Starting phenix.real_space_refine on Sat Aug 23 08:00:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xqw_33402/08_2025/7xqw_33402.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xqw_33402/08_2025/7xqw_33402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xqw_33402/08_2025/7xqw_33402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xqw_33402/08_2025/7xqw_33402.map" model { file = "/net/cci-nas-00/data/ceres_data/7xqw_33402/08_2025/7xqw_33402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xqw_33402/08_2025/7xqw_33402.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 sd= 0.416 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians W 1 12.54 5 Fe 20 7.16 5 P 5 5.49 5 S 85 5.16 5 C 6478 2.51 5 N 1847 2.21 5 O 1955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10391 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 6070 Classifications: {'peptide': 790} Link IDs: {'PTRANS': 46, 'TRANS': 743} Chain: "B" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4155 Classifications: {'peptide': 541} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 512} Chain: "A" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {' W': 1, 'FES': 1, 'MGD': 2, 'SF4': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {'FES': 1, 'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2823 SG CYS A 436 38.796 41.161 97.901 1.00 30.06 S ATOM 265 SG CYS A 102 49.846 56.059 57.111 1.00 6.05 S ATOM 366 SG CYS A 115 50.188 58.413 56.214 1.00 5.19 S ATOM 388 SG CYS A 118 54.459 56.843 55.167 1.00 6.36 S ATOM 490 SG CYS A 132 53.154 54.080 57.928 1.00 6.68 S ATOM 1137 SG CYS A 216 44.284 58.289 60.773 1.00 5.04 S ATOM 1114 SG CYS A 213 37.999 59.406 59.077 1.00 4.73 S ATOM 1497 SG CYS A 266 41.040 61.341 64.716 1.00 4.47 S ATOM 1159 SG CYS A 219 39.339 55.080 63.198 1.00 4.82 S ATOM 1470 SG CYS A 262 38.075 55.629 69.657 1.00 4.49 S ATOM 1433 SG CYS A 256 33.221 53.159 72.467 1.00 7.86 S ATOM 1451 SG CYS A 259 39.131 51.450 74.442 1.00 4.94 S ATOM 1188 SG CYS A 223 37.224 49.225 68.875 1.00 5.66 S ATOM 1718 SG CYS A 295 42.563 54.021 86.838 1.00 10.97 S ATOM 1977 SG CYS A 329 39.198 50.941 82.741 1.00 6.79 S ATOM 1743 SG CYS A 298 40.939 48.104 86.685 1.00 11.58 S ATOM 1764 SG CYS A 302 45.768 51.518 82.517 1.00 10.15 S ATOM 10068 SG CYS B 542 45.532 49.480 43.520 1.00 6.26 S ATOM 9808 SG CYS B 508 42.415 54.946 43.829 1.00 5.94 S ATOM 9788 SG CYS B 505 46.218 54.628 47.560 1.00 5.57 S ATOM 9769 SG CYS B 502 41.464 49.903 48.254 1.00 5.50 S ATOM 6791 SG CYS B 113 28.519 49.098 31.049 1.00 15.72 S ATOM 6826 SG CYS B 118 27.173 48.927 27.718 1.00 16.89 S ATOM 7038 SG CYS B 146 32.281 46.333 30.942 1.00 13.72 S ATOM 7063 SG CYS B 150 32.668 46.254 27.160 1.00 17.32 S Time building chain proxies: 2.44, per 1000 atoms: 0.23 Number of scatterers: 10391 At special positions: 0 Unit cell: (85.32, 86.4, 138.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) W 1 73.95 Fe 20 26.01 S 85 16.00 P 5 15.00 O 1955 8.00 N 1847 7.00 C 6478 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 390.2 milliseconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A1004 " pdb="FE1 FES A1004 " - pdb=" SG CYS A 102 " pdb="FE1 FES A1004 " - pdb=" N HIS A 103 " pdb="FE2 FES A1004 " - pdb=" SG CYS A 118 " pdb="FE2 FES A1004 " - pdb=" SG CYS A 132 " pdb="FE1 FES A1004 " - pdb=" SG CYS A 115 " pdb=" FES B 603 " pdb="FE1 FES B 603 " - pdb=" SG CYS B 113 " pdb="FE2 FES B 603 " - pdb=" SG CYS B 150 " pdb="FE1 FES B 603 " - pdb=" SG CYS B 118 " pdb="FE2 FES B 603 " - pdb=" SG CYS B 146 " pdb=" SF4 A1005 " pdb="FE1 SF4 A1005 " - pdb=" SG CYS A 216 " pdb="FE4 SF4 A1005 " - pdb=" SG CYS A 219 " pdb="FE2 SF4 A1005 " - pdb=" SG CYS A 213 " pdb="FE3 SF4 A1005 " - pdb=" SG CYS A 266 " pdb=" SF4 A1006 " pdb="FE2 SF4 A1006 " - pdb=" SG CYS A 256 " pdb="FE3 SF4 A1006 " - pdb=" SG CYS A 259 " pdb="FE4 SF4 A1006 " - pdb=" SG CYS A 223 " pdb="FE1 SF4 A1006 " - pdb=" SG CYS A 262 " pdb=" SF4 A1007 " pdb="FE1 SF4 A1007 " - pdb=" SG CYS A 295 " pdb="FE2 SF4 A1007 " - pdb=" SG CYS A 329 " pdb="FE3 SF4 A1007 " - pdb=" SG CYS A 298 " pdb="FE4 SF4 A1007 " - pdb=" SG CYS A 302 " pdb=" SF4 B 602 " pdb="FE3 SF4 B 602 " - pdb=" SG CYS B 505 " pdb="FE1 SF4 B 602 " - pdb=" SG CYS B 542 " pdb="FE4 SF4 B 602 " - pdb=" SG CYS B 502 " pdb="FE2 SF4 B 602 " - pdb=" SG CYS B 508 " Number of angles added : 62 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2432 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 13 sheets defined 45.8% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 86 through 95 Processing helix chain 'A' and resid 146 through 164 Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 210 through 213 Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 237 through 241 Processing helix chain 'A' and resid 262 through 266 removed outlier: 3.688A pdb=" N CYS A 266 " --> pdb=" O VAL A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 335 through 339 removed outlier: 3.556A pdb=" N TYR A 338 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 395 removed outlier: 3.583A pdb=" N LEU A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 removed outlier: 3.801A pdb=" N LEU A 400 " --> pdb=" O ARG A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 423 Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 437 through 449 Processing helix chain 'A' and resid 456 through 462 Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 477 through 491 Processing helix chain 'A' and resid 503 through 509 removed outlier: 3.589A pdb=" N ARG A 507 " --> pdb=" O THR A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 534 removed outlier: 4.052A pdb=" N MET A 523 " --> pdb=" O SER A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 545 removed outlier: 3.591A pdb=" N ILE A 542 " --> pdb=" O ASP A 538 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLY A 544 " --> pdb=" O GLN A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 556 removed outlier: 4.050A pdb=" N LEU A 552 " --> pdb=" O ASN A 548 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG A 553 " --> pdb=" O PHE A 549 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS A 555 " --> pdb=" O ALA A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 568 removed outlier: 4.422A pdb=" N SER A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL A 567 " --> pdb=" O LYS A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 585 Processing helix chain 'A' and resid 593 through 598 Processing helix chain 'A' and resid 601 through 616 removed outlier: 4.205A pdb=" N ASN A 605 " --> pdb=" O HIS A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 641 Processing helix chain 'A' and resid 656 through 668 Processing helix chain 'A' and resid 678 through 688 removed outlier: 3.803A pdb=" N HIS A 687 " --> pdb=" O MET A 683 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A 688 " --> pdb=" O ARG A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 704 Processing helix chain 'A' and resid 711 through 717 Processing helix chain 'A' and resid 773 through 785 Processing helix chain 'A' and resid 793 through 803 Processing helix chain 'A' and resid 812 through 818 Processing helix chain 'B' and resid 31 through 43 Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'B' and resid 51 through 63 Processing helix chain 'B' and resid 68 through 78 Processing helix chain 'B' and resid 81 through 90 Processing helix chain 'B' and resid 115 through 121 Processing helix chain 'B' and resid 122 through 134 removed outlier: 3.689A pdb=" N LEU B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 167 through 177 Processing helix chain 'B' and resid 189 through 196 removed outlier: 3.601A pdb=" N GLY B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 207 Processing helix chain 'B' and resid 211 through 223 Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 262 through 269 removed outlier: 3.529A pdb=" N LEU B 266 " --> pdb=" O PHE B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 287 removed outlier: 3.810A pdb=" N PHE B 275 