Starting phenix.real_space_refine on Fri Jan 24 05:09:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cuj_45935/01_2025/9cuj_45935.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cuj_45935/01_2025/9cuj_45935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cuj_45935/01_2025/9cuj_45935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cuj_45935/01_2025/9cuj_45935.map" model { file = "/net/cci-nas-00/data/ceres_data/9cuj_45935/01_2025/9cuj_45935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cuj_45935/01_2025/9cuj_45935.cif" } resolution = 2.78 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= 0.003 sd= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 20 5.49 5 S 160 5.16 5 C 14288 2.51 5 N 3336 2.21 5 O 3752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 21557 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4895 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 26, 'TRANS': 583} Chain: "B" Number of atoms: 4895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4895 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 26, 'TRANS': 583} Chain: "C" Number of atoms: 4895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4895 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 26, 'TRANS': 583} Chain: "D" Number of atoms: 4895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4895 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 26, 'TRANS': 583} Chain: "A" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 477 Unusual residues: {' CA': 1, 'PCW': 5, 'POV': 8, 'Y01': 3} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 315 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1, 'POV:plan-1': 1, 'PCW:plan-1': 5, 'PCW:plan-2': 2, 'PCW:plan-3': 5, 'PCW:plan-4': 5} Unresolved non-hydrogen planarities: 78 Chain: "B" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 476 Unusual residues: {'PCW': 5, 'POV': 8, 'Y01': 3} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 315 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1, 'POV:plan-1': 1, 'PCW:plan-1': 5, 'PCW:plan-2': 2, 'PCW:plan-3': 5, 'PCW:plan-4': 5} Unresolved non-hydrogen planarities: 78 Chain: "C" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 476 Unusual residues: {'PCW': 5, 'POV': 8, 'Y01': 3} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 315 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1, 'POV:plan-1': 1, 'PCW:plan-1': 5, 'PCW:plan-2': 2, 'PCW:plan-3': 5, 'PCW:plan-4': 5} Unresolved non-hydrogen planarities: 78 Chain: "D" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 476 Unusual residues: {'PCW': 5, 'POV': 8, 'Y01': 3} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 315 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1, 'POV:plan-1': 1, 'PCW:plan-1': 5, 'PCW:plan-2': 2, 'PCW:plan-3': 5, 'PCW:plan-4': 5} Unresolved non-hydrogen planarities: 78 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Time building chain proxies: 12.81, per 1000 atoms: 0.59 Number of scatterers: 21557 At special positions: 0 Unit cell: (131.97, 131.97, 122.01, 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) Ca 1 19.99 S 160 16.00 P 20 15.00 O 3752 8.00 N 3336 7.00 C 14288 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.49 Conformation dependent library (CDL) restraints added in 2.4 seconds 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4608 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 8 sheets defined 67.3% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 removed outlier: 3.675A pdb=" N SER A 32 " --> pdb=" O SER A 28 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 57 through 66 removed outlier: 3.546A pdb=" N LEU A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.578A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 106 removed outlier: 4.008A pdb=" N VAL A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.752A pdb=" N VAL A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.580A pdb=" N ARG A 134 " --> pdb=" O MET A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.505A pdb=" N CYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.590A pdb=" N HIS A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 204 through 206 No H-bonds generated for 'chain 'A' and resid 204 through 206' Processing helix chain 'A' and resid 208 through 222 removed outlier: 3.914A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.754A pdb=" N VAL A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.549A pdb=" N ALA A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 291 through 299 removed outlier: 3.572A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 309 removed outlier: 3.844A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 324 removed outlier: 3.581A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 349 removed outlier: 3.652A pdb=" N TYR A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 removed outlier: 4.067A pdb=" N TYR A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 404 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.867A pdb=" N PHE A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 423 removed outlier: 4.415A pdb=" N THR A 419 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 445 Processing helix chain 'A' and resid 450 through 463 removed outlier: 3.573A pdb=" N VAL A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 470 removed outlier: 3.700A pdb=" N ALA A 469 " --> pdb=" O MET A 466 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 487 Processing helix chain 'A' and resid 489 