Starting phenix.real_space_refine on Fri Jul 3 22:55:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7w2j_32262/07_2026/7w2j_32262.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w2j_32262/07_2026/7w2j_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/cci-nas-00/data/ceres_data/7w2j_32262/07_2026/7w2j_32262.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w2j_32262/07_2026/7w2j_32262.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7w2j_32262/07_2026/7w2j_32262.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7w2j_32262/07_2026/7w2j_32262.cif" model { file = "/net/cci-nas-00/data/ceres_data/7w2j_32262/07_2026/7w2j_32262.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w2j_32262/07_2026/7w2j_32262.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 5.20, per 1000 atoms: 0.31 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: 1.69 Conformation dependent library (CDL) restraints added in 704.1 milliseconds 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: 0.26 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: 2.21 Time building geometry restraints manager: 2.14 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: 9358 26.58 - 53.16: 478 53.16 - 79.74: 40 79.74 - 106.31: 18 106.31 - 132.89: 2 Dihedral angle restraints: 9896 sinusoidal: 3842 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 9893 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: 0.03 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: 0.000 Normalize map: mean=0, sd=1: 1.360 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: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.700 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 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 : 0.035 1.774 17010 Z= 1.787 Angle : 1.692 52.370 23220 Z= 0.621 Chirality : 0.556 19.468 2478 Planarity : 0.006 0.078 2986 Dihedral : 15.428 132.892 6036 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 17.82 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.011 0.001 ARG A 397 TYR 0.030 0.003 TYR D 368 PHE 0.034 0.004 PHE E 79 TRP 0.052 0.003 TRP A 111 HIS 0.016 0.002 HIS D 503 Details of bonding type rmsd/Z covalent geometry : bond 0.02956 / 1.46 (16972) covalent geometry : angle 1.48512 / 0.62 (23202) hydrogen bonds : bond 0.25783 / 17.76 ( 498) hydrogen bonds : angle 10.23269 / 7.42 ( 1434) metal coordination : bond 0.87980 / 51.96 ( 6) metal coordination : angle 29.16381 / 15.83 ( 18) Misc. bond : bond 0.19219 / 12.85 ( 32) *********************** 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 to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.538 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: 0.5573 (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: 0.1118 time to fit residues: 37.5964 Evaluate side-chains 180 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 110 HIS ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.157349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.147703 restraints weight = 22052.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.145034 restraints weight = 23761.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.144815 restraints weight = 29632.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.144824 restraints weight = 24787.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.144729 restraints weight = 26419.475| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.186 17010 Z= 0.236 Angle : 1.475 59.303 23220 Z= 0.486 Chirality : 0.066 1.652 2478 Planarity : 0.006 0.070 2986 Dihedral : 9.232 118.109 2346 Min Nonbonded Distance : 1.529 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.84 % Favored : 93.77 % Rotamer: Outliers : 0.82 % Allowed : 9.10 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % 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 are not related in a simple way. whole: -1.78 (0.18), residues: 2072 helix: -0.56 (0.20), residues: 690 sheet: -0.67 (0.39), residues: 170 loop : -1.66 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 397 TYR 0.018 0.002 TYR C 120 PHE 0.016 0.001 PHE D 270 TRP 0.020 0.002 TRP A 111 HIS 0.005 0.001 HIS D 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.23 (16972) covalent geometry : angle 1.20885 / 0.48 (23202) hydrogen bonds : bond 0.04979 / 3.40 ( 498) hydrogen bonds : angle 6.56887 / 4.71 ( 1434) metal coordination : bond 0.01612 / 0.91 ( 6) metal coordination : angle 30.37770 / 16.16 ( 18) Misc. bond : bond 0.04254 / 2.74 ( 32) *********************** 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 226 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 212 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.7016 (mp10) REVERT: B 150 TYR cc_start: 0.5390 (t80) cc_final: 0.4866 (t80) REVERT: C 224 ASP cc_start: 0.7766 (p0) cc_final: 0.7501 (p0) REVERT: D 61 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.6993 (mp10) REVERT: E 86 PHE cc_start: 0.3956 (t80) cc_final: 0.3738 (t80) REVERT: E 150 TYR cc_start: 0.5411 (t80) cc_final: 0.4901 (t80) REVERT: F 224 ASP cc_start: 0.7780 (p0) cc_final: 0.7517 (p0) outliers start: 14 outliers final: 6 residues processed: 219 average time/residue: 0.0960 time to fit residues: 33.9995 Evaluate side-chains 191 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 183 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 121 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 157 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 178 optimal weight: 9.9990 chunk 145 optimal weight: 9.9990 chunk 169 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 GLN ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.157911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 111)---------------| | r_work = 0.3633 r_free = 0.3633 target = 0.144414 restraints weight = 22473.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.143756 restraints weight = 27174.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.143529 restraints weight = 23130.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.143089 restraints weight = 25570.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.143199 restraints weight = 23143.016| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.151 17010 Z= 0.166 Angle : 1.495 86.004 23220 Z= 0.457 Chirality : 0.060 1.416 2478 Planarity : 0.005 0.058 2986 Dihedral : 9.080 118.263 2346 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.95 % Favored : 92.76 % Rotamer: Outliers : 1.29 % Allowed : 13.03 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % 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 are not related in a simple way. whole: -1.49 (0.18), residues: 2072 helix: -0.27 (0.20), residues: 704 sheet: -0.37 (0.40), residues: 166 loop : -1.56 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 133 TYR 0.018 0.002 TYR A 79 PHE 0.015 0.001 PHE A 270 TRP 0.015 0.001 TRP B 128 HIS 0.005 0.001 HIS E 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (16972) covalent geometry : angle 1.13748 / 0.45 (23202) hydrogen bonds : bond 0.04127 / 2.85 ( 498) hydrogen bonds : angle 6.04362 / 4.33 ( 1434) metal coordination : bond 0.00256 / 0.13 ( 6) metal coordination : angle 34.88941 / 21.02 ( 18) Misc. bond : bond 0.03890 / 2.16 ( 32) *********************** 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 222 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 61 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.6772 (mp10) REVERT: A 221 ASN cc_start: 0.8506 (t0) cc_final: 0.8184 (t0) REVERT: A 440 VAL cc_start: 0.7011 (m) cc_final: 0.6780 (m) REVERT: B 150 TYR cc_start: 0.5384 (t80) cc_final: 0.4858 (t80) REVERT: C 118 MET cc_start: 0.7827 (tpt) cc_final: 0.7361 (tpt) REVERT: C 224 ASP cc_start: 0.7677 (p0) cc_final: 0.7410 (p0) REVERT: C 449 LYS cc_start: 0.6685 (pptt) cc_final: 0.5668 (ptpp) REVERT: D 61 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.6794 (mp10) REVERT: D 257 MET cc_start: 0.6166 (mtm) cc_final: 0.5965 (mtp) REVERT: D 440 VAL cc_start: 0.6924 (m) cc_final: 0.6704 (m) REVERT: E 150 TYR cc_start: 0.5349 (t80) cc_final: 0.4817 (t80) REVERT: F 118 MET cc_start: 0.7823 (tpt) cc_final: 0.7372 (tpt) REVERT: F 224 ASP cc_start: 0.7664 (p0) cc_final: 0.7393 (p0) outliers start: 22 outliers final: 12 residues processed: 214 average time/residue: 0.1137 time to fit residues: 39.4527 Evaluate side-chains 201 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 364 THR Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 171 VAL 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 D residue 485 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 120 optimal weight: 4.9990 chunk 29 optimal weight: 0.4980 chunk 56 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 201 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 411 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.150527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.130705 restraints weight = 22929.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.130637 restraints weight = 28551.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.131325 restraints weight = 24108.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.131027 restraints weight = 21644.