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 311 removed outlier: 3.642A pdb=" N ALA B 311 " --> pdb=" O ALA B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 332 Processing helix chain 'B' and resid 333 through 342 Processing helix chain 'B' and resid 370 through 383 removed outlier: 3.594A pdb=" N TRP B 375 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 376 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ARG B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ASP B 378 " --> pdb=" O PHE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.871A pdb=" N TRP B 387 " --> pdb=" O GLY B 383 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS B 390 " --> pdb=" O TRP B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 427 Processing helix chain 'B' and resid 454 through 456 No H-bonds generated for 'chain 'B' and resid 454 through 456' Processing helix chain 'B' and resid 465 through 469 removed outlier: 3.523A pdb=" N TYR B 468 " --> pdb=" O LEU B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 501 Processing helix chain 'B' and resid 505 through 520 removed outlier: 3.994A pdb=" N GLN B 513 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 540 Processing helix chain 'B' and resid 542 through 549 removed outlier: 4.448A pdb=" N SER B 549 " --> pdb=" O GLY B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 559 Processing helix chain 'B' and resid 560 through 563 removed outlier: 3.625A pdb=" N PHE B 563 " --> pdb=" O PRO B 560 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 560 through 563' Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 78 removed outlier: 6.662A pdb=" N GLU A 73 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 206 through 208 Processing sheet with id=AA3, first strand: chain 'A' and resid 233 through 234 Processing sheet with id=AA4, first strand: chain 'A' and resid 289 through 293 removed outlier: 3.698A pdb=" N TYR A 315 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 374 Processing sheet with id=AA6, first strand: chain 'A' and resid 511 through 512 removed outlier: 3.833A pdb=" N ARG A 511 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE A 466 " --> pdb=" O ILE A 496 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL A 465 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N PHE A 591 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL A 467 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N SER A 588 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N HIS A 627 " --> pdb=" O SER A 588 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE A 590 " --> pdb=" O HIS A 627 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 546 through 547 Processing sheet with id=AA8, first strand: chain 'A' and resid 647 through 648 Processing sheet with id=AA9, first strand: chain 'A' and resid 749 through 752 Processing sheet with id=AB1, first strand: chain 'B' and resid 66 through 67 removed outlier: 6.413A pdb=" N ILE B 66 " --> pdb=" O VAL B 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 139 through 144 Processing sheet with id=AB3, first strand: chain 'B' and resid 319 through 324 removed outlier: 6.366A pdb=" N VAL B 291 " --> pdb=" O HIS B 321 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ARG B 323 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ILE B 293 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET B 250 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 366 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 411 through 416 removed outlier: 7.871A pdb=" N VAL B 477 " --> pdb=" O SER B 400 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N SER B 402 " --> pdb=" O VAL B 477 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ILE B 479 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N SER B 404 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N SER B 481 " --> pdb=" O SER B 404 " (cutoff:3.500A) 413 hydrogen bonds defined for protein. 