Starting phenix.real_space_refine on Sat May 10 13:58:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w9i_32367/05_2025/7w9i_32367.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w9i_32367/05_2025/7w9i_32367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w9i_32367/05_2025/7w9i_32367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w9i_32367/05_2025/7w9i_32367.map" model { file = "/net/cci-nas-00/data/ceres_data/7w9i_32367/05_2025/7w9i_32367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w9i_32367/05_2025/7w9i_32367.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.076 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 37 5.16 5 C 4101 2.51 5 N 1066 2.21 5 O 1208 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6412 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "E" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1542 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 183} Time building chain proxies: 4.54, per 1000 atoms: 0.71 Number of scatterers: 6412 At special positions: 0 Unit cell: (91.812, 84.161, 119.137, 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 37 16.00 O 1208 8.00 N 1066 7.00 C 4101 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 944.7 milliseconds 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1488 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 6 sheets defined 48.3% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 20 through 34 removed outlier: 3.711A pdb=" N LYS A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 53 removed outlier: 3.577A pdb=" N TYR A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 80 removed outlier: 3.667A pdb=" N ASN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET A 62 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.655A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 4.122A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.552A pdb=" N SER A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 152 removed outlier: 3.508A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 147 through 152' Processing helix chain 'A' and resid 158 through 167 removed outlier: 3.831A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 removed outlier: 3.923A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 removed outlier: 3.683A pdb=" N ARG A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 248 removed outlier: 3.589A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N HIS A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.829A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 297 removed outlier: 3.607A pdb=" N MET A 297 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 removed outlier: 4.188A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.979A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 324 through 331' Processing helix chain 'A' and resid 368 through 378 removed outlier: 3.609A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.536A pdb=" N ALA A 387 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.668A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 removed outlier: 3.720A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 400 through 405' Processing helix chain 'A' and resid 431 through 444 removed outlier: 3.700A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 464 removed outlier: 3.650A pdb=" N LEU A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 482 removed outlier: 4.040A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N MET A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 515 Processing helix chain 'A' and resid 516 through 533 removed outlier: 3.671A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN A 526 " --> pdb=" O GLN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.668A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.696A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.925A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 598 removed outlier: 3.623A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 removed outlier: 4.001A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 370 removed outlier: 3.766A pdb=" N TYR E 369 " --> pdb=" O TYR E 365 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN E 370 " --> pdb=" O