Starting phenix.real_space_refine on Sat May 17 10:34:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rkv_4912/05_2025/6rkv_4912.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rkv_4912/05_2025/6rkv_4912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6rkv_4912/05_2025/6rkv_4912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rkv_4912/05_2025/6rkv_4912.map" model { file = "/net/cci-nas-00/data/ceres_data/6rkv_4912/05_2025/6rkv_4912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rkv_4912/05_2025/6rkv_4912.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 P 64 5.49 5 S 54 5.16 5 C 9522 2.51 5 N 2750 2.21 5 O 3070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15460 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4022 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 21, 'TRANS': 489} Chain breaks: 2 Chain: "B" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3052 Classifications: {'peptide': 381} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 363} Chain breaks: 1 Chain: "C" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4022 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 21, 'TRANS': 489} Chain breaks: 2 Chain: "D" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3052 Classifications: {'peptide': 381} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 363} Chain breaks: 1 Chain: "F" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 288 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "E" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 288 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "G" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 368 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "H" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 368 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Time building chain proxies: 9.42, per 1000 atoms: 0.61 Number of scatterers: 15460 At special positions: 0 Unit cell: (122.32, 146.96, 123.2, 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) S 54 16.00 P 64 15.00 O 3070 8.00 N 2750 7.00 C 9522 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: 4.12 Conformation dependent library (CDL) restraints added in 1.7 seconds 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3340 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 22 sheets defined 50.0% alpha, 10.4% beta 32 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 5.48 Creating SS restraints... Processing helix chain 'A' and resid 15 through 32 removed outlier: 3.934A pdb=" N SER A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 56 Processing helix chain 'A' and resid 66 through 77 Processing helix chain 'A' and resid 82 through 94 Processing helix chain 'A' and resid 95 through 98 removed outlier: 3.635A pdb=" N LEU A 98 " --> pdb=" O PRO A 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 95 through 98' Processing helix chain 'A' and resid 130 through 134 Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 186 through 200 Processing helix chain 'A' and resid 204 through 212 removed outlier: 3.604A pdb=" N HIS A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 235 removed outlier: 4.451A pdb=" N ILE A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 283 Processing helix chain 'A' and resid 313 through 324 Processing helix chain 'A' and resid 346 through 389 removed outlier: 3.518A pdb=" N ALA A 382 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 389 " --> pdb=" O VAL A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 400 Processing helix chain 'A' and resid 402 through 413 Processing helix chain 'A' and resid 451 through 460 Processing helix chain 'A' and resid 462 through 466 removed outlier: 3.765A pdb=" N LYS A 465 " --> pdb=" O ARG A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 494 Processing helix chain 'A' and resid 494 through 513 removed outlier: 3.931A pdb=" N LEU A 498 " --> pdb=" O SER A 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 436 removed outlier: 4.415A pdb=" N SER B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 472 Processing helix chain 'B' and resid 500 through 518 Processing helix chain 'B' and resid 518 through 524 removed outlier: 4.023A pdb=" N VAL B 522 " --> pdb=" O MET B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 561 Processing helix chain 'B' and resid 577 through 598 Processing helix chain 'B' and resid 602 through 609 removed outlier: 4.061A pdb=" N LEU B 606 " --> pdb=" O PRO B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 621 removed outlier: 3.670A pdb=" N SER B 621 " --> pdb=" O ALA B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 641 removed outlier: 3.680A pdb=" N VAL B 626 " --> pdb=" O ASP B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 684 Processing helix chain 'B' and resid 684 through 699 Processing helix chain 'B' and resid 718 through 732 Processing helix chain 'B' and resid 741 through 745 removed outlier: 4.242A pdb=" N MET B 745 " --> pdb=" O