1134 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: 1.74 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 4448 1.43 - 1.64: 6039 1.64 - 1.86: 99 1.86 - 2.07: 2 2.07 - 2.28: 56 Bond restraints: 10644 Sorted by residual: bond pdb=" C12 MGD A1002 " pdb=" C13 MGD A1002 " ideal model delta sigma weight residual 1.337 1.526 -0.189 2.00e-02 2.50e+03 8.93e+01 bond pdb=" C6 MGD A1002 " pdb=" O6 MGD A1002 " ideal model delta sigma weight residual 1.220 1.403 -0.183 2.00e-02 2.50e+03 8.36e+01 bond pdb=" C6 MGD A1003 " pdb=" O6 MGD A1003 " ideal model delta sigma weight residual 1.220 1.403 -0.183 2.00e-02 2.50e+03 8.34e+01 bond pdb=" C12 MGD A1003 " pdb=" C13 MGD A1003 " ideal model delta sigma weight residual 1.337 1.519 -0.182 2.00e-02 2.50e+03 8.26e+01 bond pdb=" C17 MGD A1002 " pdb=" O17 MGD A1002 " ideal model delta sigma weight residual 1.232 1.398 -0.166 2.00e-02 2.50e+03 6.87e+01 ... (remaining 10639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 14394 3.43 - 6.85: 82 6.85 - 10.28: 22 10.28 - 13.71: 7 13.71 - 17.13: 6 Bond angle restraints: 14511 Sorted by residual: angle pdb=" C13 MGD A1003 " pdb=" C12 MGD A1003 " pdb=" S12 MGD A1003 " ideal model delta sigma weight residual 125.54 108.41 17.13 3.00e+00 1.11e-01 3.26e+01 angle pdb=" O3A MGD A1003 " pdb=" PA MGD A1003 " pdb=" O3B MGD A1003 " ideal model delta sigma weight residual 93.37 109.82 -16.45 3.00e+00 1.11e-01 3.01e+01 angle pdb=" O3B MGD A1002 " pdb=" PB MGD A1002 " pdb=" O5' MGD A1002 " ideal model delta sigma weight residual 93.25 108.57 -15.32 3.00e+00 1.11e-01 2.61e+01 angle pdb=" C13 MGD A1002 " pdb=" C12 MGD A1002 " pdb=" S12 MGD A1002 " ideal model delta sigma weight residual 125.54 110.48 15.06 3.00e+00 1.11e-01 2.52e+01 angle pdb=" O3A MGD A1002 " pdb=" PA MGD A1002 " pdb=" O3B MGD A1002 " ideal model delta sigma weight residual 93.37 108.03 -14.66 3.00e+00 1.11e-01 2.39e+01 ... (remaining 14506 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.09: 6208 32.09 - 64.18: 168 64.18 - 96.27: 23 96.27 - 128.36: 2 128.36 - 160.45: 1 Dihedral angle restraints: 6402 sinusoidal: 2606 harmonic: 3796 Sorted by residual: dihedral pdb=" CA LYS B 351 " pdb=" C LYS B 351 " pdb=" N PRO B 352 " pdb=" CA PRO B 352 " ideal model delta harmonic sigma weight residual 180.00 152.33 27.67 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" O5' MGD A1003 " pdb=" O3B MGD A1003 " pdb=" PB MGD A1003 " pdb=" PA MGD A1003 " ideal model delta sinusoidal sigma weight residual 203.73 43.28 160.45 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" CA THR A 823 " pdb=" C THR A 823 " pdb=" N TYR A 824 " pdb=" CA TYR A 824 " ideal model delta harmonic sigma weight residual -180.00 -159.85 -20.15 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 6399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1479 0.087 - 0.174: 106 0.174 - 0.261: 4 0.261 - 0.348: 1 0.348 - 0.435: 3 Chirality restraints: 1593 Sorted by residual: chirality pdb=" C4' MGD A1003 " pdb=" C3' MGD A1003 " pdb=" C5' MGD A1003 " pdb=" O4' MGD A1003 " both_signs ideal model delta sigma weight residual False -2.53 -2.10 -0.44 2.00e-01 2.50e+01 4.74e+00 chirality pdb=" CA ALA A 711 " pdb=" N ALA A 711 " pdb=" C ALA A 711 " pdb=" CB ALA A 711 " both_signs ideal model delta sigma weight residual False 2.48 2.13 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA GLU A 835 " pdb=" N GLU A 835 " pdb=" C GLU A 835 " pdb=" CB GLU A 835 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 ... (remaining 1590 not shown) Planarity restraints: 1897 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C16 MGD A1002 " 0.067 2.00e-02 2.50e+03 1.23e-01 4.14e+02 pdb=" C17 MGD A1002 " -0.008 2.00e-02 2.50e+03 pdb=" C19 MGD A1002 " -0.021 2.00e-02 2.50e+03 pdb=" C21 MGD A1002 " 0.094 2.00e-02 2.50e+03 pdb=" C23 MGD A1002 " -0.311 2.00e-02 2.50e+03 pdb=" N15 MGD A1002 " 0.110 2.00e-02 2.50e+03 pdb=" N18 MGD A1002 " -0.051 2.00e-02 2.50e+03 pdb=" N19 MGD A1002 " -0.067 2.00e-02 2.50e+03 pdb=" N20 MGD A1002 " 0.053 2.00e-02 2.50e+03 pdb=" N22 MGD A1002 " 0.176 