE1 GLU A 524 " model vdw 2.213 3.120 nonbonded pdb=" OH TYR C 305 " pdb=" OD2 ASP D 259 " model vdw 2.218 3.040 nonbonded pdb=" OD1 ASN B 66 " pdb=" OG SER B 69 " model vdw 2.228 3.040 ... (remaining 86885 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 'C' and resid 162 through 331) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.060 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.470 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 39.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11381 Z= 0.219 Angle : 0.491 8.999 15368 Z= 0.262 Chirality : 0.041 0.134 1722 Planarity : 0.003 0.059 1977 Dihedral : 13.589 87.722 4314 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.23), residues: 1372 helix: 2.18 (0.27), residues: 382 sheet: 1.20 (0.33), residues: 250 loop : -0.66 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 247 HIS 0.006 0.001 HIS D 220 PHE 0.018 0.001 PHE B 409 TYR 0.025 0.001 TYR A 103 ARG 0.002 0.000 ARG B 354 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 1.505 Fit side-chains REVERT: A 333 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7539 (mt-10) REVERT: B 133 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8310 (mt-10) outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 1.5371 time to fit residues: 519.8200 Evaluate side-chains 294 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.0770 chunk 103 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 79 optimal weight: 0.3980 chunk 124 optimal weight: 1.9990 overall best weight: 0.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN A 163 HIS A 278 GLN B 22 ASN B 50 ASN B 269 GLN B 352 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.145228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.116897 restraints weight = 13937.369| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.93 r_work: 0.3385 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.0815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11381 Z= 0.228 Angle : 0.499 6.107 15368 Z= 0.266 Chirality : 0.042 0.136 1722 Planarity : 0.004 0.043 1977 Dihedral : 4.230 18.978 1489 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.51 % Allowed : 7.45 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.23), residues: 1372 helix: 2.07 (0.27), residues: 394 sheet: 1.09 (0.32), residues: 259 loop : -0.71 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 265 HIS 0.006 0.001 HIS D 220 PHE 0.019 0.001 PHE B 409 TYR 0.012 0.001 TYR A 103 ARG 0.006 0.000 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 294 time to evaluate : 1.516 Fit side-chains revert: symmetry clash REVERT: A 192 ASP cc_start: 0.7540 (m-30) cc_final: 0.7306 (m-30) REVERT: A 250 GLU cc_start: 0.7696 (pp20) cc_final: 0.7382 (pp20) REVERT: A 333 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7688 (mt-10) REVERT: A 516 LYS cc_start: 0.8133 (mptt) cc_final: 0.7886 (mptm) REVERT: B 133 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8019 (mt-10) REVERT: B 141 ARG cc_start: 0.8068 (ttp80) cc_final: 0.7867 (ttp80) outliers start: 19 outliers final: 11 residues processed: 295 average time/residue: 1.4119 time to fit residues: 445.5336 Evaluate side-chains 309 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 298 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 302 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 2 optimal weight: 0.8980 chunk 40 optimal weight: 0.0770 chunk 118 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 68 optimal weight: 30.0000 chunk 36 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 278 GLN B 22 ASN B 43 GLN B 50 ASN B 119 GLN B 352 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.145794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.116577 restraints weight = 14035.528| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.99 r_work: 0.3386 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11381 Z= 0.209 Angle : 0.475 5.894 15368 Z= 0.254 Chirality : 0.041 0.134 1722 Planarity : 0.003 0.038 1977 Dihedral : 4.190 18.420 1489 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.59 % Allowed : 9.12 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.23), residues: 1372 helix: 2.09 (0.27), residues: 394 sheet: 1.11 (0.32), residues: 259 loop : -0.70 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 247 HIS 0.005 0.001 HIS D 220 PHE 0.018 0.001 PHE B 409 TYR 0.008 0.001 TYR A 217 ARG 0.005 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 296 time to evaluate : 1.222 Fit side-chains revert: symmetry clash REVERT: A 192 ASP cc_start: 0.7550 (m-30) cc_final: 0.7316 (m-30) REVERT: A 333 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7633 (mt-10) REVERT: A 372 GLU cc_start: 0.7990 (tp30) cc_final: 0.7790 (mm-30) REVERT: B 133 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8096 (mt-10) REVERT: B 141 ARG cc_start: 0.8084 (ttp80) cc_final: 0.7872 (ttp80) REVERT: B 399 LYS cc_start: 0.8303 (mtpp) cc_final: 0.8090 (ttmm) REVERT: C 329 MET cc_start: 0.6306 (mmm) cc_final: 