Starting phenix.real_space_refine on Sun Aug 24 16:11:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yih_33859/08_2025/7yih_33859.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yih_33859/08_2025/7yih_33859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yih_33859/08_2025/7yih_33859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yih_33859/08_2025/7yih_33859.map" model { file = "/net/cci-nas-00/data/ceres_data/7yih_33859/08_2025/7yih_33859.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yih_33859/08_2025/7yih_33859.cif" } resolution = 3.5 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= 0.001 sd= 0.041 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: 5 Type Number sf(0) Gaussians K 5 8.98 5 S 128 5.16 5 C 13796 2.51 5 N 3544 2.21 5 O 3848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21321 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' K': 5} Classifications: {'undetermined': 5, 'water': 1} Link IDs: {None: 5} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 5.20, per 1000 atoms: 0.24 Number of scatterers: 21321 At special positions: 0 Unit cell: (158.763, 158.763, 129.897, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 5 19.00 S 128 16.00 O 3848 8.00 N 3544 7.00 C 13796 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: 1.88 Conformation dependent library (CDL) restraints added in 687.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5048 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 46.4% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 150 through 154 removed outlier: 3.858A pdb=" N THR A 153 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 162 Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'A' and resid 211 through 238 removed outlier: 3.628A pdb=" N THR A 215 " --> pdb=" O CYS A 211 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 244 through 265 removed outlier: 3.827A pdb=" N LEU A 248 " --> pdb=" O ASN A 244 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 280 through 301 removed outlier: 6.284A pdb=" N VAL A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 328 removed outlier: 3.633A pdb=" N VAL A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 338 Processing helix chain 'A' and resid 345 through 375 removed outlier: 3.514A pdb=" N VAL A 375 " --> pdb=" O GLY A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 397 Processing helix chain 'A' and resid 414 through 431 Processing helix chain 'A' and resid 442 through 495 removed outlier: 3.823A pdb=" N LYS A 446 " --> pdb=" O THR A 442 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N MET A 474 " --> pdb=" O ILE A 470 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR A 475 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN A 477 " --> pdb=" O GLN A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 516 Processing helix chain 'A' and resid 520 through 527 removed outlier: 3.874A pdb=" N VAL A 524 " --> pdb=" O ASP A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 542 removed outlier: 3.551A pdb=" N ARG A 542 " --> pdb=" O VAL A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 563 Processing helix chain 'A' and resid 646 through 653 removed outlier: 3.665A pdb=" N LEU A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 664 removed outlier: 3.756A pdb=" N ASN A 658 " --> pdb=" O THR A 654 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 692 Processing helix chain 'B' and resid 83 through 88 Processing helix chain 'B' and resid 150 through 154 removed outlier: 3.858A pdb=" N THR B 153 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 211 through 238 removed outlier: 3.628A pdb=" N THR B 215 " --> pdb=" O CYS B 211 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 244 through 265 removed outlier: 3.827A pdb=" N LEU B 248 " --> pdb=" O ASN B 244 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 280 through 301 removed outlier: 6.285A pdb=" N VAL B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE B 295 " --> pdb=" O THR B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 328 removed outlier: 3.633A pdb=" N VAL B 325 " --> pdb=" O SER B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 