2.00e-02 2.50e+03 pdb=" O17 MGD A1002 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' MGD A1003 " -0.093 2.00e-02 2.50e+03 3.53e-02 3.73e+01 pdb=" C2 MGD A1003 " 0.007 2.00e-02 2.50e+03 pdb=" C4 MGD A1003 " 0.026 2.00e-02 2.50e+03 pdb=" C5 MGD A1003 " 0.006 2.00e-02 2.50e+03 pdb=" C6 MGD A1003 " -0.016 2.00e-02 2.50e+03 pdb=" C8 MGD A1003 " 0.034 2.00e-02 2.50e+03 pdb=" N1 MGD A1003 " -0.013 2.00e-02 2.50e+03 pdb=" N2 MGD A1003 " 0.006 2.00e-02 2.50e+03 pdb=" N3 MGD A1003 " 0.025 2.00e-02 2.50e+03 pdb=" N7 MGD A1003 " 0.011 2.00e-02 2.50e+03 pdb=" N9 MGD A1003 " 0.043 2.00e-02 2.50e+03 pdb=" O6 MGD A1003 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 351 " 0.038 5.00e-02 4.00e+02 5.81e-02 5.41e+00 pdb=" N PRO B 352 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 352 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 352 " 0.032 5.00e-02 4.00e+02 ... (remaining 1894 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 46 2.44 - 3.06: 7164 3.06 - 3.67: 16205 3.67 - 4.29: 25553 4.29 - 4.90: 41588 Nonbonded interactions: 90556 Sorted by model distance: nonbonded pdb=" OD2 ASP A 725 " pdb=" CG2 THR A 729 " model vdw 1.827 3.460 nonbonded pdb=" O2' FMN B 601 " pdb=" O4' FMN B 601 " model vdw 1.898 3.040 nonbonded pdb=" OD1 ASP A 725 " pdb=" N LEU A 726 " model vdw 2.154 3.120 nonbonded pdb=" OE1 GLN A 325 " pdb=" NH2 ARG A 327 " model vdw 2.204 3.120 nonbonded pdb=" O VAL A 479 " pdb=" OG1 THR A 482 " model vdw 2.211 3.040 ... (remaining 90551 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.340 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 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 : 0.008 0.189 10670 Z= 0.400 Angle : 1.140 41.255 14573 Z= 0.364 Chirality : 0.047 0.435 1593 Planarity : 0.006 0.123 1897 Dihedral : 15.296 160.449 3970 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.23), residues: 1327 helix: 0.50 (0.24), residues: 503 sheet: -0.08 (0.54), residues: 100 loop : -1.30 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 511 TYR 0.021 0.001 TYR A 824 PHE 0.013 0.001 PHE A 245 TRP 0.024 0.002 TRP B 524 HIS 0.011 0.001 HIS B 57 Details of bonding type rmsd covalent geometry : bond 0.00768 (10644) covalent geometry : angle 0.80933 (14511) hydrogen bonds : bond 0.19381 ( 413) hydrogen bonds : angle 7.89389 ( 1134) metal coordination : bond 0.03505 ( 25) metal coordination : angle 12.32487 ( 62) Misc. bond : bond 0.12434 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.351 Fit side-chains REVERT: A 389 LYS cc_start: 0.7553 (tttm) cc_final: 0.7255 (tttt) REVERT: A 555 LYS cc_start: 0.7266 (ttpt) cc_final: 0.7017 (mtmp) REVERT: A 730 GLU cc_start: 0.7358 (mp0) cc_final: 0.7019 (mp0) REVERT: B 44 THR cc_start: 0.8119 (p) cc_final: 0.7892 (t) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.5661 time to fit residues: 113.7012 Evaluate side-chains 122 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.1980 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 0.0170 chunk 55 optimal weight: 0.1980 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS A 217 ASN A 428 ASN A 669 GLN A 724 GLN A 734 HIS A 779 GLN A 810 ASN B 29 GLN B 273 HIS B 436 HIS B 492 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.159835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.136012 restraints weight = 8032.046| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.08 r_work: 0.3511 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.154 10670 Z= 0.134 Angle : 1.013 40.545 14573 Z= 0.319 Chirality : 0.045 0.176 1593 Planarity : 0.005 0.070 1897 Dihedral : 9.494 158.378 1591 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.78 % Allowed : 11.70 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.23), residues: 1327 helix: 0.72 (0.23), residues: 508 sheet: -0.18 (0.51), residues: 104 loop : -1.12 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 660 TYR 0.020 0.001 TYR A 824 PHE 0.013 0.001 PHE B 162 TRP 0.011 0.001 TRP B 524 HIS 0.009 0.001 HIS A 713 Details of bonding