LEU B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 772 through 778 removed outlier: 4.205A pdb=" N THR B 778 " --> pdb=" O ASP B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 780 through 786 Processing helix chain 'C' and resid 15 through 32 removed outlier: 3.933A pdb=" N SER C 19 " --> pdb=" O GLU C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 56 Processing helix chain 'C' and resid 66 through 77 Processing helix chain 'C' and resid 82 through 94 Processing helix chain 'C' and resid 95 through 98 removed outlier: 3.636A pdb=" N LEU C 98 " --> pdb=" O PRO C 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 95 through 98' Processing helix chain 'C' and resid 130 through 134 Processing helix chain 'C' and resid 164 through 169 Processing helix chain 'C' and resid 186 through 200 Processing helix chain 'C' and resid 204 through 212 removed outlier: 3.605A pdb=" N HIS C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 235 removed outlier: 4.451A pdb=" N ILE C 229 " --> pdb=" O GLY C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 283 Processing helix chain 'C' and resid 313 through 324 Processing helix chain 'C' and resid 346 through 389 removed outlier: 3.518A pdb=" N ALA C 382 " --> pdb=" O HIS C 378 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN C 389 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 400 Processing helix chain 'C' and resid 402 through 413 Processing helix chain 'C' and resid 451 through 460 Processing helix chain 'C' and resid 462 through 466 removed outlier: 3.765A pdb=" N LYS C 465 " --> pdb=" O ARG C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 494 Processing helix chain 'C' and resid 494 through 513 removed outlier: 3.931A pdb=" N LEU C 498 " --> pdb=" O SER C 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 436 removed outlier: 4.415A pdb=" N SER D 431 " --> pdb=" O SER D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 472 Processing helix chain 'D' and resid 500 through 518 Processing helix chain 'D' and resid 518 through 524 removed outlier: 4.023A pdb=" N VAL D 522 " --> pdb=" O MET D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 561 Processing helix chain 'D' and resid 577 through 598 Processing helix chain 'D' and resid 602 through 609 removed outlier: 4.061A pdb=" N LEU D 606 " --> pdb=" O PRO D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 621 removed outlier: 3.669A pdb=" N SER D 621 " --> pdb=" O ALA D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 641 removed outlier: 3.680A pdb=" N VAL D 626 " --> pdb=" O ASP D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 684 Processing helix chain 'D' and resid 684 through 699 Processing helix chain 'D' and resid 718 through 732 Processing helix chain 'D' and resid 741 through 745 removed outlier: 4.241A pdb=" N MET D 745 " --> pdb=" O LEU D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 755 Processing helix chain 'D' and resid 772 through 778 removed outlier: 4.205A pdb=" N THR D 778 " --> pdb=" O ASP D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 780 through 786 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 removed outlier: 3.702A pdb=" N LYS A 64 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 174 Processing sheet with id=AA4, first strand: chain 'A' and resid 327 through 328 Processing sheet with id=AA5, first strand: chain 'A' and resid 237 through 239 removed outlier: 3.730A pdb=" N GLY A 238 " --> pdb=" O ILE A 332 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 245 through 250 removed outlier: 6.961A pdb=" N ARG A 245 " --> pdb=" O HIS A 262 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 247 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLU A 257 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU A 306 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA A 291 " --> pdb=" O GLU A 306 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 335 through 337 removed outlier: 3.827A pdb=" N ALA A 336 " --> pdb=" O LYS A 343 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 441 through 446 removed outlier: 6.158A pdb=" N GLU B 419 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU B 444 " --> pdb=" O GLU B 419 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N TYR B 421 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU B 446 " --> pdb=" O TYR B 421 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B 423 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LEU B 420 " --> pdb=" O ILE B 494 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 542 through 546 Processing sheet with id=AB1, first strand: chain 'B' and resid 565 through 566 removed outlier: 3.664A pdb=" N THR B 565 " --> pdb=" O GLU B 708 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU B 708 " --> pdb=" O THR B 565 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 646 through 653 removed outlier: 3.537A pdb=" N VAL B 664 " --> pdb=" O TYR B 675 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 