SER E 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 365 through 370' Processing helix chain 'E' and resid 385 through 389 removed outlier: 3.897A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP E 389 " --> pdb=" O LYS E 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 385 through 389' Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.621A pdb=" N SER E 443 " --> pdb=" O ASN E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 506 removed outlier: 3.530A pdb=" N TYR E 505 " --> pdb=" O GLY E 502 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN E 506 " --> pdb=" O VAL E 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 502 through 506' Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 removed outlier: 4.638A pdb=" N VAL A 132 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 142 " --> pdb=" O VAL A 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.409A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.200A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.528A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474 197 hydrogen bonds defined for protein. 543 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.81 Time building geometry restraints manager: 1.80 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: 2065 1.34 - 1.46: 1673 1.46 - 1.58: 2796 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6592 Sorted by residual: bond pdb=" C VAL A 488 " pdb=" N GLU A 489 " ideal model delta sigma weight residual 1.331 1.279 0.052 2.07e-02 2.33e+03 6.20e+00 bond pdb=" C LYS E 478 " pdb=" N PRO E 479 " ideal model delta sigma weight residual 1.338 1.364 -0.026 1.90e-02 2.77e+03 1.80e+00 bond pdb=" C ARG A 177 " pdb=" N PRO A 178 " ideal model delta sigma weight residual 1.336 1.351 -0.015 1.25e-02 6.40e+03 1.49e+00 bond pdb=" C ASP A 499 " pdb=" N PRO A 500 " ideal model delta sigma weight residual 1.336 1.351 -0.015 1.25e-02 6.40e+03 1.44e+00 bond pdb=" CB VAL A 581 " pdb=" CG2 VAL A 581 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.43e+00 ... (remaining 6587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 8819 2.36 - 4.71: 118 4.71 - 7.07: 13 7.07 - 9.43: 6 9.43 - 11.79: 2 Bond angle restraints: 8958 Sorted by residual: angle pdb=" C LYS E 478 " pdb=" N PRO E 479 " pdb=" CA PRO E 479 " ideal model delta sigma weight residual 127.00 138.79 -11.79 2.40e+00 1.74e-01 2.41e+01 angle pdb=" C LYS E 478 " pdb=" N PRO E 479 " pdb=" CD PRO E 479 " ideal model delta sigma weight residual 120.60 111.48 9.12 2.20e+00 2.07e-01 1.72e+01 angle pdb=" N ARG A 582 " pdb=" CA ARG A 582 " pdb=" C ARG A 582 " ideal model delta sigma weight residual 109.81 117.59 -7.78 2.21e+00 2.05e-01 1.24e+01 angle pdb=" N ASP A 499 " pdb=" CA ASP A 499 " pdb=" C ASP A 499 " ideal model delta sigma weight residual 109.81 116.86 -7.05 2.21e+00 2.05e-01 1.02e+01 angle pdb=" CA LEU A 143 " pdb=" CB LEU A 143 " pdb=" CG LEU A 143 " ideal model delta sigma weight residual 116.30 126.28 -9.98 3.50e+00 8.16e-02 8.13e+00 ... (remaining 8953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 3450 17.85 - 35.71: 365 35.71 - 53.56: 58 53.56 - 71.41: 15 71.41 - 89.27: 5 Dihedral angle restraints: 3893 sinusoidal: 1573 harmonic: 2320 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 134.75 -41.75 1 1.00e+01 1.00e-02 2.44e+01 dihedral pdb=" CA CYS A 344 " pdb=" C CYS A 344 " pdb=" N HIS A 345 " pdb=" CA HIS A 345 " ideal model delta harmonic sigma weight residual 180.00 158.21 21.79 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA LEU E 461 " pdb=" C LEU E 461 " pdb=" N LYS E 462 " pdb=" CA LYS E 462 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 3890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 744 0.056 - 0.111: 166 0.111 - 0.167: 22 0.167 - 0.222: 1 0.222 - 0.278: 1 Chirality restraints: 934 Sorted by residual: chirality pdb=" CB ILE A 291 " pdb=" CA ILE A 291 " pdb=" CG1 ILE A 291 " pdb=" CG2 ILE A 291 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CB VAL A 364 " pdb=" CA VAL A 364 " pdb=" CG1 VAL A 364 " pdb=" CG2 VAL A 364 " both_signs ideal model delta sigma weight residual False -2.63 -2.80 0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" CB VAL E 350 " pdb=" CA VAL E 350 " pdb=" CG1 VAL E 