type rmsd covalent geometry : bond 0.00303 (10644) covalent geometry : angle 0.62993 (14511) hydrogen bonds : bond 0.04215 ( 413) hydrogen bonds : angle 5.85699 ( 1134) metal coordination : bond 0.03385 ( 25) metal coordination : angle 12.17272 ( 62) Misc. bond : bond 0.00169 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.373 Fit side-chains REVERT: A 389 LYS cc_start: 0.6969 (tttm) cc_final: 0.6483 (tttt) REVERT: A 437 HIS cc_start: 0.6729 (OUTLIER) cc_final: 0.5840 (m-70) REVERT: A 547 GLU cc_start: 0.7685 (mp0) cc_final: 0.7269 (mp0) REVERT: A 665 GLU cc_start: 0.7541 (tm-30) cc_final: 0.7316 (tp30) REVERT: A 694 MET cc_start: 0.7065 (mtm) cc_final: 0.6835 (mtp) REVERT: A 730 GLU cc_start: 0.7229 (mp0) cc_final: 0.6873 (mp0) REVERT: B 44 THR cc_start: 0.8117 (p) cc_final: 0.7741 (t) REVERT: B 271 ASP cc_start: 0.8055 (t0) cc_final: 0.7731 (t70) REVERT: B 304 GLU cc_start: 0.7703 (tp30) cc_final: 0.7457 (tt0) REVERT: B 483 GLN cc_start: 0.7781 (mp10) cc_final: 0.7488 (mm110) REVERT: B 562 LEU cc_start: 0.7697 (mt) cc_final: 0.7482 (mt) outliers start: 19 outliers final: 10 residues processed: 152 average time/residue: 0.5015 time to fit residues: 82.1997 Evaluate side-chains 134 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain B residue 458 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 25 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 103 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 114 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN A 720 HIS A 724 GLN A 810 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.154446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.128293 restraints weight = 7139.312| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.19 r_work: 0.3415 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.165 10670 Z= 0.137 Angle : 0.983 41.146 14573 Z= 0.306 Chirality : 0.045 0.198 1593 Planarity : 0.005 0.073 1897 Dihedral : 9.000 147.535 1591 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.46 % Allowed : 13.76 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.23), residues: 1327 helix: 0.70 (0.23), residues: 521 sheet: -0.34 (0.48), residues: 117 loop : -1.16 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 660 TYR 0.018 0.001 TYR A 824 PHE 0.013 0.001 PHE A 245 TRP 0.014 0.001 TRP B 524 HIS 0.004 0.001 HIS B 57 Details of bonding type rmsd covalent geometry : bond 0.00318 (10644) covalent geometry : angle 0.60473 (14511) hydrogen bonds : bond 0.03949 ( 413) hydrogen bonds : angle 5.54155 ( 1134) metal coordination : bond 0.03641 ( 25) metal coordination : angle 11.90128 ( 62) Misc. bond : bond 0.00068 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.388 Fit side-chains REVERT: A 126 ARG cc_start: 0.8005 (ttp-110) cc_final: 0.7775 (ttp80) REVERT: A 292 LYS cc_start: 0.7921 (ptmm) cc_final: 0.7659 (ttpt) REVERT: A 389 LYS cc_start: 0.6743 (tttm) cc_final: 0.6456 (tttt) REVERT: A 437 HIS cc_start: 0.6782 (OUTLIER) cc_final: 0.5807 (m-70) REVERT: A 490 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8190 (mt0) REVERT: A 491 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.6256 (mmm-85) REVERT: A 547 GLU cc_start: 0.7335 (mp0) cc_final: 0.7018 (mp0) REVERT: A 581 LEU cc_start: 0.7541 (tp) cc_final: 0.7305 (tp) REVERT: A 586 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7735 (tttp) REVERT: A 665 GLU cc_start: 0.7541 (tm-30) cc_final: 0.7291 (tp30) REVERT: A 694 MET cc_start: 0.7182 (mtm) cc_final: 0.6973 (mtp) REVERT: A 730 GLU cc_start: 0.7363 (mp0) cc_final: 0.6908 (mp0) REVERT: A 827 ASP cc_start: 0.6401 (OUTLIER) cc_final: 0.6176 (m-30) REVERT: B 44 THR cc_start: 0.8148 (p) cc_final: 0.7751 (t) REVERT: B 61 ASP cc_start: 0.7975 (m-30) cc_final: 0.7697 (m-30) REVERT: B 209 GLU cc_start: 0.5467 (mt-10) cc_final: 0.5259 (mt-10) REVERT: B 333 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7693 (tp30) REVERT: B 483 GLN cc_start: 0.7571 (mp10) cc_final: 0.7254 (mm110) outliers start: 37 outliers final: 16 residues