64 through 65 removed outlier: 3.701A pdb=" N LYS C 64 " --> pdb=" O ILE C 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AB5, first strand: chain 'C' and resid 172 through 174 Processing sheet with id=AB6, first strand: chain 'C' and resid 327 through 328 Processing sheet with id=AB7, first strand: chain 'C' and resid 237 through 239 removed outlier: 3.730A pdb=" N GLY C 238 " --> pdb=" O ILE C 332 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 245 through 250 removed outlier: 6.960A pdb=" N ARG C 245 " --> pdb=" O HIS C 262 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C 247 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLU C 257 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU C 306 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA C 291 " --> pdb=" O GLU C 306 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 335 through 337 removed outlier: 3.828A pdb=" N ALA C 336 " --> pdb=" O LYS C 343 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 441 through 446 removed outlier: 6.158A pdb=" N GLU D 419 " --> pdb=" O ALA D 442 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N LEU D 444 " --> pdb=" O GLU D 419 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TYR D 421 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU D 446 " --> pdb=" O TYR D 421 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL D 423 " --> pdb=" O LEU D 446 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU D 420 " --> pdb=" O ILE D 494 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 542 through 546 Processing sheet with id=AC3, first strand: chain 'D' and resid 565 through 566 removed outlier: 3.664A pdb=" N THR D 565 " --> pdb=" O GLU D 708 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU D 708 " --> pdb=" O THR D 565 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 646 through 653 removed outlier: 3.536A pdb=" N VAL D 664 " --> pdb=" O TYR D 675 " (cutoff:3.500A) 692 hydrogen bonds defined for protein. 1992 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 6.01 Time building geometry restraints manager: 4.72 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: 4540 1.34 - 1.45: 2427 1.45 - 1.57: 8655 1.57 - 1.69: 124 1.69 - 1.81: 102 Bond restraints: 15848 Sorted by residual: bond pdb=" C ASN D 484 " pdb=" N PRO D 485 " ideal model delta sigma weight residual 1.335 1.348 -0.013 1.28e-02 6.10e+03 1.11e+00 bond pdb=" C ASN B 484 " pdb=" N PRO B 485 " ideal model delta sigma weight residual 1.335 1.348 -0.013 1.28e-02 6.10e+03 1.07e+00 bond pdb=" CA ASN D 484 " pdb=" C ASN D 484 " ideal model delta sigma weight residual 1.524 1.536 -0.012 1.26e-02 6.30e+03 9.60e-01 bond pdb=" CA ASN B 484 " pdb=" C ASN B 484 " ideal model delta sigma weight residual 1.524 1.536 -0.012 1.26e-02 6.30e+03 9.50e-01 bond pdb=" CA ASP C 391 " pdb=" C ASP C 391 " ideal model delta sigma weight residual 1.520 1.531 -0.011 1.23e-02 6.61e+03 7.60e-01 ... (remaining 15843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 21324 1.76 - 3.53: 322 3.53 - 5.29: 29 5.29 - 7.06: 11 7.06 - 8.82: 6 Bond angle restraints: 21692 Sorted by residual: angle pdb=" N GLY D 577 " pdb=" CA GLY D 577 " pdb=" C GLY D 577 " ideal model delta sigma weight residual 111.56 115.47 -3.91 1.01e+00 9.80e-01 1.50e+01 angle pdb=" N GLY B 577 " pdb=" CA GLY B 577 " pdb=" C GLY B 577 " ideal model delta sigma weight residual 111.56 115.45 -3.89 1.01e+00 9.80e-01 1.48e+01 angle pdb=" C THR D 779 " pdb=" N LEU D 780 " pdb=" CA LEU D 780 " ideal model delta sigma weight residual 121.54 128.40 -6.86 1.91e+00 2.74e-01 1.29e+01 angle pdb=" C THR B 779 " pdb=" N LEU B 780 " pdb=" CA LEU B 780 " ideal model delta sigma weight residual 121.54 128.39 -6.85 1.91e+00 2.74e-01 1.29e+01 angle pdb=" N ASN D 484 " pdb=" CA ASN D 484 " pdb=" C ASN D 484 " ideal model delta sigma weight residual 109.81 117.41 -7.60 2.21e+00 2.05e-01 1.18e+01 ... (remaining 21687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.11: 9148 28.11 - 56.23: 366 56.23 - 84.34: 34 84.34 - 112.45: 0 112.45 - 140.56: 4 Dihedral angle restraints: 9552 sinusoidal: 4376 harmonic: 5176 Sorted by residual: dihedral pdb=" CA ALA D 655 " pdb=" C ALA D 655 " pdb=" N GLU D 656 " pdb=" CA GLU D 656 " ideal model delta harmonic sigma weight residual 180.00 160.88 19.12 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA ALA B 655 " pdb=" C ALA B 655 " pdb=" N GLU B 656 " pdb=" CA GLU B 656 " ideal model delta harmonic sigma weight residual 180.00 160.92 19.08 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" C4' DT H 26 " pdb=" C3' DT H 26 " pdb=" O3' DT H 26 " pdb=" P DT H 27 " ideal model delta sinusoidal sigma weight residual 220.00 79.44 140.56 1 3.50e+01 8.16e-04 1.39e+01 ... (remaining 9549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1879 0.040 - 0.080: 427 0.080 - 0.121: 136 0.121 - 0.161: 0 0.161 - 0.201: 2 Chirality restraints: 2444 Sorted by residual: chirality pdb=" CA ASN D 484 " pdb=" N