Starting phenix.real_space_refine on Fri Sep 27 18:07:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2j_32262/09_2024/7w2j_32262.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2j_32262/09_2024/7w2j_32262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2j_32262/09_2024/7w2j_32262.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2j_32262/09_2024/7w2j_32262.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2j_32262/09_2024/7w2j_32262.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2j_32262/09_2024/7w2j_32262.cif" } resolution = 3.6 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= 0.005 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: 6 Type Number sf(0) Gaussians Fe 12 7.16 5 P 4 5.49 5 S 90 5.16 5 C 10438 2.51 5 N 2856 2.21 5 O 3122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16522 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4143 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 36, 'TRANS': 500} Chain: "B" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain breaks: 4 Chain: "C" Number of atoms: 3149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3149 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 25, 'TRANS': 392} Chain breaks: 1 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'F3S': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'HEC': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1743 SG CYS A 226 52.601 34.063 74.352 1.00 8.79 S ATOM 1714 SG CYS A 222 51.682 31.454 77.344 1.00 8.19 S ATOM 1674 SG CYS A 216 53.050 28.269 73.790 1.00 25.28 S Restraints were copied for chains: D, E, F Time building chain proxies: 13.35, per 1000 atoms: 0.81 Number of scatterers: 16522 At special positions: 0 Unit cell: (103.077, 127.745, 119.816, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 12 26.01 S 90 16.00 P 4 15.00 O 3122 8.00 N 2856 7.00 C 10438 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=32, symmetry=0 Number of additional bonds: simple=32, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.24 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S A 602 " pdb="FE1 F3S A 602 " - pdb=" SG CYS A 226 " pdb="FE3 F3S A 602 " - pdb=" SG CYS A 222 " pdb="FE4 F3S A 602 " - pdb=" SG CYS A 216 " pdb=" F3S D 602 " pdb="FE1 F3S D 602 " - pdb=" SG CYS D 226 " pdb="FE3 F3S D 602 " - pdb=" SG CYS D 222 " pdb="FE4 F3S D 602 " - pdb=" SG CYS D 216 " Number of angles added : 18 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3860 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 16 sheets defined 39.9% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 16 through 30 Processing helix chain 'A' and resid 43 through 54 Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.545A pdb=" N LYS A 59 " --> pdb=" O PRO A 55 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 97 Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.564A pdb=" N THR A 108 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 123 removed outlier: 3.604A pdb=" N PHE A 123 " --> pdb=" O PRO A 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 124 through 130 Processing helix chain 'A' and resid 138 through 154 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 181 through 195 removed outlier: 3.919A pdb=" N ARG A 185 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 245 removed outlier: 4.350A pdb=" N ALA A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'A' and resid 350 through 353 Processing helix chain 'A' and resid 355 through 360 removed outlier: 3.982A pdb=" N ARG A 358 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER A 359 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 388 through 401 Processing helix chain 'A' and resid 440 through 462 removed outlier: 4.363A pdb=" N VAL A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.881A pdb=" N SER A 492 " --> pdb=" O PRO A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 514 removed outlier: 3.682A pdb=" N MET A 514 " --> pdb=" O GLY A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 removed outlier: 3.939A pdb=" N MET A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 541 removed outlier: 4.230A pdb=" N ASP A 535 " --> pdb=" O LEU A 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 56 Processing helix chain 'B' and resid 74 through 83 removed outlier: 3.616A pdb=" N ALA B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 