through 512 removed outlier: 5.827A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 515 No H-bonds generated for 'chain 'A' and resid 513 through 515' Processing helix chain 'A' and resid 525 through 538 Processing helix chain 'A' and resid 552 through 566 removed outlier: 4.215A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 588 removed outlier: 3.545A pdb=" N LEU A 574 " --> pdb=" O MET A 570 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 606 removed outlier: 3.575A pdb=" N ALA A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 removed outlier: 3.530A pdb=" N LEU A 612 " --> pdb=" O PRO A 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 47 removed outlier: 3.746A pdb=" N ASN B 37 " --> pdb=" O ARG B 33 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 Processing helix chain 'B' and resid 57 through 66 removed outlier: 3.546A pdb=" N LEU B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.578A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 106 removed outlier: 4.009A pdb=" N VAL B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 106' Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.753A pdb=" N VAL B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.579A pdb=" N ARG B 134 " --> pdb=" O MET B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 removed outlier: 3.506A pdb=" N CYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.590A pdb=" N HIS B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 208 through 222 removed outlier: 3.914A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 removed outlier: 3.755A pdb=" N VAL B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.550A pdb=" N ALA B 247 " --> pdb=" O PRO B 243 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.573A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 309 removed outlier: 3.844A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 324 removed outlier: 3.581A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 349 removed outlier: 3.652A pdb=" N TYR B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 removed outlier: 4.067A pdb=" N TYR B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 404 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.866A pdb=" N PHE B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 409 " --> pdb=" O PRO B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 423 removed outlier: 4.415A pdb=" N THR B 419 " --> pdb=" O PHE B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 445 Processing helix chain 'B' and resid 450 through 463 removed outlier: 3.574A pdb=" N VAL B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 470 removed outlier: 3.700A pdb=" N ALA B 469 " --> pdb=" O MET B 466 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 487 Processing helix chain 'B' and resid 489 through 512 removed outlier: 5.827A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 515 No H-bonds generated for 'chain 'B' and resid 513 through 515' Processing helix chain 'B' and resid 525 through 538 Processing helix chain 'B' and resid 552 through 566 removed outlier: 4.215A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 588 removed outlier: 3.544A pdb=" N LEU B 574 " --> pdb=" O MET B 570 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 606 removed outlier: 3.574A pdb=" N ALA B 595 " --> pdb=" O GLU B 591 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 removed outlier: 3.531A pdb=" N LEU B 612 " --> pdb=" O PRO B 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 47 removed outlier: 3.746A pdb=" N ASN C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 Processing helix chain 'C' and resid 57 through 66 removed outlier: 3.546A pdb=" N LEU C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.578A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 106 removed outlier: 4.007A pdb=" N VAL C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 106' Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.753A pdb=" N VAL C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.581A pdb=" N ARG C 134 " --> pdb=" O MET C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 173 removed outlier: 3.505A pdb=" N CYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.589A pdb=" N HIS C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 204 through 206 No H-bonds generated for 'chain 'C' and resid 204 through 206' Processing helix chain 'C' and resid 208 through 222 removed outlier: 3.914A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.755A pdb=" N VAL C 235 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.549A pdb=" N ALA C 247 " --> pdb=" O PRO C 243 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 Processing helix chain 'C' and resid 291 through 299 removed outlier: 3.573A pdb=" N ILE C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 309 removed outlier: 3.843A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 324 removed outlier: 3.582A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.651A pdb=" N TYR C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 377 removed outlier: 4.067A pdb=" N TYR C 377 " --> pdb=" O LEU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 404 Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.866A pdb=" N PHE C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 409 " --> pdb=" O PRO C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 423 removed outlier: 4.415A pdb=" N THR C 419 " --> pdb=" O PHE C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 445 Processing