ASN D 484 " pdb=" C ASN D 484 " pdb=" CB ASN D 484 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ASN B 484 " pdb=" N ASN B 484 " pdb=" C ASN B 484 " pdb=" CB ASN B 484 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ILE B 450 " pdb=" N ILE B 450 " pdb=" C ILE B 450 " pdb=" CB ILE B 450 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.61e-01 ... (remaining 2441 not shown) Planarity restraints: 2610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 780 " -0.016 2.00e-02 2.50e+03 3.13e-02 9.79e+00 pdb=" C LEU B 780 " 0.054 2.00e-02 2.50e+03 pdb=" O LEU B 780 " -0.020 2.00e-02 2.50e+03 pdb=" N MET B 781 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 780 " 0.016 2.00e-02 2.50e+03 3.12e-02 9.74e+00 pdb=" C LEU D 780 " -0.054 2.00e-02 2.50e+03 pdb=" O LEU D 780 " 0.020 2.00e-02 2.50e+03 pdb=" N MET D 781 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 182 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO C 183 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 183 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 183 " -0.023 5.00e-02 4.00e+02 ... (remaining 2607 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2771 2.78 - 3.31: 14085 3.31 - 3.84: 23957 3.84 - 4.37: 25913 4.37 - 4.90: 44911 Nonbonded interactions: 111637 Sorted by model distance: nonbonded pdb=" OE2 GLU D 454 " pdb=" NH1 ARG D 516 " model vdw 2.246 3.120 nonbonded pdb=" OE2 GLU B 454 " pdb=" NH1 ARG B 516 " model vdw 2.247 3.120 nonbonded pdb=" OD2 ASP A 39 " pdb=" NH2 ARG A 46 " model vdw 2.259 3.120 nonbonded pdb=" OD2 ASP C 39 " pdb=" NH2 ARG C 46 " model vdw 2.259 3.120 nonbonded pdb=" O LYS B 538 " pdb=" OG SER B 735 " model vdw 2.282 3.040 ... (remaining 111632 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: 0.07 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'C' } Set up NCS constraints Number of NCS constrained groups: 4 pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'H' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' } Set refine NCS operators NCS operators will be refined. 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: 2.970 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: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 40.390 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 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 : 0.002 0.025 15848 Z= 0.112 Angle : 0.534 8.819 21692 Z= 0.309 Chirality : 0.037 0.201 2444 Planarity : 0.005 0.041 2610 Dihedral : 13.181 140.565 6212 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -1.73 (0.19), residues: 1764 helix: 0.55 (0.17), residues: 836 sheet: -1.81 (0.35), residues: 210 loop : -3.10 (0.20), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 415 HIS 0.005 0.001 HIS A 399 PHE 0.013 0.001 PHE B 514 TYR 0.011 0.001 TYR A 266 ARG 0.002 0.000 ARG A 46 Details of bonding type rmsd hydrogen bonds : bond 0.16646 ( 770) hydrogen bonds : angle 5.39648 ( 2148) covalent geometry : bond 0.00202 (15848) covalent geometry : angle 0.53374 (21692) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.018 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0141 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.014 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0164 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 Evaluate side-chains 65 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 439 LYS cc_start: 0.9127 (tttp) cc_final: 0.8838 (tptp) REVERT: B 660 PHE cc_start: 0.8181 (m-10) cc_final: 0.7574 (m-10) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.2600 time to fit residues: 19.0564 Evaluate side-chains 31 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.371 Evaluate side-chains 92 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8785 (m-30) cc_final: 0.7539 (p0) REVERT: A 306 GLU cc_start: 0.8142 (tt0) cc_final: 0.7845 (tm-30) REVERT: A 307 VAL cc_start: 0.9030 (t) cc_final: 0.8790 (t) REVERT: A 326 LEU cc_start: 0.9131 (mt) cc_final: 0.8800 (tt) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2158 time to fit residues: 23.5020 Evaluate side-chains 42 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.5980 chunk 137 optimal weight: 0.0670 chunk 76 optimal weight: 0.0470 chunk 47 optimal weight: 0.1980 chunk 93 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 55 optimal weight: 0.0370 chunk 86 optimal weight: 3.9990 chunk 106 optimal weight: 0.0010 chunk 165 optimal weight: 8.9990 overall best weight: 0.0700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 HIS A 224 ASN A 357 HIS A 378 HIS A 399 HIS A 456 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.059236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.057180 restraints weight = 4144.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.057596 restraints weight = 1031.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.057818 restraints weight = 547.776| |-----------------------------------------------------------------------------| r_work (final): 0.2899 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.069043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.063309 restraints weight = 5275.