350 " pdb=" CG2 VAL E 350 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.55e-01 ... (remaining 931 not shown) Planarity restraints: 1165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 582 " 0.044 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO A 583 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 234 " 0.042 5.00e-02 4.00e+02 6.23e-02 6.21e+00 pdb=" N PRO A 235 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 520 " 0.040 5.00e-02 4.00e+02 6.02e-02 5.80e+00 pdb=" N PRO E 521 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO E 521 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 521 " 0.033 5.00e-02 4.00e+02 ... (remaining 1162 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1967 2.81 - 3.33: 5129 3.33 - 3.86: 10439 3.86 - 4.38: 12633 4.38 - 4.90: 21601 Nonbonded interactions: 51769 Sorted by model distance: nonbonded pdb=" O ALA A 501 " pdb=" OG SER A 507 " model vdw 2.289 3.040 nonbonded pdb=" OD1 ASP A 543 " pdb=" OG SER A 545 " model vdw 2.319 3.040 nonbonded pdb=" OG SER A 170 " pdb=" OE1 GLU A 171 " model vdw 2.344 3.040 nonbonded pdb=" OG SER E 371 " pdb=" OG SER E 373 " model vdw 2.348 3.040 nonbonded pdb=" OD1 ASP A 382 " pdb=" OH TYR A 385 " model vdw 2.360 3.040 ... (remaining 51764 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.410 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.570 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 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 : 0.005 0.052 6599 Z= 0.195 Angle : 0.725 11.787 8972 Z= 0.383 Chirality : 0.049 0.278 934 Planarity : 0.006 0.065 1165 Dihedral : 14.898 89.268 2384 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -5.48 (0.21), residues: 787 helix: -4.83 (0.08), residues: 351 sheet: -2.24 (0.72), residues: 49 loop : -2.53 (0.25), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 566 HIS 0.004 0.001 HIS E 519 PHE 0.015 0.002 PHE A 452 TYR 0.025 0.002 TYR E 453 ARG 0.007 0.000 ARG A 518 Details of bonding type rmsd hydrogen bonds : bond 0.31511 ( 197) hydrogen bonds : angle 11.66894 ( 543) SS BOND : bond 0.00315 ( 7) SS BOND : angle 1.33237 ( 14) covalent geometry : bond 0.00457 ( 6592) covalent geometry : angle 0.72358 ( 8958) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: A 50 TYR cc_start: 0.8635 (t80) cc_final: 0.8433 (t80) REVERT: A 62 MET cc_start: 0.7878 (ptm) cc_final: 0.7601 (ptm) REVERT: A 255 TYR cc_start: 0.7287 (m-80) cc_final: 0.7075 (m-10) REVERT: A 375 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7260 (mm-30) REVERT: A 398 GLU cc_start: 0.8189 (pt0) cc_final: 0.7875 (pt0) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2140 time to fit residues: 34.4439 Evaluate side-chains 86 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.0040 chunk 45 optimal weight: 0.3980 chunk 70 optimal weight: 0.5980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 58 ASN A 81 GLN A 89 GLN A 96 GLN A 103 ASN A 373 HIS A 378 HIS E 474 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.184724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.152927 restraints weight = 7915.386| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.11 r_work: 0.3504 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6599 Z= 0.121 Angle : 0.517 7.249 8972 Z= 0.262 Chirality : 0.042 0.156 934 Planarity : 0.005 0.044 1165 Dihedral : 4.375 17.247 861 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.30 % Allowed : 11.10 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -3.85 (0.25), residues: 787 helix: -3.21 (0.19), residues: 354 sheet: -1.55 (0.72), residues: 47 loop : -1.92 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 566 HIS 0.003 0.001 HIS A 505 PHE 0.014 0.001 PHE E 377 TYR 0.018 0.001 TYR A 202 ARG 0.004 0.000 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.04138 ( 197) hydrogen bonds : angle 5.53994 ( 543) SS BOND : bond 0.00277 ( 7) SS BOND : angle 0.76031 ( 14) covalent geometry : bond 0.00273 ( 6592) covalent geometry : angle 0.51675 ( 8958) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.8088 (tmm) cc_final: 0.7882 (tmm) REVERT: A 255 TYR cc_start: 0.7578 (m-80) cc_final: 0.7301 (m-10) REVERT: A 332 MET cc_start: 0.8552 (ttp) cc_final: 0.7442 (ttp) REVERT: A 375 