helix chain 'C' and resid 450 through 463 removed outlier: 3.573A pdb=" N VAL C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 470 removed outlier: 3.700A pdb=" N ALA C 469 " --> pdb=" O MET C 466 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 487 Processing helix chain 'C' and resid 489 through 512 removed outlier: 5.827A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 515 No H-bonds generated for 'chain 'C' and resid 513 through 515' Processing helix chain 'C' and resid 525 through 538 Processing helix chain 'C' and resid 552 through 566 removed outlier: 4.215A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 588 removed outlier: 3.545A pdb=" N LEU C 574 " --> pdb=" O MET C 570 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 606 removed outlier: 3.575A pdb=" N ALA C 595 " --> pdb=" O GLU C 591 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 removed outlier: 3.530A pdb=" N LEU C 612 " --> pdb=" O PRO C 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 47 removed outlier: 3.747A pdb=" N ASN D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 57 through 66 removed outlier: 3.546A pdb=" N LEU D 61 " --> pdb=" O ASP D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.577A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 106 removed outlier: 4.008A pdb=" N VAL D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 106' Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.752A pdb=" N VAL D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.580A pdb=" N ARG D 134 " --> pdb=" O MET D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 173 removed outlier: 3.506A pdb=" N CYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.589A pdb=" N HIS D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 203 Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 208 through 222 removed outlier: 3.914A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 removed outlier: 3.754A pdb=" N VAL D 235 " --> pdb=" O LEU D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 removed outlier: 3.549A pdb=" N ALA D 247 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 291 through 299 removed outlier: 3.573A pdb=" N ILE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 309 removed outlier: 3.843A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 324 removed outlier: 3.581A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 349 removed outlier: 3.651A pdb=" N TYR D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 377 removed outlier: 4.067A pdb=" N TYR D 377 " --> pdb=" O LEU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 404 Processing helix chain 'D' and resid 404 through 410 removed outlier: 3.866A pdb=" N PHE D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG D 409 " --> pdb=" O PRO D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 423 removed outlier: 4.415A pdb=" N THR D 419 " --> pdb=" O PHE D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 445 Processing helix chain 'D' and resid 450 through 463 removed outlier: 3.574A pdb=" N VAL D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 470 removed outlier: 3.700A pdb=" N ALA D 469 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 487 Processing helix chain 'D' and resid 489 through 512 removed outlier: 5.827A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 515 No H-bonds generated for 'chain 'D' and resid 513 through 515' Processing helix chain 'D' and resid 525 through 538 Processing helix chain 'D' and resid 552 through 566 removed outlier: 4.215A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 588 removed outlier: 3.544A pdb=" N LEU D 574 " --> pdb=" O MET D 570 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP D 580 " --> pdb=" O ALA D 576 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 606 removed outlier: 3.574A pdb=" N ALA D 595 " --> pdb=" O GLU D 591 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 removed outlier: 3.530A pdb=" N LEU D 612 " --> pdb=" O PRO D 609 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 268 removed outlier: 6.690A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 268 removed outlier: 6.691A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 265 through 268 removed outlier: 6.691A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 265 through 268 removed outlier: 6.691A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1010 hydrogen bonds defined for protein. 2922 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: 6.39 Time building geometry restraints manager: 6.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 3204 1.30 - 1.43: 5461 1.43 - 1.56: 12808 1.56 - 1.69: 175 1.69 - 1.81: 272 Bond restraints: 21920 Sorted by residual: bond pdb=" C29 POV A 803 " pdb="C210 POV A 803 " ideal model delta sigma weight residual 1.333 1.552 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C29 POV B 805 " pdb="C210 POV B 805 " ideal model delta sigma weight residual 1.333 1.552 -0.219 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C29 POV D 809 " pdb="C210 POV D 809 " ideal model delta sigma weight residual 1.333 1.551 -0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C29 POV C 805 " pdb="C210 POV C 805 " ideal model delta sigma weight residual 1.333 1.551 -0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C29 POV C 808 " pdb="C210 POV C 808 " ideal model delta sigma weight residual 1.333 1.550 -0.217 2.00e-02 2.50e+03 1.17e+02 ... (remaining 21915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 28517 