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.064693 restraints weight = 1926.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.065172 restraints weight = 1138.951| |-----------------------------------------------------------------------------| r_work (final): 0.3183 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.056264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.046205 restraints weight = 27609.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.047158 restraints weight = 21183.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.047938 restraints weight = 17191.530| |-----------------------------------------------------------------------------| r_work (final): 0.3195 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.044665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.037845 restraints weight = 34069.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.038871 restraints weight = 21031.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.039662 restraints weight = 14807.173| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15848 Z= 0.125 Angle : 0.584 7.782 21692 Z= 0.304 Chirality : 0.040 0.193 2444 Planarity : 0.005 0.047 2610 Dihedral : 16.975 141.102 2668 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -0.77 (0.20), residues: 1764 helix: 1.73 (0.18), residues: 824 sheet: -1.54 (0.35), residues: 208 loop : -3.02 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 415 HIS 0.004 0.001 HIS C 45 PHE 0.004 0.001 PHE D 649 TYR 0.013 0.001 TYR A 478 ARG 0.010 0.001 ARG D 438 Details of bonding type rmsd hydrogen bonds : bond 0.06934 ( 770) hydrogen bonds : angle 4.76107 ( 2148) covalent geometry : bond 0.00258 (15848) covalent geometry : angle 0.58364 (21692) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0137 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0153 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Evaluate side-chains 35 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 439 LYS cc_start: 0.9189 (tttp) cc_final: 0.8873 (tptp) REVERT: B 535 TYR cc_start: 0.8477 (m-10) cc_final: 0.8048 (m-10) REVERT: B 583 LEU cc_start: 0.8776 (mm) cc_final: 0.8330 (pp) REVERT: B 660 PHE cc_start: 0.7983 (m-10) cc_final: 0.7752 (m-10) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.2283 time to fit residues: 9.4516 Evaluate side-chains 25 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.354 Evaluate side-chains 51 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.9318 (t0) cc_final: 0.9031 (t0) REVERT: A 113 ASP cc_start: 0.8903 (m-30) cc_final: 0.7988 (p0) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1976 time to fit residues: 12.4128 Evaluate side-chains 34 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 801, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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: 60.3102 > 50: distance: 2 - 3: 8.348 distance: 3 - 4: 8.374 distance: 3 - 6: 39.502 distance: 4 - 5: 18.551 distance: 4 - 13: 13.807 distance: 5 - 36: 43.613 distance: 6 - 7: 26.492 distance: 7 - 8: 16.482 distance: 8 - 9: 29.027 distance: 9 - 10: 46.973 distance: 10 - 11: 20.229 distance: 10 - 12: 36.285 distance: 14 - 15: 32.081 distance: 14 - 17: 13.376 distance: 15 - 16: 33.041 distance: 15 - 18: 14.497 distance: 16 - 44: 43.901 distance: 18 - 19: 17.598 distance: 19 - 20: 25.339 distance: 19 - 22: 22.311 distance: 20 - 21: 15.649 distance: 20 - 28: 27.264 distance: 22 - 23: 24.663 distance: 23 - 24: 29.548 distance: 23 - 25: 42.818 distance: 24 - 26: 18.877 distance: 25 - 27: 8.689 distance: 26 - 27: 51.422 distance: 28 - 29: 10.987 distance: 29 - 30: 17.982 distance: 29 - 32: 26.800 distance: 30 - 31: 5.752 distance: 30 - 36: 12.572 distance: 31 - 58: 29.252 distance: 32 - 33: 19.411 distance: 32 - 34: 12.468 distance: 33 - 35: 7.852 distance: 36 - 37: 18.238 distance: 37 - 38: 22.222 distance: 37 - 40: 26.594 distance: 38 - 39: 12.262 distance: 38 - 44: 11.657 distance: 39 - 66: 11.569 distance: 40 - 41: 11.207 distance: 41 - 42: 21.544 distance: 41 - 43: 28.741 distance: 44 - 45: 10.077 distance: 45 - 46: 32.271 distance: 45 - 48: 23.240 distance: 46 - 47: 26.642 distance: 46 - 53: 16.347 distance: 47 - 71: 30.375 distance: 48 - 49: 15.623 distance: 49 - 50: 6.387 distance: 50 - 51: 30.274 distance: 50 - 52: 29.091 distance: 53 - 54: 18.825 distance: 54 - 55: 10.255 distance: 54 - 57: 40.000 distance: 55 - 56: 14.012 distance: 55 - 58: 18.640 distance: 58 - 59: 29.778 distance: 59 - 60: 6.940 distance: 59 - 62: 28.457 distance: 60 - 61: 18.688 distance: 60 - 66: 23.406 distance: 62 - 63: 10.474 distance: 63 - 64: 21.933 distance: 63 - 65: 16.214 distance: 66 - 67: 38.064 distance: 67 - 68: 26.100 distance: 67 - 70: 23.942 distance: 68 - 69: 17.433 distance: 68 - 71: 12.927 distance: 71 - 72: 32.950 distance: 72 - 73: 16.204