93 removed outlier: 4.248A pdb=" N LYS B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA B 92 " --> pdb=" O THR B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 124 removed outlier: 4.140A pdb=" N ILE B 124 " --> pdb=" O LEU B 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 121 through 124' Processing helix chain 'B' and resid 125 through 130 Processing helix chain 'C' and resid 41 through 51 removed outlier: 3.544A pdb=" N ALA C 47 " --> pdb=" O GLY C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 106 removed outlier: 3.530A pdb=" N ALA C 102 " --> pdb=" O GLN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 127 through 141 removed outlier: 3.508A pdb=" N LYS C 132 " --> pdb=" O ASP C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'C' and resid 163 through 172 Processing helix chain 'C' and resid 185 through 196 removed outlier: 3.546A pdb=" N GLY C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP C 196 " --> pdb=" O ARG C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 206 Processing helix chain 'C' and resid 245 through 256 removed outlier: 3.504A pdb=" N THR C 255 " --> pdb=" O GLN C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 278 Processing helix chain 'C' and resid 279 through 293 removed outlier: 3.609A pdb=" N ILE C 283 " --> pdb=" O PRO C 279 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA C 285 " --> pdb=" O ALA C 281 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 341 removed outlier: 3.752A pdb=" N GLU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 383 Processing helix chain 'C' and resid 408 through 423 removed outlier: 4.190A pdb=" N ALA C 413 " --> pdb=" O ASP C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 441 removed outlier: 3.564A pdb=" N GLN C 437 " --> pdb=" O ASP C 433 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 451 Processing helix chain 'C' and resid 452 through 471 removed outlier: 3.560A pdb=" N MET C 456 " --> pdb=" O SER C 452 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 459 " --> pdb=" O VAL C 455 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE C 468 " --> pdb=" O ILE C 464 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL C 471 " --> pdb=" O ALA C 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 30 Processing helix chain 'D' and resid 43 through 54 Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.545A pdb=" N LYS D 59 " --> pdb=" O PRO D 55 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN D 61 " --> pdb=" O ASP D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 97 Processing helix chain 'D' and resid 105 through 110 removed outlier: 3.563A pdb=" N THR D 108 " --> pdb=" O GLY D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 123 removed outlier: 3.603A pdb=" N PHE D 123 " --> pdb=" O PRO D 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 120 through 123' Processing helix chain 'D' and resid 124 through 130 Processing helix chain 'D' and resid 138 through 154 Proline residue: D 144 - end of helix Processing helix chain 'D' and resid 181 through 195 removed outlier: 3.919A pdb=" N ARG D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 245 removed outlier: 4.350A pdb=" N ALA D 237 " --> pdb=" O ASN D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 301 Processing helix chain 'D' and resid 350 through 353 Processing helix chain 'D' and resid 355 through 360 removed outlier: 3.983A pdb=" N ARG D 358 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER D 359 " --> pdb=" O ASP D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 384 Processing helix chain 'D' and resid 388 through 401 Processing helix chain 'D' and resid 440 through 462 removed outlier: 4.364A pdb=" N VAL D 444 " --> pdb=" O VAL D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 492 removed outlier: 3.881A pdb=" N SER D 492 " --> pdb=" O PRO D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 514 removed outlier: 3.682A pdb=" N MET D 514 " --> pdb=" O GLY D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 531 removed outlier: 3.940A pdb=" N MET D 526 " --> pdb=" O SER D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 541 removed outlier: 4.229A pdb=" N ASP D 535 " --> pdb=" O LEU D 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 56 Processing helix chain 'E' and resid 74 through 83 removed outlier: 3.616A pdb=" N ALA E 