338 Processing helix chain 'B' and resid 345 through 375 removed outlier: 3.514A pdb=" N VAL B 375 " --> pdb=" O GLY B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 397 Processing helix chain 'B' and resid 414 through 431 Processing helix chain 'B' and resid 442 through 495 removed outlier: 3.823A pdb=" N LYS B 446 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET B 447 " --> pdb=" O ASP B 443 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N MET B 474 " --> pdb=" O ILE B 470 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR B 475 " --> pdb=" O PHE B 471 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN B 477 " --> pdb=" O GLN B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 516 Processing helix chain 'B' and resid 520 through 527 removed outlier: 3.874A pdb=" N VAL B 524 " --> pdb=" O ASP B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 542 removed outlier: 3.551A pdb=" N ARG B 542 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 563 Processing helix chain 'B' and resid 646 through 653 removed outlier: 3.665A pdb=" N LEU B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 664 removed outlier: 3.756A pdb=" N ASN B 658 " --> pdb=" O THR B 654 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER B 659 " --> pdb=" O ALA B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 692 Processing helix chain 'C' and resid 83 through 88 Processing helix chain 'C' and resid 150 through 154 removed outlier: 3.858A pdb=" N THR C 153 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 183 through 187 Processing helix chain 'C' and resid 211 through 238 removed outlier: 3.628A pdb=" N THR C 215 " --> pdb=" O CYS C 211 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 244 through 265 removed outlier: 3.827A pdb=" N LEU C 248 " --> pdb=" O ASN C 244 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 280 through 301 removed outlier: 6.285A pdb=" N VAL C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE C 295 " --> pdb=" O THR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 328 removed outlier: 3.633A pdb=" N VAL C 325 " --> pdb=" O SER C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 338 Processing helix chain 'C' and resid 345 through 375 removed outlier: 3.514A pdb=" N VAL C 375 " --> pdb=" O GLY C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 397 Processing helix chain 'C' and resid 414 through 431 Processing helix chain 'C' and resid 442 through 495 removed outlier: 3.823A pdb=" N LYS C 446 " --> pdb=" O THR C 442 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET C 447 " --> pdb=" O ASP C 443 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N MET C 474 " --> pdb=" O ILE C 470 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR C 475 " --> pdb=" O PHE C 471 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN C 477 " --> pdb=" O GLN C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 516 Processing helix chain 'C' and resid 520 through 527 removed outlier: 3.874A pdb=" N VAL C 524 " --> pdb=" O ASP C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 542 removed outlier: 3.551A pdb=" N ARG C 542 " --> pdb=" O VAL C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 563 Processing helix chain 'C' and resid 646 through 653 removed outlier: 3.665A pdb=" N LEU C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 664 removed outlier: 3.756A pdb=" N ASN C 658 " --> pdb=" O THR C 654 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER C 659 " --> pdb=" O ALA C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 692 Processing helix chain 'D' and resid 83 through 88 Processing helix chain 'D' and resid 150 through 154 removed outlier: 3.858A pdb=" N THR D 153 " --> pdb=" O ALA D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 162 Processing helix chain 'D' and resid 183 through 187 Processing helix chain 'D' and resid 211 through 238 removed outlier: 3.628A pdb=" N THR D 215 " --> pdb=" O CYS D 211 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 244 through 265 removed outlier: 3.827A pdb=" N LEU D 248 " --> pdb=" O ASN D 244 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 268 