processed: 160 average time/residue: 0.5678 time to fit residues: 97.9141 Evaluate side-chains 140 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 586 LYS Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 827 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 553 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 102 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 GLN A 734 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.148272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.123941 restraints weight = 6467.653| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.07 r_work: 0.3343 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.202 10670 Z= 0.203 Angle : 1.047 42.558 14573 Z= 0.342 Chirality : 0.048 0.209 1593 Planarity : 0.005 0.075 1897 Dihedral : 8.786 142.318 1591 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.59 % Allowed : 15.17 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.23), residues: 1327 helix: 0.41 (0.22), residues: 530 sheet: -0.45 (0.47), residues: 117 loop : -1.28 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 236 TYR 0.026 0.002 TYR A 824 PHE 0.017 0.002 PHE A 245 TRP 0.027 0.002 TRP B 524 HIS 0.004 0.001 HIS B 57 Details of bonding type rmsd covalent geometry : bond 0.00489 (10644) covalent geometry : angle 0.68267 (14511) hydrogen bonds : bond 0.04426 ( 413) hydrogen bonds : angle 5.65034 ( 1134) metal coordination : bond 0.04487 ( 25) metal coordination : angle 12.18502 ( 62) Misc. bond : bond 0.00056 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 116 time to evaluate : 0.408 Fit side-chains REVERT: A 389 LYS cc_start: 0.6890 (tttm) cc_final: 0.6526 (tttt) REVERT: A 415 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7977 (mp) REVERT: A 437 HIS cc_start: 0.7040 (OUTLIER) cc_final: 0.6009 (m-70) REVERT: A 464 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7434 (mt-10) REVERT: A 490 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8197 (mt0) REVERT: A 491 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.6286 (mmm-85) REVERT: A 547 GLU cc_start: 0.7430 (mp0) cc_final: 0.7123 (mp0) REVERT: A 589 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.7961 (tt) REVERT: A 630 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.6489 (mtt-85) REVERT: A 665 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7269 (tp30) REVERT: A 730 GLU cc_start: 0.7607 (mp0) cc_final: 0.7121 (mp0) REVERT: A 810 ASN cc_start: 0.7568 (t0) cc_final: 0.7250 (t0) REVERT: B 44 THR cc_start: 0.8229 (p) cc_final: 0.7842 (t) REVERT: B 333 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7640 (tp30) REVERT: B 483 GLN cc_start: 0.7619 (mp10) cc_final: 0.7307 (mm110) outliers start: 49 outliers final: 22 residues processed: 150 average time/residue: 0.5876 time to fit residues: 95.1208 Evaluate side-chains 138 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 630 ARG Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 454 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 72 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 94 optimal weight: 8.9990 chunk 0 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS A 281 GLN ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.151962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.126998 restraints weight = 6276.916| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.09 r_work: 0.3398 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.159 10670 Z= 0.138 Angle : 0.994 43.899 14573 Z= 0.306 Chirality : 0.045 0.198 1593 Planarity : 0.005 0.073 1897 Dihedral : 8.502 138.243 1591 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.31 % Allowed : 15.73 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.23), residues: 1327 helix: 0.60 (0.23), residues: 523 sheet: -0.50 (0.47), residues: 117 loop : -1.23 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 236 TYR 0.019 0.001 TYR A 824 PHE 0.015 0.001 PHE A 245 TRP 0.017 0.001 TRP B 524 HIS 0.003 0.001 HIS B 57 Details of bonding type rmsd covalent geometry : bond 0.00325 (10644) covalent geometry : angle 0.60772 (14511) hydrogen bonds : bond 0.03775 ( 413) hydrogen bonds : angle 5.47385 ( 1134) metal coordination : bond 0.03493 ( 25) metal coordination : angle 12.08206 ( 62) Misc. bond : bond 0.00065 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2654 Ramachandran restraints generated. 