78 " --> pdb=" O ALA E 74 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 93 removed outlier: 4.249A pdb=" N LYS E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA E 92 " --> pdb=" O THR E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 124 removed outlier: 4.141A pdb=" N ILE E 124 " --> pdb=" O LEU E 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 121 through 124' Processing helix chain 'E' and resid 125 through 130 Processing helix chain 'F' and resid 41 through 51 removed outlier: 3.545A pdb=" N ALA F 47 " --> pdb=" O GLY F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 106 removed outlier: 3.530A pdb=" N ALA F 102 " --> pdb=" O GLN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 124 Processing helix chain 'F' and resid 127 through 141 removed outlier: 3.508A pdb=" N LYS F 132 " --> pdb=" O ASP F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 163 through 172 Processing helix chain 'F' and resid 185 through 196 removed outlier: 3.545A pdb=" N GLY F 191 " --> pdb=" O ASP F 187 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP F 196 " --> pdb=" O ARG F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 206 Processing helix chain 'F' and resid 245 through 256 removed outlier: 3.504A pdb=" N THR F 255 " --> pdb=" O GLN F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 272 Processing helix chain 'F' and resid 274 through 278 Processing helix chain 'F' and resid 279 through 293 removed outlier: 3.609A pdb=" N ILE F 283 " --> pdb=" O PRO F 279 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA F 285 " --> pdb=" O ALA F 281 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER F 292 " --> pdb=" O THR F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 341 removed outlier: 3.751A pdb=" N GLU F 340 " --> pdb=" O ALA F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 383 Processing helix chain 'F' and resid 408 through 423 removed outlier: 4.188A pdb=" N ALA F 413 " --> pdb=" O ASP F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 441 removed outlier: 3.564A pdb=" N GLN F 437 " --> pdb=" O ASP F 433 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 451 Processing helix chain 'F' and resid 452 through 471 removed outlier: 3.561A pdb=" N MET F 456 " --> pdb=" O SER F 452 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU F 459 " --> pdb=" O VAL F 455 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA F 467 " --> pdb=" O GLY F 463 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE F 468 " --> pdb=" O ILE F 464 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL F 471 " --> pdb=" O ALA F 467 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 247 through 250 removed outlier: 6.378A pdb=" N VAL A 33 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ILE A 249 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A 35 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N SER A 7 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ALA A 282 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ASP A 9 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR A 284 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA A 282 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N THR A 266 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N VAL A 254 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 250 removed outlier: 6.378A pdb=" N VAL A 33 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ILE A 249 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A 35 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N SER A 7 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ALA A 282 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ASP A 9 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR A 284 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N PHE A 507 " --> pdb=" O LYS A 283 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N PHE A 285 " --> pdb=" O PHE A 507 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 327 through 332 removed outlier: 3.690A pdb=" N ILE A 405 " --> pdb=" O MET A 329 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE A 331 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N TYR A 406 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY A 367 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN A 408 " --> pdb=" O GLN A 365 