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.131161 restraints weight = 20025.307| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.173 17010 Z= 0.249 Angle : 1.564 84.762 23220 Z= 0.491 Chirality : 0.064 1.468 2478 Planarity : 0.006 0.064 2986 Dihedral : 9.424 127.433 2346 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.54 % Favored : 91.12 % Rotamer: Outliers : 2.93 % Allowed : 13.97 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % 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 are not related in a simple way. whole: -1.56 (0.18), residues: 2072 helix: -0.32 (0.20), residues: 706 sheet: -0.36 (0.39), residues: 170 loop : -1.62 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 262 TYR 0.019 0.002 TYR B 150 PHE 0.026 0.002 PHE E 144 TRP 0.015 0.002 TRP E 128 HIS 0.008 0.001 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.25 (16972) covalent geometry : angle 1.21142 / 0.48 (23202) hydrogen bonds : bond 0.04564 / 3.12 ( 498) hydrogen bonds : angle 6.04525 / 4.33 ( 1434) metal coordination : bond 0.00088 / 0.05 ( 6) metal coordination : angle 35.52655 / 21.32 ( 18) Misc. bond : bond 0.05004 / 2.85 ( 32) *********************** 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 241 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 191 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7525 (tt) REVERT: A 257 MET cc_start: 0.6290 (mtm) cc_final: 0.5995 (mtp) REVERT: C 118 MET cc_start: 0.8397 (tpt) cc_final: 0.8132 (tpt) REVERT: C 224 ASP cc_start: 0.7725 (p0) cc_final: 0.7499 (p0) REVERT: D 13 ILE cc_start: 0.7811 (OUTLIER) cc_final: 0.7498 (tt) REVERT: F 118 MET cc_start: 0.8404 (tpt) cc_final: 0.8125 (tpt) REVERT: F 182 HIS cc_start: 0.5886 (m-70) cc_final: 0.5539 (m170) REVERT: F 224 ASP cc_start: 0.7756 (p0) cc_final: 0.7513 (p0) outliers start: 50 outliers final: 31 residues processed: 222 average time/residue: 0.1036 time to fit residues: 37.9131 Evaluate side-chains 217 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 33 VAL 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 368 TYR 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 137 THR Chi-restraints excluded: chain B residue 157 VAL 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 253 LEU Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 45 SER 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 368 TYR 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 137 THR Chi-restraints excluded: chain E residue 157 VAL 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 Chi-restraints excluded: chain F residue 253 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 154 optimal weight: 6.9990 chunk 167 optimal weight: 9.9990 chunk 163 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 72 optimal weight: 0.2980 chunk 55 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.159157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.149260 restraints weight = 22149.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.146146 restraints weight = 23531.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 75)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.145640 restraints weight = 25113.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 90)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.141644 restraints weight = 24287.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 82)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.141305 restraints weight = 25895.541| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 17010 Z= 0.167 Angle : 1.480 83.731 23220 Z= 0.449 Chirality : 0.061 1.443 2478 Planarity : 0.005 0.060 2986 Dihedral : 9.084 120.129 2346 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.27 % Favored : 93.53 % Rotamer: Outliers : 2.52 % Allowed : 15.55 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % 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 are not related in a simple way. whole: -1.26 (0.19), residues: 2072 helix: -0.07 (0.20), residues: 708 sheet: -0.05 (0.41), residues: 166 loop : -1.45 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 262 TYR 0.017 0.001 TYR A 79 PHE 0.016 0.001 PHE D 270 TRP 0.012 0.001 TRP B 128 HIS 0.005 0.001 HIS E 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (16972) covalent geometry : angle 1.12631 / 0.44 (23202) hydrogen bonds : bond 0.03757 / 2.61 ( 498) hydrogen bonds : angle 5.73534 / 4.10 ( 1434) metal coordination : bond 0.00172 / 0.11 ( 6) metal coordination : angle 34.52313 / 20.85 ( 18) Misc. bond : bond 0.03637 / 2.30 ( 32) *********************** 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 250 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 207 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7493 (tt) REVERT: A 57 ASP cc_start: 0.6782 (t0) cc_final: 0.6562 (t0) REVERT: C 224 ASP cc_start: 0.7564 (p0) cc_final: 0.7319 (p0) REVERT: C 449 LYS cc_start: 0.6542 (pptt) cc_final: 0.5434 (ptpp) REVERT: D 57 ASP cc_start: 0.6779 (t0) cc_final: 0.6565 (t0) REVERT: F 182 HIS cc_start: 0.5851 (m-70) cc_final: 0.5396 (m170) REVERT: F 224 ASP cc_start: 0.7586 (p0) cc_final: 0.7344 (p0) outliers start: 43 outliers final: 32 residues processed: 235 average time/residue: 0.1207 time to fit residues: 44.2429 Evaluate side-chains 225 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE 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 294 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 