0.5773 (mmm) REVERT: D 321 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8490 (mtpp) outliers start: 20 outliers final: 9 residues processed: 299 average time/residue: 1.3731 time to fit residues: 441.3347 Evaluate side-chains 304 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 294 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 321 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 59 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 71 optimal weight: 0.0060 chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN A 278 GLN B 22 ASN ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN B 119 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.144480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.116114 restraints weight = 14023.109| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.94 r_work: 0.3359 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 11381 Z= 0.408 Angle : 0.560 7.678 15368 Z= 0.295 Chirality : 0.045 0.138 1722 Planarity : 0.004 0.037 1977 Dihedral : 4.520 18.298 1489 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.90 % Allowed : 10.55 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.23), residues: 1372 helix: 1.85 (0.26), residues: 393 sheet: 0.96 (0.32), residues: 273 loop : -0.78 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 247 HIS 0.007 0.001 HIS B 246 PHE 0.025 0.002 PHE B 409 TYR 0.013 0.002 TYR A 409 ARG 0.007 0.001 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 291 time to evaluate : 1.253 Fit side-chains REVERT: A 79 ASP cc_start: 0.7637 (t0) cc_final: 0.7393 (t0) REVERT: A 130 ARG cc_start: 0.7664 (ptp-110) cc_final: 0.7456 (ttm110) REVERT: A 172 GLU cc_start: 0.7464 (tp30) cc_final: 0.7123 (tp30) REVERT: A 192 ASP cc_start: 0.7593 (m-30) cc_final: 0.7358 (m-30) REVERT: A 333 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7815 (mt-10) REVERT: B 133 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8140 (mt-10) REVERT: B 141 ARG cc_start: 0.8136 (ttp80) cc_final: 0.7919 (ttp80) REVERT: B 457 LEU cc_start: 0.8605 (tp) cc_final: 0.8404 (tp) REVERT: C 329 MET cc_start: 0.6413 (mmm) cc_final: 0.5817 (mmm) outliers start: 24 outliers final: 13 residues processed: 295 average time/residue: 1.4144 time to fit residues: 447.2697 Evaluate side-chains 301 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 288 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 302 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 67 optimal weight: 0.0970 chunk 60 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN A 152 ASN A 163 HIS A 278 GLN B 22 ASN B 43 GLN B 50 ASN B 119 GLN B 269 GLN B 352 GLN ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.146121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.116548 restraints weight = 13875.802| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.05 r_work: 0.3364 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11381 Z= 0.263 Angle : 0.498 6.607 15368 Z= 0.266 Chirality : 0.042 0.143 1722 Planarity : 0.003 0.041 1977 Dihedral : 4.391 17.805 1489 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.74 % Allowed : 11.82 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.23), residues: 1372 helix: 1.98 (0.27), residues: 394 sheet: 1.07 (0.32), residues: 260 loop : -0.77 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 247 HIS 0.006 0.001 HIS D 220 PHE 0.021 0.001 PHE B 409 TYR 0.009 0.001 TYR A 71 ARG 0.008 0.000 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 286 time to evaluate : 1.315 Fit side-chains REVERT: A 91 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6593 (mm-30) REVERT: A 172 GLU cc_start: 0.7465 (tp30) cc_final: 0.7124 (tp30) REVERT: A 192 ASP cc_start: 0.7629 (m-30) cc_final: 0.7384 (m-30) REVERT: A 333 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7824 (mt-10) REVERT: B 141 ARG cc_start: 0.8127 (ttp80) cc_final: 0.7905 (ttp80) REVERT: B 457 LEU cc_start: 0.8581 (tp) cc_final: 0.8378 (tp) REVERT: C 329 MET cc_start: 0.6418 (mmm) cc_final: 0.5772 (mmm) outliers start: 22 outliers final: 15 residues processed: 290 average time/residue: 1.4307 time to fit residues: 443.0972 Evaluate side-chains 299 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 283 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 302 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 128 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 ASN B 43 GLN B 50 ASN B 119 GLN B 269 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.144806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.115400 restraints weight = 14079.656| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.02 r_work: 0.3344 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 11381 Z= 0.428 Angle : 0.572 7.591 15368 Z= 0.301 Chirality : 0.045 0.156 1722 Planarity : 0.004 0.037 1977 Dihedral : 4.593 17.909 1489 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.54 % Allowed : 12.05 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.23), residues: 1372 helix: 