1327 Oldfield, 0 Emsley, 1327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 127 time to evaluate : 0.370 Fit side-chains REVERT: A 389 LYS cc_start: 0.6851 (tttm) cc_final: 0.6583 (tttt) REVERT: A 415 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7866 (mp) REVERT: A 491 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.6303 (mmm-85) REVERT: A 547 GLU cc_start: 0.7273 (mp0) cc_final: 0.6985 (mp0) REVERT: A 646 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7356 (pmm) REVERT: A 665 GLU cc_start: 0.7454 (tm-30) cc_final: 0.7240 (tp30) REVERT: A 730 GLU cc_start: 0.7494 (mp0) cc_final: 0.7076 (mp0) REVERT: A 810 ASN cc_start: 0.7458 (t0) cc_final: 0.7164 (t0) REVERT: B 44 THR cc_start: 0.8279 (p) cc_final: 0.7900 (t) REVERT: B 61 ASP cc_start: 0.8014 (m-30) cc_final: 0.7718 (m-30) REVERT: B 333 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7644 (tp30) REVERT: B 432 ILE cc_start: 0.7007 (OUTLIER) cc_final: 0.6636 (mt) REVERT: B 483 GLN cc_start: 0.7665 (mp10) cc_final: 0.7406 (mm110) outliers start: 46 outliers final: 26 residues processed: 160 average time/residue: 0.6006 time to fit residues: 103.3161 Evaluate side-chains 145 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 553 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.6787 > 50: distance: 110 - 114: 8.499 distance: 111 - 133: 21.739 distance: 114 - 115: 5.667 distance: 114 - 120: 19.916 distance: 115 - 118: 15.550 distance: 116 - 117: 17.076 distance: 116 - 121: 8.762 distance: 117 - 138: 16.840 distance: 118 - 119: 35.771 distance: 119 - 120: 33.720 distance: 122 - 123: 8.455 distance: 122 - 125: 8.395 distance: 123 - 124: 7.765 distance: 123 - 128: 12.491 distance: 124 - 145: 21.554 distance: 125 - 126: 14.300 distance: 125 - 127: 10.218 distance: 128 - 129: 15.220 distance: 129 - 130: 7.131 distance: 129 - 132: 7.825 distance: 130 - 131: 14.071 distance: 130 - 133: 15.178 distance: 131 - 156: 42.360 distance: 133 - 134: 17.088 distance: 134 - 135: 19.297 distance: 134 - 137: 17.040 distance: 135 - 136: 14.284 distance: 135 - 138: 25.838 distance: 136 - 164: 13.916 distance: 138 - 139: 6.036 distance: 139 - 140: 16.587 distance: 139 - 142: 25.525 distance: 140 - 141: 14.578 distance: 140 - 145: 9.471 distance: 141 - 173: 8.790 distance: 142 - 143: 29.613 distance: 142 - 144: 49.756 distance: 145 - 146: 5.834 distance: 146 - 147: 12.172 distance: 146 - 149: 11.647 distance: 147 - 148: 17.745 distance: 147 - 156: 30.646 distance: 148 - 181: 33.299 distance: 149 - 150: 15.914 distance: 150 - 151: 22.594 distance: 150 - 152: 13.364 distance: 151 - 153: 22.748 distance: 152 - 154: 16.881 distance: 153 - 155: 23.647 distance: 154 - 155: 20.130 distance: 156 - 157: 18.590 distance: 157 - 158: 12.203 distance: 157 - 160: 11.923 distance: 158 - 159: 12.137 distance: 158 - 164: 5.410 distance: 159 - 186: 20.361 distance: 160 - 161: 20.684 distance: 161 - 162: 15.192 distance: 161 - 163: 16.236 distance: 164 - 165: 11.583 distance: 165 - 166: 35.299 distance: 165 - 168: 12.646 distance: 166 - 167: 47.060 distance: 166 - 173: 24.032 distance: 167 - 193: 33.500 distance: 168 - 169: 23.116 distance: 169 - 170: 13.470 distance: 170 - 171: 15.207 distance: 171 - 172: 16.975 distance: 173 - 174: 39.033 distance: 174 - 175: 27.167 distance: 174 - 177: 38.237 distance: 175 - 176: 41.961 distance: 175 - 181: 30.861 distance: 176 - 200: 27.909 distance: 177 - 178: 25.771 distance: 178 - 179: 26.191 distance: 178 - 180: 37.015 distance: 181 - 182: 9.079 distance: 182 - 183: 13.441 distance: 182 - 185: 8.541 distance: 183 - 184: 10.614 distance: 183 - 186: 13.121 distance: 184 - 208: 25.319