450 ILE 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 137 THR 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 D residue 33 VAL Chi-restraints excluded: chain D residue 45 SER 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 368 TYR Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain D residue 450 ILE 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 137 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 21 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 164 optimal weight: 0.3980 chunk 92 optimal weight: 0.1980 chunk 90 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 chunk 172 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN B 123 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 89 GLN E 123 GLN F 347 HIS ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.153646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.140314 restraints weight = 22871.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.139554 restraints weight = 35676.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.140227 restraints weight = 33071.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.140323 restraints weight = 24256.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.140462 restraints weight = 22752.821| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 17010 Z= 0.152 Angle : 1.454 83.377 23220 Z= 0.438 Chirality : 0.060 1.449 2478 Planarity : 0.005 0.059 2986 Dihedral : 8.898 116.343 2346 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.27 % Favored : 93.63 % Rotamer: Outliers : 2.93 % Allowed : 16.26 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % 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 are not related in a simple way. whole: -1.01 (0.19), residues: 2072 helix: 0.11 (0.20), residues: 722 sheet: 0.35 (0.41), residues: 166 loop : -1.35 (0.19), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 397 TYR 0.018 0.001 TYR F 135 PHE 0.014 0.001 PHE A 270 TRP 0.014 0.001 TRP B 128 HIS 0.004 0.001 HIS D 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (16972) covalent geometry : angle 1.10544 / 0.43 (23202) hydrogen bonds : bond 0.03434 / 2.40 ( 498) hydrogen bonds : angle 5.58058 / 4.00 ( 1434) metal coordination : bond 0.00091 / 0.06 ( 6) metal coordination : angle 33.96925 / 20.60 ( 18) Misc. bond : bond 0.03654 / 2.58 ( 32) *********************** REFINEMENT MACRO_CYCLE 6 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 258 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 208 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7464 (tt) REVERT: A 61 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.6583 (mp10) REVERT: A 226 CYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7139 (p) REVERT: C 449 LYS cc_start: 0.6657 (pptt) cc_final: 0.5590 (ptpp) REVERT: C 456 MET cc_start: 0.5622 (tpt) cc_final: 0.5257 (tpt) REVERT: D 13 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7501 (tt) REVERT: D 61 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.6651 (mp10) REVERT: D 226 CYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7110 (p) REVERT: F 456 MET cc_start: 0.5556 (tpt) cc_final: 0.4766 (tpp) outliers start: 50 outliers final: 32 residues processed: 240 average time/residue: 0.1128 time to fit residues: 43.3917 Evaluate side-chains 228 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 190 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE 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 226 CYS Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 368 TYR 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 C residue 80 SER Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 226 CYS 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 368 TYR Chi-restraints excluded: chain D residue 458 ILE 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 Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 253 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 23 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 chunk 3 optimal weight: 0.1980 chunk 131 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 168 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 120 optimal weight: 0.5980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 ASN ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** F 347 HIS ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.154329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.140770 restraints weight = 22718.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.140119 restraints weight = 31703.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.140431 restraints weight = 31361.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.140673 restraints weight = 24345.