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7249 (mm-30) REVERT: A 398 GLU cc_start: 0.8434 (pt0) cc_final: 0.8173 (pt0) REVERT: A 479 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7535 (tm-30) REVERT: E 452 ARG cc_start: 0.8369 (mtm-85) cc_final: 0.8144 (mtm180) REVERT: E 508 TYR cc_start: 0.8483 (m-80) cc_final: 0.7827 (m-80) outliers start: 9 outliers final: 5 residues processed: 107 average time/residue: 0.1516 time to fit residues: 22.9995 Evaluate side-chains 90 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 519 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 67 optimal weight: 0.0570 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.184129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.151931 restraints weight = 8001.419| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.08 r_work: 0.3461 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6599 Z= 0.126 Angle : 0.503 7.126 8972 Z= 0.250 Chirality : 0.042 0.149 934 Planarity : 0.004 0.036 1165 Dihedral : 4.105 16.291 861 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.59 % Allowed : 12.54 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.27), residues: 787 helix: -2.15 (0.24), residues: 352 sheet: -1.42 (0.67), residues: 47 loop : -1.62 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 566 HIS 0.003 0.001 HIS E 519 PHE 0.012 0.001 PHE E 377 TYR 0.017 0.001 TYR A 202 ARG 0.005 0.000 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 197) hydrogen bonds : angle 4.87871 ( 543) SS BOND : bond 0.00292 ( 7) SS BOND : angle 0.75513 ( 14) covalent geometry : bond 0.00293 ( 6592) covalent geometry : angle 0.50221 ( 8958) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.767 Fit side-chains REVERT: A 157 ASP cc_start: 0.7347 (t0) cc_final: 0.7076 (t0) REVERT: A 255 TYR cc_start: 0.7611 (m-80) cc_final: 0.7379 (m-10) REVERT: A 332 MET cc_start: 0.8654 (ttp) cc_final: 0.7833 (ttp) REVERT: A 375 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7540 (mm-30) REVERT: A 398 GLU cc_start: 0.8487 (pt0) cc_final: 0.8192 (pt0) REVERT: A 479 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7513 (tm-30) REVERT: E 508 TYR cc_start: 0.8474 (m-80) cc_final: 0.7835 (m-80) outliers start: 11 outliers final: 8 residues processed: 98 average time/residue: 0.1554 time to fit residues: 21.7542 Evaluate side-chains 93 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 519 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 0.5980 chunk 24 optimal weight: 8.9990 chunk 63 optimal weight: 0.0980 chunk 13 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 71 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.180694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.148809 restraints weight = 7885.835| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.04 r_work: 0.3472 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6599 Z= 0.114 Angle : 0.493 7.377 8972 Z= 0.240 Chirality : 0.042 0.124 934 Planarity : 0.003 0.035 1165 Dihedral : 3.929 14.999 861 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.59 % Allowed : 14.84 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.28), residues: 787 helix: -1.54 (0.26), residues: 356 sheet: -1.37 (0.68), residues: 50 loop : -1.38 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 566 HIS 0.002 0.001 HIS E 519 PHE 0.008 0.001 PHE A 369 TYR 0.016 0.001 TYR A 202 ARG 0.004 0.000 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.03248 ( 197) hydrogen bonds : angle 4.48544 ( 543) SS BOND : bond 0.00245 ( 7) SS BOND : angle 0.67984 ( 14) covalent geometry : bond 0.00264 ( 6592) covalent geometry : angle 0.49260 ( 8958) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.744 Fit side-chains REVERT: A 157 ASP cc_start: 0.7313 (t0) cc_final: 0.7021 (t0) REVERT: A 255 TYR cc_start: 0.7594 (m-80) cc_final: 0.7356 (m-10) REVERT: A 332 MET cc_start: 0.8625 (ttp) cc_final: 0.7423 (ttp) REVERT: A 375 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7468 (mm-30) REVERT: A 398 GLU cc_start: 0.8523 (pt0) cc_final: 0.8176 (pt0) REVERT: A 479 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7433 (tm-30) REVERT: E 508 TYR cc_start: 0.8435 (m-80) cc_final: 0.7809 (m-80) outliers start: 11 outliers final: 9 residues