No H-bonds generated for 'chain 'D' and resid 266 through 268' Processing helix chain 'D' and resid 280 through 301 removed outlier: 6.285A pdb=" N VAL D 294 " --> pdb=" O LYS D 290 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE D 295 " --> pdb=" O THR D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 328 removed outlier: 3.633A pdb=" N VAL D 325 " --> pdb=" O SER D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 338 Processing helix chain 'D' and resid 345 through 375 removed outlier: 3.514A pdb=" N VAL D 375 " --> pdb=" O GLY D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 397 Processing helix chain 'D' and resid 414 through 431 Processing helix chain 'D' and resid 442 through 495 removed outlier: 3.823A pdb=" N LYS D 446 " --> pdb=" O THR D 442 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET D 447 " --> pdb=" O ASP D 443 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N MET D 474 " --> pdb=" O ILE D 470 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR D 475 " --> pdb=" O PHE D 471 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN D 477 " --> pdb=" O GLN D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 516 Processing helix chain 'D' and resid 520 through 527 removed outlier: 3.874A pdb=" N VAL D 524 " --> pdb=" O ASP D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 542 removed outlier: 3.551A pdb=" N ARG D 542 " --> pdb=" O VAL D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 563 Processing helix chain 'D' and resid 646 through 653 removed outlier: 3.665A pdb=" N LEU D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 664 removed outlier: 3.756A pdb=" N ASN D 658 " --> pdb=" O THR D 654 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER D 659 " --> pdb=" O ALA D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 692 Processing sheet with id=AA1, first strand: chain 'A' and resid 270 through 271 removed outlier: 4.075A pdb=" N PHE A 270 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 567 through 571 removed outlier: 3.661A pdb=" N SER A 592 " --> pdb=" O ASP A 637 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N HIS A 639 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL A 590 " --> pdb=" O HIS A 639 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 602 through 607 removed outlier: 3.636A pdb=" N GLU A 602 " --> pdb=" O GLN A 599 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL A 597 " --> pdb=" O VAL A 604 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE A 606 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEU A 595 " --> pdb=" O ILE A 606 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 596 " --> pdb=" O ARG A 631 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 270 through 271 removed outlier: 4.075A pdb=" N PHE B 270 " --> pdb=" O ILE B 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 567 through 571 removed outlier: 3.663A pdb=" N SER B 592 " --> pdb=" O ASP B 637 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N HIS B 639 " --> pdb=" O VAL B 590 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL B 590 " --> pdb=" O HIS B 639 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 602 through 607 removed outlier: 3.636A pdb=" N GLU B 602 " --> pdb=" O GLN B 599 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL B 597 " --> pdb=" O VAL B 604 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE B 606 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEU B 595 " --> pdb=" O ILE B 606 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU B 596 " --> pdb=" O ARG B 631 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 270 through 271 removed outlier: 4.075A pdb=" N PHE C 270 " --> pdb=" O ILE C 278 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 567 through 571 removed outlier: 3.663A pdb=" N SER C 592 " --> pdb=" O ASP C 637 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N HIS C 639 " --> pdb=" O VAL C 590 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL C 590 " --> pdb=" O HIS C 639 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 602 through 607 removed outlier: 3.636A pdb=" N GLU C 602 " --> pdb=" O GLN C 599 