3.25 - 6.50: 676 6.50 - 9.75: 159 9.75 - 12.99: 68 12.99 - 16.24: 16 Bond angle restraints: 29436 Sorted by residual: angle pdb=" C GLU C 68 " pdb=" N ASP C 69 " pdb=" CA ASP C 69 " ideal model delta sigma weight residual 121.54 133.83 -12.29 1.91e+00 2.74e-01 4.14e+01 angle pdb=" C GLU A 68 " pdb=" N ASP A 69 " pdb=" CA ASP A 69 " ideal model delta sigma weight residual 121.54 133.82 -12.28 1.91e+00 2.74e-01 4.14e+01 angle pdb=" C GLU D 68 " pdb=" N ASP D 69 " pdb=" CA ASP D 69 " ideal model delta sigma weight residual 121.54 133.77 -12.23 1.91e+00 2.74e-01 4.10e+01 angle pdb=" C GLU B 68 " pdb=" N ASP B 69 " pdb=" CA ASP B 69 " ideal model delta sigma weight residual 121.54 133.77 -12.23 1.91e+00 2.74e-01 4.10e+01 angle pdb=" C29 POV A 806 " pdb="C210 POV A 806 " pdb="C211 POV A 806 " ideal model delta sigma weight residual 127.67 111.43 16.24 3.00e+00 1.11e-01 2.93e+01 ... (remaining 29431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.26: 13225 30.26 - 60.52: 696 60.52 - 90.78: 69 90.78 - 121.04: 14 121.04 - 151.30: 12 Dihedral angle restraints: 14016 sinusoidal: 6880 harmonic: 7136 Sorted by residual: dihedral pdb=" CA ASP C 69 " pdb=" C ASP C 69 " pdb=" N CYS C 70 " pdb=" CA CYS C 70 " ideal model delta harmonic sigma weight residual 180.00 153.16 26.84 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA ASP B 69 " pdb=" C ASP B 69 " pdb=" N CYS B 70 " pdb=" CA CYS B 70 " ideal model delta harmonic sigma weight residual 180.00 153.18 26.82 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA ASP A 69 " pdb=" C ASP A 69 " pdb=" N CYS A 70 " pdb=" CA CYS A 70 " ideal model delta harmonic sigma weight residual 180.00 153.19 26.81 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 14013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2767 0.074 - 0.148: 395 0.148 - 0.222: 30 0.222 - 0.296: 0 0.296 - 0.370: 12 Chirality restraints: 3204 Sorted by residual: chirality pdb=" CG LEU D 458 " pdb=" CB LEU D 458 " pdb=" CD1 LEU D 458 " pdb=" CD2 LEU D 458 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CG LEU B 458 " pdb=" CB LEU B 458 " pdb=" CD1 LEU B 458 " pdb=" CD2 LEU B 458 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CG LEU A 458 " pdb=" CB LEU A 458 " pdb=" CD1 LEU A 458 " pdb=" CD2 LEU A 458 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.38e+00 ... (remaining 3201 not shown) Planarity restraints: 3552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV B 805 " 0.299 2.00e-02 2.50e+03 2.99e-01 8.96e+02 pdb=" C29 POV B 805 " -0.297 2.00e-02 2.50e+03 pdb="C210 POV B 805 " -0.302 2.00e-02 2.50e+03 pdb="C211 POV B 805 " 0.299 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 809 " -0.292 2.00e-02 2.50e+03 2.93e-01 8.58e+02 pdb=" C29 POV D 809 " 0.288 2.00e-02 2.50e+03 pdb="C210 POV D 809 " 0.298 2.00e-02 2.50e+03 pdb="C211 POV D 809 " -0.294 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A 803 " -0.287 2.00e-02 2.50e+03 2.90e-01 8.43e+02 pdb=" C29 POV A 803 " 0.278 2.00e-02 2.50e+03 pdb="C210 POV A 803 " 0.302 2.00e-02 2.50e+03 pdb="C211 POV A 803 " -0.293 2.00e-02 2.50e+03 ... (remaining 3549 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5834 2.81 - 3.33: 17911 3.33 - 3.86: 33584 3.86 - 4.38: 43816 4.38 - 4.90: 72872 Nonbonded interactions: 174017 Sorted by model distance: nonbonded pdb=" O ALA C 563 " pdb=" OG1 THR C 567 " model vdw 2.291 3.040 nonbonded pdb=" O ALA A 563 " pdb=" OG1 THR A 567 " model vdw 2.292 3.040 nonbonded pdb=" O ALA B 563 " pdb=" OG1 THR B 567 " model vdw 2.292 3.040 nonbonded pdb=" O ALA D 563 " pdb=" OG1 THR D 567 " model vdw 2.292 3.040 nonbonded pdb=" OE2 GLU A 535 " pdb=" O HOH A 901 " model vdw 2.312 3.040 ... (remaining 174012 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' and (resid 28 through 637 or resid 806)) selection = (chain 'B' and (resid 28 through 637 or (resid 806 and (name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name O21 or name O22 or name C210 or name C211 or name C212 or na \ me C213 or name C214 or name C215 or name C216)))) selection = (chain 'C' and (resid 28 through 637 or (resid 806 and (name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name O21 or name O22 or name C210 or name C211 or name C212 or na \ me C213 or name C214 or name C215 or name C216)))) selection = (chain 'D' and (resid 28 through 637 or (resid 806 and (name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name O21 or name O22 or name C210 or name C211 or name C212 or na \ me C213 or name C214 or name C215 or name C216)))) } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.020 Extract box with map and model: 0.900 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 45.830 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 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 : 0.011 0.219 21920 Z= 0.665 Angle : 1.393 16.244 29436 Z= 0.640 Chirality : 0.054 0.370 3204 Planarity : 0.013 0.299 3552 Dihedral : 17.597 151.303 9408 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.51 % Allowed : 3.02 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.66 (0.11), residues: 2432 helix: -4.26 (0.06), residues: 1456 sheet: -2.58 (0.65), residues: 76 loop : -2.56 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 629 HIS 0.012 0.003 HIS C 522 PHE 0.028 0.003 PHE B 169 TYR 0.027 0.003 TYR A 377 ARG 0.008 0.001 ARG A 589 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 500 time to evaluate : 2.339 Fit side-chains REVERT: A 47 SER cc_start: 0.6063 (m) cc_final: 0.5480 (p) REVERT: A 93 GLU cc_start: 