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN A 365 " --> pdb=" O ASN A 408 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 366 " --> pdb=" O ILE A 349 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 70 through 72 Processing sheet with id=AA6, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AA7, first strand: chain 'C' and resid 257 through 258 Processing sheet with id=AA8, first strand: chain 'C' and resid 385 through 387 Processing sheet with id=AA9, first strand: chain 'D' and resid 247 through 250 removed outlier: 6.377A pdb=" N VAL D 33 " --> pdb=" O LYS D 247 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ILE D 249 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU D 35 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N SER D 7 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ALA D 282 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ASP D 9 " --> pdb=" O ALA D 282 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR D 284 " --> pdb=" O ASP D 9 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA D 282 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N THR D 266 " --> pdb=" O ALA D 282 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR D 271 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL D 254 " --> pdb=" O TYR D 271 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 247 through 250 removed outlier: 6.377A pdb=" N VAL D 33 " --> pdb=" O LYS D 247 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ILE D 249 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU D 35 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N SER D 7 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ALA D 282 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ASP D 9 " --> pdb=" O ALA D 282 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR D 284 " --> pdb=" O ASP D 9 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N PHE D 507 " --> pdb=" O LYS D 283 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N PHE D 285 " --> pdb=" O PHE D 507 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 87 through 89 Processing sheet with id=AB3, first strand: chain 'D' and resid 327 through 332 removed outlier: 3.691A pdb=" N ILE D 405 " --> pdb=" O MET D 329 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE D 331 " --> pdb=" O VAL D 403 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N TYR D 406 " --> pdb=" O GLY D 367 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY D 367 " --> pdb=" O TYR D 406 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN D 408 " --> pdb=" O GLN D 365 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN D 365 " --> pdb=" O ASN D 408 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE D 366 " --> pdb=" O ILE D 349 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 70 through 72 Processing sheet with id=AB5, first strand: chain 'F' and resid 224 through 225 Processing sheet with id=AB6, first strand: chain 'F' and resid 257 through 258 Processing sheet with id=AB7, first strand: chain 'F' and resid 385 through 387 510 hydrogen bonds defined for protein. 1434 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: 4.37 Time building geometry restraints manager: 5.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.77: 16809 1.77 - 2.33: 157 2.33 - 2.89: 0 2.89 - 3.45: 0 3.45 - 4.01: 6 Bond restraints: 16972 Sorted by residual: bond pdb=" S4 F3S D 602 " pdb="FE1 F3S D 602 " ideal model delta sigma weight residual 2.233 4.007 -1.774 2.00e-02 2.50e+03 7.87e+03 bond pdb=" S4 F3S A 602 " pdb="FE1 F3S A 602 " ideal model delta sigma weight residual 2.233 4.007 -1.774 2.00e-02 2.50e+03 7.86e+03 bond pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 2.258 3.759 -1.501 2.00e-02 2.50e+03 5.63e+03 bond pdb=" S1 F3S D 602 " pdb="FE4 F3S D 602 " ideal model delta sigma weight residual 2.258 3.758 -1.500 2.00e-02 2.50e+03 5.63e+03 bond pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 2.300 3.463 -1.163 2.00e-02 2.50e+03 3.38e+03 ... (remaining 16967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.47: 23176 10.47 - 20.95: 6 20.95 - 31.42: 6 31.42 - 41.90: 8 41.90 - 52.37: 6 Bond angle restraints: 23202 Sorted by residual: angle pdb=" S3 F3S D 602 " pdb="FE1 F3S D 602 " pdb=" S4 F3S D 602 " ideal model delta sigma weight residual 112.59 60.22 52.37 3.00e+00 1.11e-01 3.05e+02 angle pdb=" S3 F3S A 602 " pdb="FE1 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 112.59 60.24 52.35 3.00e+00 1.11e-01 3.05e+02 angle pdb=" S1 F3S D 602 " pdb="FE4 F3S D 602 " pdb=" S3 F3S D 602 " ideal model delta sigma weight residual 114.75 66.85 47.90 3.00e+00 1.11e-01 2.55e+02 angle pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " pdb=" S3 F3S A 602 " ideal model delta sigma weight residual 114.75 66.85 47.90 3.00e+00 1.11e-01 2.55e+02 angle pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " pdb=" S2 F3S A 602 " ideal model delta sigma weight residual 103.63 61.46 42.17 3.00e+00 1.11e-01 1.98e+02 ... (remaining 23197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.58: 9424 26.58 - 53.16: 494 53.16 - 79.74: 42 79.74 - 106.31: 20 106.31 - 132.89: 2 Dihedral angle restraints: 9982 sinusoidal: 3928 harmonic: 6054 Sorted by residual: dihedral pdb=" CA PHE A 80 " pdb=" C PHE A 80 " pdb=" N PRO A 81 " pdb=" CA PRO A 81 " ideal model delta harmonic sigma weight residual -180.00 -132.52 -47.48 0 5.00e+00 4.00e-02 9.02e+01 dihedral pdb=" CA PHE D 80 " pdb=" C PHE D 80 " pdb=" N PRO D 81 " pdb=" CA PRO D 81 " ideal model delta harmonic sigma weight residual -180.00 -132.58 -47.42 0 5.00e+00 4.00e-02 8.99e+01 dihedral pdb=" CA PHE F 156 " pdb=" C PHE F 156 " pdb=" N PRO F 157 " pdb=" CA PRO F 157 " ideal model delta harmonic sigma weight residual 180.00 -139.15 -40.85 0 5.00e+00 4.00e-02 6.68e+01 ... (remaining 9979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.894: 2476 3.894 - 7.787: 0 7.787 - 11.681: 0 11.681 - 15.574: 0 15.574 - 19.468: 2 Chirality restraints: 2478 Sorted by residual: chirality pdb=" S2 F3S A 602 " pdb="FE1 F3S A 602 " pdb="FE3 F3S A 602 " pdb="FE4 F3S A 602 " both_signs ideal model delta sigma weight residual False 10.77 -8.70 19.47 2.00e-01 2.50e+01 9.48e+03 chirality pdb=" S2 F3S D 602 " pdb="FE1 F3S D 602 " pdb="FE3 F3S D 602 " pdb="FE4 F3S D 602 " both_signs ideal model delta sigma weight residual False 10.77 -8.70 19.47 2.00e-01 2.50e+01 9.47e+03 chirality pdb=" CB ILE B 133 " pdb=" CA ILE B 133 " pdb=" CG1 ILE B 133 " pdb=" CG2 ILE B 133 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 2475 not shown) Planarity restraints: 2986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC C 502 " -0.019 2.00e-02 2.50e+03 4.68e-02 4.93e+01 pdb=" C2C HEC C 502 " 0.127 2.00e-02 2.50e+03 pdb=" C3C HEC C 502 " -0.006 2.00e-02 2.50e+03 pdb=" C4C HEC C 502 " -0.002 2.00e-02 2.50e+03 pdb=" CAC HEC C 502 " -0.034 2.00e-02 2.50e+03 pdb=" CHC HEC C 502 " -0.024 2.00e-02 2.50e+03 pdb=" CHD HEC C 502 " 0.004 2.00e-02 2.50e+03 pdb=" CMC HEC C 502 " -0.036 2.00e-02 2.50e+03 pdb=" NC HEC C 502 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC F 502 " -0.018 2.00e-02 2.50e+03 4.66e-02 4.89e+01 pdb=" C2C HEC F 502 " 0.127 2.00e-02 2.50e+03 pdb=" C3C HEC F 502 " -0.006 2.00e-02 2.50e+03 pdb=" C4C HEC F 502 " -0.003 2.00e-02 2.50e+03 pdb=" CAC HEC F 502 " -0.034 2.00e-02 2.50e+03 pdb=" CHC HEC F 502 " -0.024 2.00e-02 2.50e+03 pdb=" CHD HEC F 502 " 0.004 2.00e-02 2.50e+03 pdb=" CMC HEC F 502 " -0.036 2.00e-02 2.50e+03 pdb=" NC HEC F 502 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC F 503 " 0.013 2.00e-02 2.50e+03 2.95e-02 1.95e+01 pdb=" C2C HEC F 503 " -0.080 2.00e-02 2.50e+03 pdb=" C3C HEC F 503 " 0.005 2.00e-02 2.50e+03 pdb=" C4C HEC F 503 " -0.000 2.00e-02 2.50e+03 pdb=" CAC HEC F 503 " 0.022 2.00e-02 2.50e+03 pdb=" CHC HEC F 503 " 0.015 2.00e-02 2.50e+03 pdb=" CHD HEC F 503 " -0.002 2.00e-02 2.50e+03 pdb=" CMC HEC F 503 " 0.022 2.00e-02 2.50e+03 pdb=" NC HEC F 503 " 0.006 2.00e-02 2.50e+03 ... (remaining 2983 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 246 2.59 - 3.17: 15383 3.17 - 3.74: 25522 3.74 - 4.32: 37186 4.32 - 4.90: 59514 Nonbonded interactions: 137851 Sorted by model distance: nonbonded pdb=" SG CYS A 226 " pdb=" S1 F3S A 602 " model vdw 2.011 3.760 nonbonded pdb=" SG CYS D 226 " pdb=" S1 F3S D 602 " model vdw 2.012 3.760 nonbonded pdb=" SG CYS A 222 " pdb=" S3 F3S A 602 " model vdw 2.013 3.760 nonbonded pdb=" SG CYS D 222 " pdb=" S3 F3S D 602 " model vdw 2.013 3.760 nonbonded pdb=" OH TYR A 68 " pdb=" O PRO A 224 " model vdw 2.090 3.040 ... (remaining 137846 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.530 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: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 43.170 