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL C 597 " --> pdb=" O VAL C 604 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE C 606 " --> pdb=" O LEU C 595 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEU C 595 " --> pdb=" O ILE C 606 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU C 596 " --> pdb=" O ARG C 631 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 270 through 271 removed outlier: 4.075A pdb=" N PHE D 270 " --> pdb=" O ILE D 278 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 567 through 571 removed outlier: 3.661A pdb=" N SER D 592 " --> pdb=" O ASP D 637 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N HIS D 639 " --> pdb=" O VAL D 590 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL D 590 " --> pdb=" O HIS D 639 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 602 through 607 removed outlier: 3.636A pdb=" N GLU D 602 " --> pdb=" O GLN D 599 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL D 597 " --> pdb=" O VAL D 604 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE D 606 " --> pdb=" O LEU D 595 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LEU D 595 " --> pdb=" O ILE D 606 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU D 596 " --> pdb=" O ARG D 631 " (cutoff:3.500A) 860 hydrogen bonds defined for protein. 2484 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: 2.66 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6656 1.34 - 1.46: 4337 1.46 - 1.58: 10619 1.58 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 21804 Sorted by residual: bond pdb=" N TRP B 38 " pdb=" CA TRP B 38 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.41e-02 5.03e+03 3.70e+00 bond pdb=" N TRP C 38 " pdb=" CA TRP C 38 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.41e-02 5.03e+03 3.70e+00 bond pdb=" N TRP D 38 " pdb=" CA TRP D 38 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.41e-02 5.03e+03 3.70e+00 bond pdb=" N TRP A 38 " pdb=" CA TRP A 38 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.41e-02 5.03e+03 3.70e+00 bond pdb=" N VAL C 36 " pdb=" CA VAL C 36 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.25e-02 6.40e+03 3.12e+00 ... (remaining 21799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 28980 2.36 - 4.72: 536 4.72 - 7.08: 40 7.08 - 9.45: 16 9.45 - 11.81: 12 Bond angle restraints: 29584 Sorted by residual: angle pdb=" N PRO A 39 " pdb=" CA PRO A 39 " pdb=" C PRO A 39 " ideal model delta sigma weight residual 112.47 124.04 -11.57 2.06e+00 2.36e-01 3.15e+01 angle pdb=" N PRO D 39 " pdb=" CA PRO D 39 " pdb=" C PRO D 39 " ideal model delta sigma weight residual 112.47 124.04 -11.57 2.06e+00 2.36e-01 3.15e+01 angle pdb=" N PRO B 39 " pdb=" CA PRO B 39 " pdb=" C PRO B 39 " ideal model delta sigma weight residual 112.47 124.04 -11.57 2.06e+00 2.36e-01 3.15e+01 angle pdb=" N PRO C 39 " pdb=" CA PRO C 39 " pdb=" C PRO C 39 " ideal model delta sigma weight residual 112.47 124.04 -11.57 2.06e+00 2.36e-01 3.15e+01 angle pdb=" CA PRO A 549 " pdb=" N PRO A 549 " pdb=" CD PRO A 549 " ideal model delta sigma weight residual 112.00 104.71 7.29 1.40e+00 5.10e-01 2.71e+01 ... (remaining 29579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 11627 17.95 - 35.91: 1105 35.91 - 53.86: 160 53.86 - 71.81: 24 71.81 - 89.77: 16 Dihedral angle restraints: 12932 sinusoidal: 5144 harmonic: 7788 Sorted by residual: dihedral pdb=" CA PRO C 39 " pdb=" C PRO C 39 " pdb=" N VAL C 40 " pdb=" CA VAL C 40 " ideal model delta harmonic sigma weight residual 180.00 146.66 33.34 0 5.00e+00 4.00e-02 4.45e+01 dihedral pdb=" CA PRO B 39 " pdb=" C PRO B 39 " pdb=" N VAL B 40 " pdb=" CA VAL B 40 " ideal model delta harmonic sigma weight residual 180.00 146.66 33.34 0 5.00e+00 4.00e-02 4.45e+01 dihedral pdb=" CA PRO A 39 " pdb=" C PRO A 39 " pdb=" N VAL A 40 " pdb=" CA VAL A 40 " ideal model delta harmonic sigma weight residual 180.00 146.66 33.34 0 5.00e+00 4.00e-02 4.45e+01 ... (remaining 12929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3116 0.077 - 0.154: 276 0.154 - 0.231: 8 0.231 - 0.308: 0 0.308 - 0.384: 4 Chirality restraints: 3404 Sorted by residual: chirality pdb=" CA PRO A 39 " pdb=" N PRO A 39 " pdb=" C PRO A 39 " pdb=" CB PRO A 39 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA PRO B 39 " pdb=" N PRO B 39 " pdb=" C PRO B 39 " pdb=" CB PRO B 39 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA PRO D 39 " pdb=" N PRO D 39 " pdb=" C PRO D 39 " pdb=" CB PRO D 39 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.38 2.00e-01 2.50e+01 3.69e+00 ... (remaining 3401 not shown) Planarity restraints: 3668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 548 " 0.108 5.00e-02 4.00e+02 1.59e-01 4.06e+01 pdb=" N PRO C 549 " -0.275 5.00e-02 4.00e+02 pdb=" CA PRO C 549 " 0.090 5.00e-02 4.00e+02 pdb=" CD PRO C 549 " 0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 548 " -0.108 5.00e-02 4.00e+02 1.59e-01 4.06e+01 pdb=" N PRO D 549 " 0.275 5.00e-02 4.00e+02 pdb=" CA PRO D 549 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO D 549 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 548 " -0.108 5.00e-02 4.00e+02 1.59e-01 4.06e+01 pdb=" N PRO A 549 " 0.275 5.00e-02 4.00e+02 pdb=" CA PRO A 549 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO A 549 " -0.078 5.00e-02 4.00e+02 ... (remaining 3665 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.68: 480 2.68 - 3.30: 24200 3.30 - 3.91: 40714 3.91 - 4.53: 52640 4.53 - 5.14: 83488 Nonbonded interactions: 201522 Sorted by model distance: nonbonded pdb=" O ARG A 677 " pdb=" N TRP D 38 " model vdw 2.066 3.120 nonbonded pdb=" N TRP A 38 " pdb=" O ARG B 677 " model vdw 2.066 3.120 nonbonded pdb=" N TRP C 38 " pdb=" O ARG D 677 " model vdw 2.066 3.120 nonbonded pdb=" N TRP B 38 " pdb=" O ARG C 677 " model vdw 2.066 3.120 nonbonded pdb=" N VAL B 36 " pdb=" O LYS C 678 " model vdw 2.233 3.120 ... (remaining 201517 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 11 through 692) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 4.750 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: 0.410 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.450 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 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 : 0.004 0.079 21804 Z= 0.181 Angle : 0.783 11.808 29584 Z= 0.436 Chirality : 0.047 0.384 3404 Planarity : 0.008 0.159 3668 Dihedral : 14.228 89.766 7884 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 1.07 % Allowed : 13.91 % Favored : 85.02 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.65 (0.16), residues: 2616 helix: 0.17 (0.15), residues: 1184 sheet: 0.42 (0.91), residues: 48 loop : -3.85 (0.14), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 327 TYR 0.014 0.002 TYR A 42 PHE 0.011 0.001 PHE C 293 TRP 0.023 0.002 TRP C 38 HIS 0.005 0.001 HIS C 570 Details of bonding type rmsd covalent geometry : bond 0.00371 (21804) covalent geometry : angle 0.78313 (29584) hydrogen bonds : bond 0.13364 ( 860) hydrogen bonds : angle 5.20462 ( 2484) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.777 Fit side-chains REVERT: A 394 LEU cc_start: 0.8471 (tp) cc_final: 0.8191 (tp) REVERT: B 394 LEU cc_start: 0.8462 (tp) cc_final: 0.8181 (tp) REVERT: C 394 LEU cc_start: 0.8479 (tp) cc_final: 0.8230 (tp) REVERT: D 394 LEU cc_start: 0.8484 (tp) cc_final: 0.8197 (tp) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.1332 time to fit residues: 53.2865 Evaluate side-chains 200 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 570 HIS B 118 HIS B 570 HIS C 118 HIS C 570 HIS D 118 HIS D 570 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.215795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.193180 restraints weight = 26926.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.188751 restraints weight = 41919.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.186372 restraints weight = 40255.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.184990 restraints weight = 42130.