0.6607 (mp0) cc_final: 0.6277 (mt-10) REVERT: A 96 MET cc_start: 0.5079 (mtm) cc_final: 0.4695 (mtm) REVERT: A 110 MET cc_start: 0.6739 (mtt) cc_final: 0.6473 (mtt) REVERT: A 139 ARG cc_start: 0.6568 (mtt-85) cc_final: 0.6211 (mpt180) REVERT: A 177 GLU cc_start: 0.7095 (mp0) cc_final: 0.6571 (mp0) REVERT: A 311 THR cc_start: 0.6079 (OUTLIER) cc_final: 0.5162 (m) REVERT: A 375 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7623 (mt-10) REVERT: A 379 THR cc_start: 0.7517 (t) cc_final: 0.7167 (p) REVERT: A 381 LYS cc_start: 0.7950 (mtmt) cc_final: 0.7566 (mtpt) REVERT: A 589 ARG cc_start: 0.7035 (tmm160) cc_final: 0.6758 (ttm-80) REVERT: A 590 ASP cc_start: 0.7399 (m-30) cc_final: 0.7130 (m-30) REVERT: A 608 LEU cc_start: 0.7416 (mt) cc_final: 0.7174 (mt) REVERT: A 637 GLN cc_start: 0.5700 (mp10) cc_final: 0.5143 (mp-120) REVERT: B 47 SER cc_start: 0.6198 (m) cc_final: 0.5746 (p) REVERT: B 93 GLU cc_start: 0.6723 (mp0) cc_final: 0.6357 (mt-10) REVERT: B 96 MET cc_start: 0.5230 (mtm) cc_final: 0.4907 (mtm) REVERT: B 139 ARG cc_start: 0.6899 (mtt-85) cc_final: 0.6494 (mpt180) REVERT: B 177 GLU cc_start: 0.7101 (mp0) cc_final: 0.6683 (mp0) REVERT: B 263 ARG cc_start: 0.7611 (mtt-85) cc_final: 0.7323 (mtm-85) REVERT: B 311 THR cc_start: 0.6097 (OUTLIER) cc_final: 0.5236 (m) REVERT: B 379 THR cc_start: 0.7899 (t) cc_final: 0.7673 (p) REVERT: B 381 LYS cc_start: 0.7994 (mtmt) cc_final: 0.7746 (mtpt) REVERT: B 392 THR cc_start: 0.8465 (t) cc_final: 0.8205 (m) REVERT: B 458 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8414 (mt) REVERT: B 497 MET cc_start: 0.8172 (mtt) cc_final: 0.7936 (mtm) REVERT: B 524 TYR cc_start: 0.8037 (p90) cc_final: 0.7793 (p90) REVERT: B 535 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7336 (mt-10) REVERT: B 590 ASP cc_start: 0.7573 (m-30) cc_final: 0.7309 (m-30) REVERT: B 637 GLN cc_start: 0.6029 (mp10) cc_final: 0.5400 (mp-120) REVERT: C 78 MET cc_start: 0.7261 (mmt) cc_final: 0.6949 (mmp) REVERT: C 93 GLU cc_start: 0.6660 (mp0) cc_final: 0.6296 (mt-10) REVERT: C 96 MET cc_start: 0.5037 (mtm) cc_final: 0.4706 (mtm) REVERT: C 139 ARG cc_start: 0.6683 (mtt-85) cc_final: 0.6321 (mtm180) REVERT: C 177 GLU cc_start: 0.7106 (mp0) cc_final: 0.6614 (mp0) REVERT: C 263 ARG cc_start: 0.7597 (mtt-85) cc_final: 0.7281 (mtm-85) REVERT: C 311 THR cc_start: 0.6077 (OUTLIER) cc_final: 0.5111 (m) REVERT: C 375 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7555 (mt-10) REVERT: C 379 THR cc_start: 0.7870 (t) cc_final: 0.7530 (p) REVERT: C 381 LYS cc_start: 0.7866 (mtmt) cc_final: 0.7596 (mtpt) REVERT: C 392 THR cc_start: 0.8431 (t) cc_final: 0.8204 (m) REVERT: C 458 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8406 (mt) REVERT: C 497 MET cc_start: 0.8073 (mtt) cc_final: 0.7808 (mtm) REVERT: C 524 TYR cc_start: 0.7991 (p90) cc_final: 0.7682 (p90) REVERT: C 535 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7441 (mt-10) REVERT: C 589 ARG cc_start: 0.7232 (tmm160) cc_final: 0.6930 (ttm-80) REVERT: C 590 ASP cc_start: 0.7567 (m-30) cc_final: 0.7296 (m-30) REVERT: C 637 GLN cc_start: 0.5940 (mp10) cc_final: 0.5294 (mp-120) REVERT: D 78 MET cc_start: 0.7305 (mmt) cc_final: 0.6987 (mmp) REVERT: D 93 GLU cc_start: 0.6671 (mp0) cc_final: 0.6297 (mt-10) REVERT: D 96 MET cc_start: 0.5035 (mtm) cc_final: 0.4663 (mtm) REVERT: D 139 ARG cc_start: 0.6702 (mtt-85) cc_final: 0.6309 (mtm180) REVERT: D 177 GLU cc_start: 0.7101 (mp0) cc_final: 0.6590 (mp0) REVERT: D 263 ARG cc_start: 0.7642 (mtt-85) cc_final: 0.7197 (mtm-85) REVERT: D 311 THR cc_start: 0.6051 (OUTLIER) cc_final: 0.5117 (m) REVERT: D 375 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7534 (mt-10) REVERT: D 379 THR cc_start: 0.7801 (t) cc_final: 0.7372 (p) REVERT: D 381 LYS cc_start: 0.7896 (mtmt) cc_final: 0.7610 (mtpt) REVERT: D 392 THR cc_start: 0.8456 (t) cc_final: 0.8222 (m) REVERT: D 458 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8390 (mt) REVERT: D 497 MET cc_start: 0.8075 (mtt) cc_final: 0.7817 (mtm) REVERT: D 535 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7475 (mt-10) REVERT: D 589 ARG cc_start: 0.7207 (tmm160) cc_final: 0.6879 (ttm-80) REVERT: D 590 ASP cc_start: 0.7538 (m-30) cc_final: 0.7243 (m-30) REVERT: D 608 LEU cc_start: 0.7376 (mt) cc_final: 0.7175 (mt) REVERT: D 637 GLN cc_start: 0.5748 (mp10) cc_final: 0.5201 (mp-120) outliers start: 32 outliers final: 5 residues processed: 528 average time/residue: 1.3618 time to fit residues: 814.9963 Evaluate side-chains 378 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 366 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 6.9990 chunk 184 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 191 optimal weight: 10.0000 chunk 74 optimal weight: 0.0470 chunk 116 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 221 optimal weight: 10.0000 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 118 GLN A 122 HIS A 174 ASN A 225 HIS A 369 GLN A 370 GLN A 546 ASN A 572 ASN B 37 ASN B 118 GLN B 122 HIS B 174 ASN B 225 HIS B 369 GLN B 370 GLN B 546 ASN B 572 ASN B 582 HIS C 37 ASN C 118 GLN C 122 HIS C 174 ASN C 225 HIS C 369 GLN C 370 GLN C 546 ASN C 572 ASN C 582 HIS D 37 ASN D 118 GLN D 122 HIS D 174 ASN D 225 HIS D 369 GLN D 370 GLN D 546 ASN D 572 ASN D 582 HIS Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.196829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.131745 restraints weight = 20770.813| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.88 r_work: 0.3236 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 