processed: 96 average time/residue: 0.1658 time to fit residues: 22.5345 Evaluate side-chains 95 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 519 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 3.9990 chunk 26 optimal weight: 0.0470 chunk 22 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 0.1980 chunk 42 optimal weight: 0.9990 chunk 46 optimal weight: 0.2980 chunk 50 optimal weight: 0.5980 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.186012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.153372 restraints weight = 7953.879| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.99 r_work: 0.3516 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6599 Z= 0.098 Angle : 0.473 7.745 8972 Z= 0.230 Chirality : 0.041 0.120 934 Planarity : 0.003 0.036 1165 Dihedral : 3.748 13.987 861 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.16 % Allowed : 15.42 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.29), residues: 787 helix: -1.14 (0.27), residues: 361 sheet: -1.09 (0.69), residues: 50 loop : -1.18 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 566 HIS 0.002 0.001 HIS A 505 PHE 0.008 0.001 PHE A 369 TYR 0.021 0.001 TYR A 202 ARG 0.004 0.000 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.03011 ( 197) hydrogen bonds : angle 4.27342 ( 543) SS BOND : bond 0.00201 ( 7) SS BOND : angle 0.64291 ( 14) covalent geometry : bond 0.00225 ( 6592) covalent geometry : angle 0.47290 ( 8958) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.669 Fit side-chains REVERT: A 119 ILE cc_start: 0.7013 (OUTLIER) cc_final: 0.6594 (tp) REVERT: A 157 ASP cc_start: 0.7325 (t0) cc_final: 0.7116 (t0) REVERT: A 332 MET cc_start: 0.8596 (ttp) cc_final: 0.7406 (ttp) REVERT: A 375 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7418 (mm-30) REVERT: A 479 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7332 (tm-30) REVERT: E 506 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8586 (mm-40) outliers start: 15 outliers final: 10 residues processed: 98 average time/residue: 0.1585 time to fit residues: 21.8060 Evaluate side-chains 93 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 519 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 54 optimal weight: 0.0000 chunk 71 optimal weight: 1.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.181108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.149407 restraints weight = 7766.948| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.02 r_work: 0.3484 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6599 Z= 0.115 Angle : 0.487 7.414 8972 Z= 0.237 Chirality : 0.042 0.120 934 Planarity : 0.003 0.041 1165 Dihedral : 3.781 15.056 861 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.02 % Allowed : 15.71 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.29), residues: 787 helix: -0.88 (0.28), residues: 360 sheet: -0.96 (0.70), residues: 50 loop : -1.12 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 566 HIS 0.002 0.001 HIS E 519 PHE 0.010 0.001 PHE A 369 TYR 0.012 0.001 TYR E 453 ARG 0.003 0.000 ARG A 518 Details of bonding type rmsd hydrogen bonds : bond 0.03037 ( 197) hydrogen bonds : angle 4.23392 ( 543) SS BOND : bond 0.00242 ( 7) SS BOND : angle 0.69124 ( 14) covalent geometry : bond 0.00270 ( 6592) covalent geometry : angle 0.48704 ( 8958) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.720 Fit side-chains REVERT: A 119 ILE cc_start: 0.7015 (OUTLIER) cc_final: 0.6556 (tp) REVERT: A 332 MET cc_start: 0.8613 (ttp) cc_final: 0.7451 (ttp) REVERT: A 375 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7448 (mm-30) REVERT: A 479 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7372 (tm-30) REVERT: E 506 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8556 (mm-40) outliers start: 14 outliers final: 11 residues processed: 92 average time/residue: 0.1588 time to fit residues: 20.8858 Evaluate side-chains 93 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 519 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 50 optimal weight: 0.0070 chunk 13 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.181519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.149700 restraints weight = 7901.355| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.92 