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.050 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 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 : 0.030 1.774 16972 Z= 1.807 Angle : 1.485 52.370 23202 Z= 0.618 Chirality : 0.556 19.468 2478 Planarity : 0.006 0.078 2986 Dihedral : 15.658 132.892 6122 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.96 % Favored : 88.66 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % 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: -2.64 (0.17), residues: 2072 helix: -1.63 (0.19), residues: 670 sheet: -1.40 (0.36), residues: 182 loop : -1.91 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP A 111 HIS 0.016 0.002 HIS D 503 PHE 0.034 0.004 PHE E 79 TYR 0.030 0.003 TYR D 368 ARG 0.011 0.001 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 86 PHE cc_start: 0.4663 (t80) cc_final: 0.4278 (t80) REVERT: B 148 LEU cc_start: 0.8433 (mt) cc_final: 0.8193 (mt) REVERT: B 150 TYR cc_start: 0.5574 (t80) cc_final: 0.5275 (t80) REVERT: C 410 GLU cc_start: 0.6098 (tp30) cc_final: 0.5835 (tp30) REVERT: E 86 PHE cc_start: 0.4701 (t80) cc_final: 0.4272 (t80) REVERT: E 148 LEU cc_start: 0.8457 (mt) cc_final: 0.8233 (mt) REVERT: E 150 TYR cc_start: 0.5648 (t80) cc_final: 0.5356 (t80) REVERT: F 135 TYR cc_start: 0.6874 (t80) cc_final: 0.6654 (t80) REVERT: F 410 GLU cc_start: 0.6060 (tp30) cc_final: 0.5821 (tp30) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.2700 time to fit residues: 89.8132 Evaluate side-chains 180 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 8.9990 chunk 156 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 53 optimal weight: 0.0570 chunk 105 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 overall best weight: 1.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 503 HIS C 124 ASN C 238 GLN ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 503 HIS F 124 ASN ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.192 16972 Z= 0.332 Angle : 1.192 54.002 23202 Z= 0.478 Chirality : 0.071 1.892 2478 Planarity : 0.006 0.067 2986 Dihedral : 10.157 117.892 2432 Min Nonbonded Distance : 1.477 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.23 % Favored : 93.29 % Rotamer: Outliers : 0.82 % Allowed : 9.68 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % 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: -1.82 (0.18), residues: 2072 helix: -0.60 (0.20), residues: 694 sheet: -0.71 (0.39), residues: 170 loop : -1.69 (0.18), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 111 HIS 0.005 0.001 HIS A 503 PHE 0.016 0.001 PHE A 270 TYR 0.017 0.002 TYR C 120 ARG 0.007 0.001 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 209 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.7039 (mp10) REVERT: B 150 TYR cc_start: 0.5336 (t80) cc_final: 0.4829 (t80) REVERT: C 224 ASP cc_start: 0.7789 (p0) cc_final: 0.7537 (p0) REVERT: D 61 GLN cc_start: 0.7434 (OUTLIER) cc_final: 0.6946 (mp10) REVERT: E 86 PHE cc_start: 0.4043 (t80) cc_final: 0.3809 (t80) REVERT: E 150 TYR cc_start: 0.5290 (t80) cc_final: 0.4805 (t80) REVERT: F 224 ASP cc_start: 0.7718 (p0) cc_final: 0.7478 (p0) outliers start: 14 outliers final: 6 residues processed: 216 average time/residue: 0.2462 time to fit residues: 84.5921 Evaluate side-chains 188 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 180 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain F residue 80 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 10.0000 chunk 58 optimal weight: 0.0170 chunk 155 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 187 optimal weight: 10.0000 chunk 202 optimal weight: 9.9990 chunk 166 optimal weight: 9.9990 chunk 185 optimal weight: 0.2980 chunk 63 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 HIS ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 GLN ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 HIS ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 411 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 16972 Z= 0.215 Angle : 1.116 86.056 23202 Z= 0.438 Chirality : 0.062 1.512 2478 Planarity : 0.005 0.058 2986 Dihedral : 9.797 112.389 2432 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.37 % Favored : 93.53 % Rotamer: Outliers : 1.76 % Allowed : 12.62 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % 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: -1.34 (0.19), residues: 