21920 Z= 0.296 Angle : 0.687 7.992 29436 Z= 0.344 Chirality : 0.043 0.279 3204 Planarity : 0.006 0.046 3552 Dihedral : 19.029 178.568 4720 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.60 % Allowed : 7.84 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.15), residues: 2432 helix: -1.59 (0.11), residues: 1460 sheet: -2.14 (0.66), residues: 76 loop : -1.70 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 613 HIS 0.006 0.001 HIS A 201 PHE 0.023 0.002 PHE B 537 TYR 0.017 0.002 TYR D 377 ARG 0.009 0.001 ARG D 146 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 408 time to evaluate : 2.219 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.6268 (OUTLIER) cc_final: 0.5904 (tm) REVERT: A 96 MET cc_start: 0.5411 (mtm) cc_final: 0.5118 (mtm) REVERT: A 177 GLU cc_start: 0.7111 (mp0) cc_final: 0.6783 (mp0) REVERT: A 375 GLU cc_start: 0.8238 (mt-10) cc_final: 0.8005 (mt-10) REVERT: A 378 MET cc_start: 0.8312 (mtt) cc_final: 0.7953 (mtp) REVERT: A 381 LYS cc_start: 0.7362 (mtmt) cc_final: 0.7162 (mtpt) REVERT: A 458 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8560 (mt) REVERT: A 535 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7660 (mt-10) REVERT: A 608 LEU cc_start: 0.7750 (mt) cc_final: 0.7428 (mt) REVERT: A 618 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7633 (mt) REVERT: A 637 GLN cc_start: 0.6225 (mp10) cc_final: 0.5960 (mp-120) REVERT: B 51 LEU cc_start: 0.6244 (OUTLIER) cc_final: 0.5891 (tm) REVERT: B 93 GLU cc_start: 0.7035 (mp0) cc_final: 0.6667 (mp0) REVERT: B 96 MET cc_start: 0.5233 (mtm) cc_final: 0.4934 (mtm) REVERT: B 177 GLU cc_start: 0.7126 (mp0) cc_final: 0.6752 (mp0) REVERT: B 315 GLU cc_start: 0.8243 (mp0) cc_final: 0.8031 (mp0) REVERT: B 381 LYS cc_start: 0.7347 (mtmt) cc_final: 0.7033 (mtpt) REVERT: B 392 THR cc_start: 0.8305 (t) cc_final: 0.7952 (m) REVERT: B 535 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7846 (mt-10) REVERT: B 590 ASP cc_start: 0.7910 (m-30) cc_final: 0.7675 (m-30) REVERT: B 610 ARG cc_start: 0.6592 (tpm170) cc_final: 0.6227 (tpt170) REVERT: B 618 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7556 (mt) REVERT: B 637 GLN cc_start: 0.6191 (mp10) cc_final: 0.5872 (mp-120) REVERT: C 78 MET cc_start: 0.7584 (mmt) cc_final: 0.7258 (mmp) REVERT: C 93 GLU cc_start: 0.7021 (mp0) cc_final: 0.6641 (mp0) REVERT: C 96 MET cc_start: 0.5349 (mtm) cc_final: 0.4970 (mtm) REVERT: C 177 GLU cc_start: 0.7142 (mp0) cc_final: 0.6806 (mp0) REVERT: C 375 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7940 (mt-10) REVERT: C 378 MET cc_start: 0.8351 (mtp) cc_final: 0.8102 (mtm) REVERT: C 381 LYS cc_start: 0.7309 (mtmt) cc_final: 0.7000 (mtpt) REVERT: C 392 THR cc_start: 0.8322 (t) cc_final: 0.7975 (m) REVERT: C 535 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7607 (mt-10) REVERT: C 610 ARG cc_start: 0.6722 (tpm170) cc_final: 0.6364 (tpt170) REVERT: C 618 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7556 (mt) REVERT: C 637 GLN cc_start: 0.6134 (mp10) cc_final: 0.5879 (mp-120) REVERT: D 37 ASN cc_start: 0.8053 (m110) cc_final: 0.7846 (m110) REVERT: D 78 MET cc_start: 0.7646 (mmt) cc_final: 0.7227 (mmp) REVERT: D 93 GLU cc_start: 0.7041 (mp0) cc_final: 0.6662 (mp0) REVERT: D 96 MET cc_start: 0.5281 (mtm) cc_final: 0.4922 (mtm) REVERT: D 177 GLU cc_start: 0.7111 (mp0) cc_final: 0.6767 (mp0) REVERT: D 375 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7949 (mt-10) REVERT: D 381 LYS cc_start: 0.7366 (mtmt) cc_final: 0.7111 (mtpt) REVERT: D 392 THR cc_start: 0.8315 (t) cc_final: 0.7959 (m) REVERT: D 535 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7766 (mt-10) REVERT: D 608 LEU cc_start: 0.7731 (mt) cc_final: 0.7424 (mt) REVERT: D 610 ARG cc_start: 0.6681 (tpm170) cc_final: 0.6330 (tpt170) REVERT: D 618 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7574 (mt) REVERT: D 637 GLN cc_start: 0.6198 (mp10) cc_final: 0.5944 (mp-120) outliers start: 55 outliers final: 23 residues processed: 440 average time/residue: 1.3529 time to fit residues: 676.2735 Evaluate side-chains 382 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 352 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 117 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 188 optimal weight: 4.9990 chunk 166 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 212 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 174 ASN A 197 ASN B 37 ASN B 197 ASN C 37 ASN C 197 ASN D 174 ASN D 197 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.197942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.136471 restraints weight = 20663.893| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.83 r_work: 0.3269 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21920 Z= 0.189 Angle : 0.570 7.807 29436 Z= 0.287 Chirality : 0.040 0.220 3204 Planarity : 0.005 0.040 3552 Dihedral : 17.522 157.894 4718 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.55 % Allowed : 11.20 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.17), residues: 2432 helix: -0.04 (0.13), residues: 1460 sheet: -1.96 (0.63), residues: 76 loop : -1.27 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 593 HIS 0.004 0.001 HIS B 265 PHE 0.014 0.001 PHE A 537 TYR 0.013 0.002 TYR C 467 ARG 0.009 0.001 ARG C 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 374 time to evaluate : 2.174 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.6364 (OUTLIER) cc_final: 0.6003 (tm) REVERT: A 93 GLU cc_start: 0.7324 (mp0) cc_final: 0.6533 (mp0) REVERT: A 96 MET cc_start: 