1.75 (0.26), residues: 393 sheet: 0.94 (0.31), residues: 273 loop : -0.84 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 247 HIS 0.007 0.001 HIS B 246 PHE 0.026 0.002 PHE B 409 TYR 0.013 0.002 TYR A 71 ARG 0.007 0.001 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 298 time to evaluate : 1.262 Fit side-chains REVERT: A 91 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6633 (mm-30) REVERT: A 172 GLU cc_start: 0.7493 (tp30) cc_final: 0.7136 (tp30) REVERT: A 192 ASP cc_start: 0.7634 (m-30) cc_final: 0.7391 (m-30) REVERT: A 333 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7860 (mt-10) REVERT: A 516 LYS cc_start: 0.8140 (mptt) cc_final: 0.7900 (mptm) REVERT: B 141 ARG cc_start: 0.8169 (ttp80) cc_final: 0.7943 (ttp80) REVERT: B 457 LEU cc_start: 0.8595 (tp) cc_final: 0.8381 (tp) REVERT: C 329 MET cc_start: 0.6424 (mmm) cc_final: 0.5777 (mmm) outliers start: 32 outliers final: 23 residues processed: 308 average time/residue: 1.4018 time to fit residues: 462.3137 Evaluate side-chains 317 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 293 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 302 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 72 optimal weight: 0.0020 chunk 40 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN A 163 HIS A 278 GLN B 6 ASN B 22 ASN B 43 GLN B 50 ASN B 119 GLN B 352 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.146588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.117182 restraints weight = 14051.788| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.06 r_work: 0.3371 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11381 Z= 0.206 Angle : 0.493 6.144 15368 Z= 0.264 Chirality : 0.041 0.152 1722 Planarity : 0.004 0.040 1977 Dihedral : 4.381 17.662 1489 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.98 % Allowed : 13.01 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.23), residues: 1372 helix: 2.02 (0.27), residues: 394 sheet: 1.06 (0.32), residues: 258 loop : -0.79 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 247 HIS 0.005 0.001 HIS D 220 PHE 0.020 0.001 PHE B 409 TYR 0.008 0.001 TYR A 71 ARG 0.010 0.000 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 286 time to evaluate : 1.231 Fit side-chains REVERT: A 91 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6600 (mm-30) REVERT: A 172 GLU cc_start: 0.7456 (tp30) cc_final: 0.7110 (tp30) REVERT: A 333 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7822 (mt-10) REVERT: B 141 ARG cc_start: 0.8062 (ttp80) cc_final: 0.7845 (ttp80) REVERT: B 457 LEU cc_start: 0.8574 (tp) cc_final: 0.8353 (tp) REVERT: C 329 MET cc_start: 0.6409 (mmm) cc_final: 0.5748 (mmm) REVERT: D 321 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8503 (mtpp) outliers start: 25 outliers final: 18 residues processed: 294 average time/residue: 1.4061 time to fit residues: 442.2765 Evaluate side-chains 302 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 282 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 527 GLN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 321 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- 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: 71.7875 > 50: distance: 53 - 93: 33.548 distance: 56 - 90: 32.207 distance: 77 - 82: 34.106 distance: 82 - 83: 20.932 distance: 82 - 156: 34.535 distance: 83 - 84: 12.942 distance: 83 - 86: 41.187 distance: 84 - 85: 51.683 distance: 84 - 90: 23.701 distance: 85 - 153: 32.506 distance: 86 - 87: 13.949 distance: 87 - 88: 40.090 distance: 87 - 89: 54.222 distance: 91 - 92: 56.624 distance: 92 - 97: 39.326 distance: 94 - 95: 37.801 distance: 94 - 96: 3.059 distance: 97 - 98: 39.806 distance: 97 - 142: 69.147 distance: 98 - 99: 41.280 distance: 99 - 100: 39.970 distance: 100 - 139: 66.397 distance: 101 - 102: 40.422 distance: 102 - 103: 39.282 distance: 102 - 105: 55.961 distance: 103 - 104: 16.792 distance: 103 - 109: 14.248 distance: 105 - 106: 39.166 distance: 106 - 107: 4.012 distance: 106 - 108: 38.516 distance: 109 - 110: 22.313 distance: 110 - 111: 39.953 distance: 113 - 114: 40.060 distance: 113 - 115: 39.267 distance: 116 - 117: 38.737 distance: 117 - 118: 50.758 distance: 117 - 120: 56.216 distance: 118 - 119: 32.407 distance: 118 - 125: 39.573 distance: 120 - 121: 40.990 distance: 122 - 123: 40.484 distance: 125 - 126: 56.300 distance: 125 - 131: 15.188 distance: 126 - 129: 39.200 distance: 130 - 131: 26.423 distance: 132 - 133: 20.736 distance: 132 - 138: 40.497 distance: 133 - 134: 56.857 distance: 133 - 136: 39.292 distance: 134 - 139: 39.739 distance: 136 - 137: 39.596 distance: 137 - 138: 40.114 distance: 139 - 140: 32.918 distance: 140 - 141: 24.576 distance: 140 - 143: 31.676 distance: 141 - 142: 40.274 distance: 141 - 146: 42.663 distance: 143 - 144: 50.585 distance: 143 - 145: 36.385 distance: 146 - 147: 42.413 distance: 147 - 148: 39.697 distance: 147 - 150: 38.893 distance: 148 - 149: 26.763 distance: 148 - 153: 35.392 distance: 150 - 151: 7.371 distance: 150 - 152: 40.337