2072 helix: -0.15 (0.20), residues: 718 sheet: -0.32 (0.39), residues: 166 loop : -1.47 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 111 HIS 0.005 0.001 HIS C 105 PHE 0.013 0.001 PHE A 270 TYR 0.017 0.001 TYR A 79 ARG 0.007 0.001 ARG D 133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 220 time to evaluate : 1.833 Fit side-chains REVERT: A 61 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.6705 (mp10) REVERT: A 211 ASP cc_start: 0.8234 (t70) cc_final: 0.7007 (t0) REVERT: A 221 ASN cc_start: 0.8379 (t0) cc_final: 0.8132 (t0) REVERT: A 440 VAL cc_start: 0.6719 (m) cc_final: 0.6509 (m) REVERT: C 118 MET cc_start: 0.7796 (tpt) cc_final: 0.7229 (tpt) REVERT: C 182 HIS cc_start: 0.5866 (m-70) cc_final: 0.5592 (m-70) REVERT: C 449 LYS cc_start: 0.6547 (pptt) cc_final: 0.5447 (ptpp) REVERT: D 61 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.6787 (mp10) REVERT: D 211 ASP cc_start: 0.8244 (t70) cc_final: 0.7036 (t0) REVERT: D 221 ASN cc_start: 0.8339 (t0) cc_final: 0.8122 (t0) REVERT: D 440 VAL cc_start: 0.6729 (m) cc_final: 0.6527 (m) REVERT: F 118 MET cc_start: 0.7784 (tpt) cc_final: 0.7228 (tpt) REVERT: F 224 ASP cc_start: 0.7651 (p0) cc_final: 0.7367 (p0) outliers start: 30 outliers final: 19 residues processed: 236 average time/residue: 0.2597 time to fit residues: 94.6974 Evaluate side-chains 213 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 192 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 61 GLN Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 80 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 0.7980 chunk 140 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 199 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 178 optimal weight: 0.7980 chunk 53 optimal weight: 0.3980 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 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN C 347 HIS ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 ASN E 89 GLN F 347 HIS ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 16972 Z= 0.222 Angle : 1.089 84.077 23202 Z= 0.426 Chirality : 0.059 1.416 2478 Planarity : 0.005 0.056 2986 Dihedral : 9.636 110.899 2432 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.79 % Favored : 94.11 % Rotamer: Outliers : 2.35 % Allowed : 13.62 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.19), residues: 2072 helix: 0.13 (0.20), residues: 718 sheet: 0.26 (0.39), residues: 166 loop : -1.27 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 128 HIS 0.004 0.001 HIS F 105 PHE 0.019 0.001 PHE C 64 TYR 0.018 0.001 TYR A 79 ARG 0.006 0.000 ARG D 397 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 216 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.6841 (t0) cc_final: 0.6566 (t0) REVERT: A 211 ASP cc_start: 0.8250 (t70) cc_final: 0.6937 (t0) REVERT: C 118 MET cc_start: 0.8053 (tpt) cc_final: 0.7765 (tpt) REVERT: C 182 HIS cc_start: 0.5953 (m-70) cc_final: 0.5718 (m-70) REVERT: C 190 ARG cc_start: 0.6423 (tpp80) cc_final: 0.6177 (tpp80) REVERT: C 449 LYS cc_start: 0.6554 (pptt) cc_final: 0.5460 (ptpp) REVERT: C 456 MET cc_start: 0.5798 (tpt) cc_final: 0.5358 (tpt) REVERT: D 61 GLN cc_start: 0.7390 (OUTLIER) cc_final: 0.6711 (mp10) REVERT: D 211 ASP cc_start: 0.8204 (t70) cc_final: 0.6939 (t0) REVERT: D 221 ASN cc_start: 0.8432 (t0) cc_final: 0.8214 (t0) REVERT: F 118 MET cc_start: 0.8036 (tpt) cc_final: 0.7749 (tpt) REVERT: F 190 ARG cc_start: 0.6382 (tpp80) cc_final: 0.6125 (tpp80) REVERT: F 449 LYS cc_start: 0.6627 (pptt) cc_final: 0.5485 (ptpp) REVERT: F 456 MET cc_start: 0.5845 (tpt) cc_final: 0.5532 (tpt) outliers start: 40 outliers final: 23 residues processed: 240 average time/residue: 0.2549 time to fit residues: 95.4348 Evaluate side-chains 214 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 190 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 57 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 0.0050 chunk 178 optimal weight: 0.5980 chunk 50 optimal weight: 8.9990 overall best weight: 1.