0.5394 (mtm) cc_final: 0.5028 (mtm) REVERT: A 131 ASN cc_start: 0.6848 (m110) cc_final: 0.6284 (m-40) REVERT: A 177 GLU cc_start: 0.7088 (mp0) cc_final: 0.6821 (mp0) REVERT: A 311 THR cc_start: 0.5475 (OUTLIER) cc_final: 0.4849 (p) REVERT: A 315 GLU cc_start: 0.8101 (mp0) cc_final: 0.7896 (mp0) REVERT: A 375 GLU cc_start: 0.8260 (mt-10) cc_final: 0.8011 (mt-10) REVERT: A 378 MET cc_start: 0.8365 (mtt) cc_final: 0.8156 (mtp) REVERT: A 458 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8657 (mt) REVERT: A 535 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7692 (mt-10) REVERT: A 591 GLU cc_start: 0.7979 (pt0) cc_final: 0.7517 (mp0) REVERT: A 608 LEU cc_start: 0.7697 (mt) cc_final: 0.7377 (mt) REVERT: A 618 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7651 (mt) REVERT: A 637 GLN cc_start: 0.6285 (mp10) cc_final: 0.6036 (mp-120) REVERT: B 51 LEU cc_start: 0.6360 (OUTLIER) cc_final: 0.6013 (tm) REVERT: B 93 GLU cc_start: 0.6984 (mp0) cc_final: 0.6654 (mp0) REVERT: B 96 MET cc_start: 0.5355 (mtm) cc_final: 0.4968 (mtm) REVERT: B 131 ASN cc_start: 0.6850 (m110) cc_final: 0.6296 (m-40) REVERT: B 177 GLU cc_start: 0.7124 (mp0) cc_final: 0.6798 (mp0) REVERT: B 311 THR cc_start: 0.5440 (OUTLIER) cc_final: 0.4784 (p) REVERT: B 535 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7713 (mt-10) REVERT: B 588 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7757 (pt0) REVERT: B 590 ASP cc_start: 0.7885 (m-30) cc_final: 0.7654 (m-30) REVERT: B 610 ARG cc_start: 0.6518 (tpm170) cc_final: 0.6299 (tpt170) REVERT: B 618 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7577 (mt) REVERT: B 637 GLN cc_start: 0.6356 (mp10) cc_final: 0.6112 (mp-120) REVERT: C 93 GLU cc_start: 0.6973 (mp0) cc_final: 0.6628 (mp0) REVERT: C 96 MET cc_start: 0.5409 (mtm) cc_final: 0.5004 (mtm) REVERT: C 131 ASN cc_start: 0.6836 (m110) cc_final: 0.6280 (m-40) REVERT: C 177 GLU cc_start: 0.7055 (mp0) cc_final: 0.6829 (mp0) REVERT: C 311 THR cc_start: 0.5364 (OUTLIER) cc_final: 0.4712 (p) REVERT: C 375 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7971 (mt-10) REVERT: C 535 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7671 (mt-10) REVERT: C 610 ARG cc_start: 0.6551 (tpm170) cc_final: 0.6336 (tpt170) REVERT: C 618 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7586 (mt) REVERT: C 637 GLN cc_start: 0.6251 (mp10) cc_final: 0.6025 (mp-120) REVERT: D 93 GLU cc_start: 0.6973 (mp0) cc_final: 0.6654 (mp0) REVERT: D 96 MET cc_start: 0.5354 (mtm) cc_final: 0.4923 (mtm) REVERT: D 131 ASN cc_start: 0.6880 (OUTLIER) cc_final: 0.6318 (m-40) REVERT: D 146 ARG cc_start: 0.7394 (mtp-110) cc_final: 0.7079 (mtp-110) REVERT: D 177 GLU cc_start: 0.7069 (mp0) cc_final: 0.6786 (mp0) REVERT: D 311 THR cc_start: 0.5354 (OUTLIER) cc_final: 0.4858 (p) REVERT: D 375 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7925 (mt-10) REVERT: D 535 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7715 (mt-10) REVERT: D 608 LEU cc_start: 0.7667 (mt) cc_final: 0.7382 (mt) REVERT: D 610 ARG cc_start: 0.6509 (tpm170) cc_final: 0.6102 (tpt170) REVERT: D 618 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7592 (mt) REVERT: D 637 GLN cc_start: 0.6268 (mp10) cc_final: 0.6030 (mp-120) outliers start: 54 outliers final: 16 residues processed: 419 average time/residue: 1.3168 time to fit residues: 631.7533 Evaluate side-chains 369 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 340 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 139 optimal weight: 0.7980 chunk 11 optimal weight: 20.0000 chunk 175 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 68 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 117 optimal weight: 0.1980 chunk 174 optimal weight: 0.4980 chunk 163 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 36 GLN C 185 HIS D 36 GLN D 37 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.199932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.137610 restraints weight = 20992.718| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.01 r_work: 0.3296 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 21920 Z= 0.145 Angle : 0.527 7.531 29436 Z= 0.265 Chirality : 0.039 0.186 3204 Planarity : 0.004 0.039 3552 Dihedral : 16.132 141.739 4718 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.46 % Allowed : 12.38 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.17), residues: 2432 helix: 0.73 (0.14), residues: 1452 sheet: -1.48 (0.64), residues: 76 loop : -1.13 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 593 HIS 0.006 0.001 HIS C 185 PHE 0.014 0.001 PHE A 408 TYR 0.011 0.001 TYR B 467 ARG 0.007 0.000 ARG D 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 383 time to evaluate : 2.280 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.6257 (OUTLIER) cc_final: 0.5908 (tm) REVERT: A 93 GLU cc_start: 0.7257 (mp0) cc_final: 0.6471 (mp0) REVERT: A 96 MET cc_start: 0.5397 (mtm) cc_final: 0.4975 (mtm) REVERT: A 131 ASN cc_start: 0.6797 (m110) cc_final: 0.6269 (m-40) REVERT: A 177 GLU cc_start: 0.7119 (mp0) cc_final: 0.6792 (pm20) REVERT: A 311 THR cc_start: 0.5347 (OUTLIER) cc_final: 0.4735 (p) REVERT: A 375 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7923 (mt-10) REVERT: A 378 MET cc_start: 0.8334 (mtt) cc_final: 0.8064 (mtm) REVERT: A 379 THR cc_start: 0.7156 (OUTLIER) cc_final: 0.6900 (p) REVERT: A 491 MET cc_start: 0.8077 (mmp) cc_final: 0.7758 (mmp) REVERT: A 535 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7727 (mt-10) REVERT: A 591 GLU cc_start: 0.7909 (pt0) cc_final: 