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.183719 restraints weight = 37776.143| |-----------------------------------------------------------------------------| r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 21804 Z= 0.347 Angle : 0.919 11.249 29584 Z= 0.494 Chirality : 0.054 0.374 3404 Planarity : 0.007 0.107 3668 Dihedral : 6.476 32.483 2864 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 1.07 % Allowed : 15.14 % Favored : 83.79 % Rotamer: Outliers : 1.34 % Allowed : 12.61 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.08 (0.16), residues: 2616 helix: -0.07 (0.15), residues: 1192 sheet: -2.38 (0.52), residues: 112 loop : -4.16 (0.14), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 327 TYR 0.021 0.002 TYR C 419 PHE 0.020 0.002 PHE C 107 TRP 0.018 0.002 TRP C 38 HIS 0.006 0.002 HIS B 539 Details of bonding type rmsd covalent geometry : bond 0.00828 (21804) covalent geometry : angle 0.91892 (29584) hydrogen bonds : bond 0.07564 ( 860) hydrogen bonds : angle 5.02233 ( 2484) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 224 time to evaluate : 0.731 Fit side-chains REVERT: A 55 ARG cc_start: 0.4484 (mpt180) cc_final: 0.3221 (mpt180) REVERT: A 59 MET cc_start: 0.2148 (tpt) cc_final: 0.1893 (tpt) REVERT: A 671 ARG cc_start: 0.7112 (tpt170) cc_final: 0.6891 (tpt170) REVERT: B 55 ARG cc_start: 0.4491 (mpt180) cc_final: 0.3227 (mpt180) REVERT: B 59 MET cc_start: 0.2142 (tpt) cc_final: 0.1893 (tpt) REVERT: B 671 ARG cc_start: 0.7108 (tpt170) cc_final: 0.6888 (tpt170) REVERT: C 55 ARG cc_start: 0.4490 (mpt180) cc_final: 0.3230 (mpt180) REVERT: C 59 MET cc_start: 0.2150 (tpt) cc_final: 0.1899 (tpt) REVERT: C 671 ARG cc_start: 0.7104 (tpt170) cc_final: 0.6884 (tpt170) REVERT: D 55 ARG cc_start: 0.4487 (mpt180) cc_final: 0.3227 (mpt180) REVERT: D 59 MET cc_start: 0.2142 (tpt) cc_final: 0.1890 (tpt) REVERT: D 671 ARG cc_start: 0.7107 (tpt170) cc_final: 0.6886 (tpt170) outliers start: 32 outliers final: 24 residues processed: 252 average time/residue: 0.1435 time to fit residues: 55.6822 Evaluate side-chains 208 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 558 CYS Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.5441 > 50: distance: 50 - 55: 20.590 distance: 55 - 56: 16.430 distance: 56 - 57: 13.006 distance: 56 - 59: 16.320 distance: 57 - 58: 40.798 distance: 57 - 62: 19.999 distance: 59 - 60: 47.367 distance: 59 - 61: 23.397 distance: 62 - 63: 16.681 distance: 63 - 64: 13.330 distance: 63 - 66: 29.197 distance: 64 - 65: 42.095 distance: 64 - 73: 14.031 distance: 66 - 67: 6.730 distance: 67 - 68: 22.835 distance: 67 - 69: 24.643 distance: 68 - 70: 21.912 distance: 69 - 71: 6.665 distance: 70 - 72: 21.722 distance: 71 - 72: 23.075 distance: 73 - 74: 11.909 distance: 74 - 75: 13.780 distance: 75 - 76: 12.581 distance: 75 - 77: 18.450 distance: 77 - 78: 21.067 distance: 78 - 79: 5.843 distance: 78 - 81: 20.117 distance: 79 - 80: 23.217 distance: 79 - 85: 6.678 distance: 81 - 82: 31.137 distance: 82 - 83: 25.347 distance: 82 - 84: 21.722 distance: 85 - 86: 13.253 distance: 86 - 87: 10.398 distance: 86 - 89: 11.549 distance: 87 - 88: 5.354 distance: 87 - 93: 19.807 distance: 89 - 90: 19.506 distance: 89 - 91: 22.892 distance: 90 - 92: 18.610 distance: 93 - 94: 11.958 distance: 94 - 95: 7.891 distance: 94 - 97: 7.506 distance: 95 - 96: 13.357 distance: 95 - 104: 10.933 distance: 97 - 98: 15.255 distance: 98 - 99: 11.044 distance: 98 - 100: 8.828 distance: 99 - 101: 9.497 distance: 100 - 102: 14.273 distance: 104 - 105: 10.504 distance: 105 - 106: 6.724 distance: 105 - 108: 5.190 distance: 106 - 107: 6.772 distance: 106 - 118: 14.302 distance: 108 - 109: 8.992 distance: 109 - 110: 8.683 distance: 109 - 111: 7.943 distance: 110 - 112: 8.232 distance: 111 - 113: 16.554 distance: 111 - 114: 18.477 distance: 112 - 113: 20.885 distance: 113 - 115: 20.959 distance: 114 - 116: 7.479 distance: 115 - 117: 5.727 distance: 116 - 117: 9.705 distance: 118 - 119: 13.680 distance: 119 - 120: 5.888 distance: 119 - 122: 10.675 distance: 120 - 121: 5.409 distance: 120 - 127: 22.414 distance: 122 - 123: 19.003 distance: 123 - 124: 16.261 distance: 124 - 125: 18.873 distance: 125 - 126: 20.482 distance: 127 - 128: 11.222 distance: 128 - 129: 3.167 distance: 128 - 131: 4.920 distance: 129 - 130: 6.063 distance: 131 - 132: 8.671 distance: 132 - 133: 6.416 distance: 133 - 134: 6.388 distance: 133 - 135: 10.433 distance: 136 - 137: 5.333 distance: 137 - 138: 6.302 distance: 138 - 143: 7.466 distance: 140 - 141: 8.595 distance: 140 - 142: 8.876