r_work: 0.3488 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6599 Z= 0.140 Angle : 0.513 7.490 8972 Z= 0.248 Chirality : 0.042 0.121 934 Planarity : 0.003 0.046 1165 Dihedral : 3.911 15.084 861 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.74 % Allowed : 15.71 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.29), residues: 787 helix: -0.80 (0.28), residues: 365 sheet: -0.61 (0.71), residues: 47 loop : -1.13 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 566 HIS 0.003 0.001 HIS E 519 PHE 0.011 0.001 PHE A 369 TYR 0.017 0.001 TYR A 202 ARG 0.003 0.000 ARG A 518 Details of bonding type rmsd hydrogen bonds : bond 0.03174 ( 197) hydrogen bonds : angle 4.30736 ( 543) SS BOND : bond 0.00309 ( 7) SS BOND : angle 0.75737 ( 14) covalent geometry : bond 0.00332 ( 6592) covalent geometry : angle 0.51269 ( 8958) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.684 Fit side-chains REVERT: A 22 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: A 119 ILE cc_start: 0.7080 (OUTLIER) cc_final: 0.6576 (tp) REVERT: A 323 MET cc_start: 0.7741 (mmm) cc_final: 0.7016 (tpp) REVERT: A 332 MET cc_start: 0.8708 (ttp) cc_final: 0.7533 (ttp) REVERT: A 375 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7602 (mm-30) REVERT: A 479 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7577 (tm-30) REVERT: E 506 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8677 (mm-40) outliers start: 19 outliers final: 14 residues processed: 96 average time/residue: 0.1493 time to fit residues: 20.4970 Evaluate side-chains 97 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 519 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.1707 > 50: distance: 101 - 129: 16.059 distance: 109 - 137: 29.224 distance: 123 - 129: 16.880 distance: 129 - 130: 12.518 distance: 130 - 131: 27.527 distance: 130 - 133: 33.298 distance: 131 - 132: 31.300 distance: 131 - 137: 36.672 distance: 133 - 134: 42.274 distance: 134 - 135: 20.008 distance: 134 - 136: 21.499 distance: 137 - 138: 19.438 distance: 138 - 139: 13.805 distance: 138 - 141: 32.331 distance: 139 - 140: 9.771 distance: 139 - 148: 54.855 distance: 141 - 142: 10.118 distance: 142 - 143: 5.556 distance: 143 - 144: 27.583 distance: 144 - 145: 45.551 distance: 145 - 146: 45.950 distance: 145 - 147: 50.154 distance: 148 - 149: 56.431 distance: 149 - 150: 44.940 distance: 149 - 152: 48.490 distance: 150 - 151: 11.981 distance: 150 - 156: 29.653 distance: 152 - 153: 21.488 distance: 153 - 154: 14.348 distance: 153 - 155: 20.710 distance: 156 - 157: 39.975 distance: 157 - 158: 24.328 distance: 158 - 159: 17.834 distance: 158 - 160: 23.578 distance: 160 - 161: 28.361 distance: 161 - 162: 10.554 distance: 161 - 164: 36.897 distance: 162 - 169: 35.833 distance: 164 - 165: 35.146 distance: 165 - 166: 27.679 distance: 166 - 167: 8.991 distance: 167 - 168: 7.937 distance: 169 - 170: 39.922 distance: 170 - 171: 18.222 distance: 170 - 173: 60.259 distance: 171 - 172: 19.047 distance: 171 - 175: 48.410 distance: 173 - 174: 45.254 distance: 175 - 176: 56.887 distance: 176 - 177: 27.478 distance: 176 - 179: 32.065 distance: 177 - 178: 44.306 distance: 177 - 184: 25.086 distance: 179 - 180: 27.477 distance: 180 - 181: 33.310 distance: 181 - 182: 7.161 distance: 181 - 183: 7.891 distance: 184 - 185: 57.590 distance: 184 - 190: 27.863 distance: 185 - 186: 38.384 distance: 185 - 188: 26.545 distance: 186 - 187: 25.370 distance: 186 - 191: 26.029 distance: 187 - 220: 14.790 distance: 188 - 189: 16.820 distance: 189 - 190: 41.278 distance: 191 - 192: 25.841 distance: 192 - 193: 7.331 distance: 192 - 195: 23.231 distance: 193 - 194: 11.649 distance: 193 - 205: 14.518 distance: 194 - 225: 15.516 distance: 195 - 196: 10.979 distance: 196 - 197: 10.918 distance: 196 - 198: 12.275 distance: 197 - 199: 16.501 distance: 198 - 200: 27.764 distance: 198 - 201: 14.007 distance: 199 - 200: 20.417 distance: 200 - 202: 36.414 distance: 201 - 203: 27.078 distance: 202 - 204: 25.031 distance: 203 - 204: 35.658 distance: 205 - 206: 23.358 distance: 206 - 207: 25.332 distance: 206 - 209: 15.139 distance: 207 - 208: 16.606 distance: 207 - 212: 13.652 distance: 208 - 232: 24.114 distance: 209 - 210: 12.511 distance: 209 - 211: 41.972