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.140785 restraints weight = 22337.432| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 17010 Z= 0.151 Angle : 1.445 83.370 23220 Z= 0.435 Chirality : 0.060 1.449 2478 Planarity : 0.005 0.061 2986 Dihedral : 8.805 114.459 2346 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.18 % Favored : 93.73 % Rotamer: Outliers : 3.17 % Allowed : 16.90 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % 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 are not related in a simple way. whole: -0.85 (0.19), residues: 2072 helix: 0.28 (0.20), residues: 722 sheet: 0.41 (0.42), residues: 162 loop : -1.27 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 397 TYR 0.018 0.001 TYR F 135 PHE 0.012 0.001 PHE D 270 TRP 0.013 0.001 TRP B 128 HIS 0.003 0.001 HIS E 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (16972) covalent geometry : angle 1.09733 / 0.43 (23202) hydrogen bonds : bond 0.03348 / 2.34 ( 498) hydrogen bonds : angle 5.48378 / 3.93 ( 1434) metal coordination : bond 0.00104 / 0.07 ( 6) metal coordination : angle 33.76616 / 20.51 ( 18) Misc. bond : bond 0.04478 / 3.14 ( 32) *********************** REFINEMENT MACRO_CYCLE 7 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 257 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 203 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7509 (tt) REVERT: A 61 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.6704 (mp10) REVERT: A 221 ASN cc_start: 0.8466 (t0) cc_final: 0.8104 (t0) REVERT: A 226 CYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7199 (p) REVERT: C 182 HIS cc_start: 0.5755 (m-70) cc_final: 0.5376 (m170) REVERT: C 449 LYS cc_start: 0.6699 (pptt) cc_final: 0.5672 (ptpp) REVERT: C 456 MET cc_start: 0.5556 (tpt) cc_final: 0.4665 (tpp) REVERT: D 61 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.6553 (mp10) REVERT: D 221 ASN cc_start: 0.8443 (t0) cc_final: 0.8082 (t0) REVERT: D 226 CYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7177 (p) REVERT: F 456 MET cc_start: 0.5546 (tpt) cc_final: 0.4713 (tpp) outliers start: 54 outliers final: 41 residues processed: 241 average time/residue: 0.1059 time to fit residues: 41.7619 Evaluate side-chains 236 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 190 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE 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 146 TYR Chi-restraints excluded: chain A residue 226 CYS 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 368 TYR 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 132 VAL Chi-restraints excluded: chain B residue 137 THR 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 253 LEU Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 137 THR 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 Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 343 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.6823 > 50: distance: 91 - 112: 20.280 distance: 106 - 112: 17.654 distance: 112 - 113: 13.456 distance: 113 - 114: 8.628 distance: 114 - 115: 12.451 distance: 114 - 116: 36.499 distance: 116 - 117: 21.410 distance: 117 - 118: 8.818 distance: 117 - 120: 16.903 distance: 118 - 119: 35.477 distance: 118 - 127: 27.124 distance: 120 - 121: 20.876 distance: 121 - 122: 9.539 distance: 121 - 123: 21.523 distance: 122 - 124: 33.842 distance: 123 - 125: 22.955 distance: 124 - 126: 13.316 distance: 125 - 126: 23.739 distance: 127 - 128: 22.126 distance: 128 - 129: 9.912 distance: 128 - 131: 40.749 distance: 129 - 130: 6.058 distance: 129 - 133: 23.308 distance: 131 - 132: 30.832 distance: 133 - 134: 11.484 distance: 134 - 135: 31.368 distance: 134 - 137: 22.195 distance: 135 - 136: 35.798 distance: 135 - 141: 6.589 distance: 137 - 138: 40.606 distance: 138 - 139: 16.336 distance: 138 - 140: 17.305 distance: 141 - 142: 12.600 distance: 142 - 143: 32.304 distance: 142 - 145: 26.390 distance: 143 - 144: 14.090 distance: 143 - 148: 46.033 distance: 145 - 146: 16.113 distance: 145 - 147: 16.988 distance: 148 - 149: 10.469 distance: 148 - 154: 40.925 distance: 149 - 150: 16.683 distance: 149 - 152: 16.527 distance: 150 - 151: 16.006 distance: 150 - 155: 9.833 distance: 152 - 153: 29.920 distance: 153 - 154: 27.596 distance: 155 - 156: 17.842 distance: 156 - 157: 21.326 distance: 156 - 159: 25.351 distance: 157 - 158: 10.157 distance: 157 - 162: 4.237 distance: 159 - 160: 24.676 distance: 159 - 161: 35.773 distance: 163 - 164: 7.070 distance: 163 - 166: 4.842 distance: 164 - 165: 15.568 distance: 164 - 169: 10.353 distance: 166 - 167: 6.094 distance: 167 - 168: 4.451 distance: 169 - 170: 15.229 distance: 170 - 171: 39.433 distance: 170 - 173: 9.129 distance: 171 - 172: 4.038 distance: 171 - 178: 22.239 distance: 173 - 174: 22.356 distance: 174 - 175: 23.499 distance: 175 - 176: 12.168 distance: 175 - 177: 16.429 distance: 178 - 179: 20.282 distance: 179 - 180: 19.722 distance: 179 - 182: 40.645 distance: 180 - 181: 29.006 distance: 180 - 183: 21.834