0.7497 (mp0) REVERT: A 608 LEU cc_start: 0.7621 (mt) cc_final: 0.7355 (mt) REVERT: A 618 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7632 (mt) REVERT: A 637 GLN cc_start: 0.6286 (mp10) cc_final: 0.5999 (mp-120) REVERT: B 51 LEU cc_start: 0.6337 (OUTLIER) cc_final: 0.5979 (tm) REVERT: B 93 GLU cc_start: 0.6959 (mp0) cc_final: 0.6631 (mp0) REVERT: B 96 MET cc_start: 0.5389 (mtm) cc_final: 0.4965 (mtm) REVERT: B 131 ASN cc_start: 0.6797 (OUTLIER) cc_final: 0.6290 (m-40) REVERT: B 177 GLU cc_start: 0.7073 (mp0) cc_final: 0.6771 (mp0) REVERT: B 311 THR cc_start: 0.5485 (OUTLIER) cc_final: 0.4845 (p) REVERT: B 378 MET cc_start: 0.8286 (mtm) cc_final: 0.8058 (mtp) REVERT: B 458 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8574 (mt) REVERT: B 535 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7683 (mt-10) REVERT: B 590 ASP cc_start: 0.7866 (m-30) cc_final: 0.7662 (m-30) REVERT: B 591 GLU cc_start: 0.7938 (pt0) cc_final: 0.7526 (mp0) REVERT: B 610 ARG cc_start: 0.6435 (tpm170) cc_final: 0.6104 (tpt170) REVERT: B 618 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7530 (mt) REVERT: B 637 GLN cc_start: 0.6368 (mp10) cc_final: 0.6147 (mp-120) REVERT: C 93 GLU cc_start: 0.6891 (mp0) cc_final: 0.6549 (mp0) REVERT: C 96 MET cc_start: 0.5395 (mtm) cc_final: 0.5000 (mtm) REVERT: C 131 ASN cc_start: 0.6780 (m110) cc_final: 0.6272 (m-40) REVERT: C 177 GLU cc_start: 0.7059 (mp0) cc_final: 0.6773 (pm20) REVERT: C 311 THR cc_start: 0.5518 (OUTLIER) cc_final: 0.4943 (p) REVERT: C 356 THR cc_start: 0.8456 (p) cc_final: 0.8251 (p) REVERT: C 458 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8580 (mt) REVERT: C 535 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7637 (mt-10) REVERT: C 591 GLU cc_start: 0.7917 (pt0) cc_final: 0.7505 (mp0) REVERT: C 610 ARG cc_start: 0.6432 (tpm170) cc_final: 0.6181 (tpm170) REVERT: C 618 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7564 (mt) REVERT: C 637 GLN cc_start: 0.6270 (mp10) cc_final: 0.6017 (mp-120) REVERT: D 93 GLU cc_start: 0.6981 (mp0) cc_final: 0.6646 (mp0) REVERT: D 96 MET cc_start: 0.5513 (mtm) cc_final: 0.5110 (mtm) REVERT: D 131 ASN cc_start: 0.6804 (OUTLIER) cc_final: 0.6277 (m-40) REVERT: D 177 GLU cc_start: 0.7093 (mp0) cc_final: 0.6790 (mp0) REVERT: D 311 THR cc_start: 0.5360 (OUTLIER) cc_final: 0.4740 (p) REVERT: D 315 GLU cc_start: 0.7992 (mp0) cc_final: 0.7770 (mp0) REVERT: D 375 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7963 (mt-10) REVERT: D 458 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8571 (mt) REVERT: D 535 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7697 (mt-10) REVERT: D 591 GLU cc_start: 0.7891 (pt0) cc_final: 0.7481 (mp0) REVERT: D 608 LEU cc_start: 0.7550 (mt) cc_final: 0.7231 (mt) REVERT: D 610 ARG cc_start: 0.6329 (tpm170) cc_final: 0.6028 (tpt170) REVERT: D 618 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7570 (mt) REVERT: D 637 GLN cc_start: 0.6342 (mp10) cc_final: 0.6043 (mp-120) outliers start: 52 outliers final: 11 residues processed: 424 average time/residue: 1.3080 time to fit residues: 634.4904 Evaluate side-chains 381 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 354 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.1461 > 50: distance: 56 - 61: 35.537 distance: 61 - 62: 47.411 distance: 62 - 63: 63.116 distance: 62 - 65: 41.369 distance: 63 - 69: 39.043 distance: 65 - 66: 44.489 distance: 66 - 67: 45.142 distance: 66 - 68: 36.825 distance: 69 - 70: 69.520 distance: 70 - 71: 59.309 distance: 70 - 73: 53.657 distance: 71 - 72: 57.913 distance: 71 - 79: 62.683 distance: 74 - 75: 45.583 distance: 74 - 76: 41.341 distance: 75 - 77: 18.678 distance: 76 - 78: 46.806 distance: 77 - 78: 43.443 distance: 79 - 80: 45.294 distance: 80 - 81: 30.521 distance: 80 - 83: 15.328 distance: 81 - 82: 41.223 distance: 81 - 88: 28.337 distance: 83 - 84: 11.232 distance: 84 - 85: 57.307 distance: 85 - 87: 39.123 distance: 88 - 89: 57.409 distance: 89 - 90: 41.320 distance: 90 - 91: 27.263 distance: 90 - 92: 25.658 distance: 92 - 93: 39.981 distance: 93 - 94: 51.764 distance: 93 - 96: 33.024 distance: 94 - 95: 44.665 distance: 94 - 100: 50.342 distance: 96 - 97: 24.244 distance: 97 - 99: 21.396 distance: 100 - 101: 39.588 distance: 101 - 102: 56.524 distance: 101 - 104: 13.980 distance: 102 - 103: 51.087 distance: 102 - 107: 33.518 distance: 103 - 134: 54.764 distance: 104 - 105: 9.795 distance: 104 - 106: 15.929 distance: 107 - 108: 5.383 distance: 107 - 113: 29.470 distance: 108 - 109: 30.464 distance: 108 - 111: 26.759 distance: 109 - 110: 5.387 distance: 109 - 114: 29.428 distance: 111 - 112: 29.817 distance: 112 - 113: 27.884 distance: 114 - 115: 27.293 distance: 115 - 116: 51.157 distance: 115 - 118: 18.895 distance: 116 - 117: 23.215 distance: 116 - 125: 49.266 distance: 118 - 119: 35.073 distance: 119 - 120: 9.452 distance: 119 - 121: 55.204 distance: 120 - 122: 56.616 distance: 121 - 123: 7.626 distance: 122 - 124: 6.272 distance: 123 - 124: 14.610 distance: 125 - 126: 11.688 distance: 126 - 127: 18.274 distance: 126 - 129: 17.087 distance: 127 - 128: 25.784 distance: 127 - 134: 18.490 distance: 128 - 151: 27.688 distance: 129 - 130: 27.731 distance: 130 - 131: 14.671 distance: 131 - 132: 16.517 distance: 132 - 133: 17.627 distance: 134 - 135: 10.278 distance: 135 - 136: 29.345 distance: 135 - 138: 31.040 distance: 136 - 137: 17.804 distance: 136 - 142: 35.727 distance: 137 - 158: 29.628 distance: 138 - 139: 40.223 distance: 139 - 140: 34.235 distance: 139 - 141: 41.320