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 HIS ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN C 347 HIS ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 ASN ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 ASN E 89 GLN E 123 GLN F 347 HIS ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 16972 Z= 0.238 Angle : 1.095 83.669 23202 Z= 0.426 Chirality : 0.060 1.462 2478 Planarity : 0.005 0.056 2986 Dihedral : 9.638 112.391 2432 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.94 % Favored : 93.97 % Rotamer: Outliers : 2.29 % Allowed : 14.85 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.19), residues: 2072 helix: 0.25 (0.20), residues: 718 sheet: 0.30 (0.40), residues: 166 loop : -1.21 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 111 HIS 0.007 0.001 HIS D 278 PHE 0.023 0.001 PHE B 144 TYR 0.016 0.001 TYR F 135 ARG 0.004 0.000 ARG D 205 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 201 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.6708 (mp10) REVERT: A 211 ASP cc_start: 0.8244 (t70) cc_final: 0.6934 (t0) REVERT: A 221 ASN cc_start: 0.8379 (t0) cc_final: 0.8106 (t0) REVERT: C 182 HIS cc_start: 0.5967 (m-70) cc_final: 0.5738 (m-70) REVERT: C 190 ARG cc_start: 0.6385 (tpp80) cc_final: 0.6168 (tpp80) REVERT: C 449 LYS cc_start: 0.6582 (pptt) cc_final: 0.5503 (ptpp) REVERT: C 456 MET cc_start: 0.5776 (tpt) cc_final: 0.5432 (tpt) REVERT: D 61 GLN cc_start: 0.7456 (OUTLIER) cc_final: 0.6658 (mp10) REVERT: D 211 ASP cc_start: 0.8211 (t70) cc_final: 0.6921 (t0) REVERT: D 221 ASN cc_start: 0.8455 (t0) cc_final: 0.8134 (t0) REVERT: F 190 ARG cc_start: 0.6476 (tpp80) cc_final: 0.6231 (tpp80) REVERT: F 456 MET cc_start: 0.5808 (tpt) cc_final: 0.5485 (tpt) outliers start: 39 outliers final: 28 residues processed: 229 average time/residue: 0.2483 time to fit residues: 89.3797 Evaluate side-chains 219 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 189 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 61 GLN Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 57 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.2676 > 50: distance: 76 - 81: 10.763 distance: 81 - 82: 12.427 distance: 82 - 83: 30.260 distance: 82 - 85: 14.355 distance: 83 - 84: 36.648 distance: 83 - 89: 9.963 distance: 85 - 86: 20.312 distance: 86 - 87: 9.462 distance: 86 - 88: 14.791 distance: 89 - 90: 8.711 distance: 90 - 91: 26.738 distance: 90 - 93: 34.052 distance: 91 - 92: 16.498 distance: 91 - 98: 18.690 distance: 93 - 94: 9.345 distance: 94 - 95: 12.389 distance: 95 - 96: 12.224 distance: 96 - 97: 7.533 distance: 98 - 99: 10.312 distance: 99 - 100: 12.268 distance: 99 - 102: 19.705 distance: 100 - 101: 15.560 distance: 100 - 112: 25.979 distance: 102 - 103: 18.163 distance: 103 - 104: 8.315 distance: 103 - 105: 8.065 distance: 104 - 106: 12.179 distance: 105 - 107: 4.760 distance: 105 - 108: 6.573 distance: 106 - 107: 4.423 distance: 107 - 109: 7.384 distance: 108 - 110: 7.374 distance: 109 - 111: 6.322 distance: 110 - 111: 10.699 distance: 112 - 113: 14.580 distance: 113 - 114: 11.808 distance: 113 - 116: 22.162 distance: 114 - 115: 16.077 distance: 114 - 120: 14.630 distance: 116 - 117: 3.544 distance: 117 - 118: 20.891 distance: 117 - 119: 29.721 distance: 120 - 121: 12.470 distance: 121 - 122: 7.042 distance: 121 - 124: 7.767 distance: 122 - 123: 12.025 distance: 122 - 131: 7.510 distance: 124 - 125: 17.781 distance: 125 - 126: 27.147 distance: 126 - 127: 16.207 distance: 127 - 128: 16.796 distance: 128 - 129: 21.418 distance: 128 - 130: 28.150 distance: 131 - 132: 9.319 distance: 132 - 133: 5.845 distance: 132 - 135: 7.920 distance: 133 - 134: 18.098 distance: 133 - 138: 7.029 distance: 135 - 136: 30.594 distance: 135 - 137: 28.888 distance: 138 - 139: 11.455 distance: 139 - 140: 21.821 distance: 139 - 142: 12.437 distance: 140 - 141: 20.101 distance: 140 - 148: 20.583 distance: 142 - 143: 8.893 distance: 143 - 144: 20.569 distance: 143 - 145: 20.200 distance: 144 - 146: 18.125 distance: 145 - 147: 18.940 distance: 146 - 147: 9.101 distance: 148 - 149: 14.102 distance: 149 - 150: 8.524 distance: 149 - 152: 17.861 distance: 150 - 151: 35.713 distance: 150 - 156: 14.673 distance: 152 - 153: 18.029 distance: 153 - 154: 24.221 distance: 153 - 155: 23.353 distance: 156 - 157: 12.396 distance: 157 - 158: 23.182 distance: 157 - 160: 7.306 distance: 158 - 159: 26.635 distance: 158 - 166: 11.035 distance: 160 - 161: 20.153 distance: 161 - 162: 16.472 distance: 161 - 163: 8.610 distance: 162 - 164: 12.538 distance: 163 - 165: 8.562 distance: 164 - 165: 16.264 distance: 166 - 167: 5.330 distance: 167 - 168: 9.125 distance: 167 - 170: 21.219 distance: 168 - 169: 29.844 distance: 168 - 172: 4.863 distance: 170 - 171: 26.541