Starting phenix.real_space_refine (version: 1.21rc1) on Sat May 6 20:59:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rkv_4912/05_2023/6rkv_4912.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rkv_4912/05_2023/6rkv_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rkv_4912/05_2023/6rkv_4912.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rkv_4912/05_2023/6rkv_4912.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rkv_4912/05_2023/6rkv_4912.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rkv_4912/05_2023/6rkv_4912.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Residue "A ARG 46": "NH1" <-> "NH2" Residue "A ARG 99": "NH1" <-> "NH2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ARG 433": "NH1" <-> "NH2" Residue "A ARG 490": "NH1" <-> "NH2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "B ARG 438": "NH1" <-> "NH2" Residue "B ARG 489": "NH1" <-> "NH2" Residue "B ARG 516": "NH1" <-> "NH2" Residue "B ARG 667": "NH1" <-> "NH2" Residue "B ARG 689": "NH1" <-> "NH2" Residue "C ARG 46": "NH1" <-> "NH2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "C ARG 121": "NH1" <-> "NH2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "C ARG 356": "NH1" <-> "NH2" Residue "C ARG 433": "NH1" <-> "NH2" Residue "C ARG 490": "NH1" <-> "NH2" Residue "C ARG 517": "NH1" <-> "NH2" Residue "D ARG 438": "NH1" <-> "NH2" Residue "D ARG 489": "NH1" <-> "NH2" Residue "D ARG 516": "NH1" <-> "NH2" Residue "D ARG 667": "NH1" <-> "NH2" Residue "D ARG 689": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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: 8.22, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 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: 6.50 Conformation dependent library (CDL) restraints added in 2.2 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: 4.50 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: 5.53 Time building geometry restraints manager: 6.72 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: 99.81 - 106.64: 792 106.64 - 113.48: 8660 113.48 - 120.31: 5846 120.31 - 127.15: 6135 127.15 - 133.98: 259 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: 9116 28.11 - 56.23: 326 56.23 - 84.34: 34 84.34 - 112.45: 0 112.45 - 140.56: 4 Dihedral angle restraints: 9480 sinusoidal: 4304 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 9477 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 2.520 nonbonded pdb=" OE2 GLU B 454 " pdb=" NH1 ARG B 516 " model vdw 2.247 2.520 nonbonded pdb=" OD2 ASP A 39 " pdb=" NH2 ARG A 46 " model vdw 2.259 2.520 nonbonded pdb=" OD2 ASP C 39 " pdb=" NH2 ARG C 46 " model vdw 2.259 2.520 nonbonded pdb=" O LYS B 538 " pdb=" OG SER B 735 " model vdw 2.282 2.440 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints Number of NCS constrained groups: 4 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'H' } 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: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.580 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 43.920 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.260 ------------------------------------------------------------------------------- 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= 0.127 Angle : 0.534 8.819 21692 Z= 0.309 Chirality : 0.037 0.201 2444 Planarity : 0.005 0.041 2610 Dihedral : 12.796 140.565 6140 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 % 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 *********************** 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 92 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.497 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 outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2241 time to fit residues: 24.2788 Evaluate side-chains 39 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.489 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6459 Evaluate side-chains 65 residues out of total 327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.2565 time to fit residues: 18.9268 Evaluate side-chains 29 residues out of total 327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.398 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5416 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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: 0.0142 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0046 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0168 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0056 ------------------------------------------------------------------------------- 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: 0.0040 chunk 137 optimal weight: 0.0770 chunk 76 optimal weight: 0.0030 chunk 47 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 142 optimal weight: 8.9990 chunk 55 optimal weight: 0.1980 chunk 86 optimal weight: 0.0270 chunk 106 optimal weight: 0.0870 chunk 165 optimal weight: 2.9990 overall best weight: 0.0396 ------------------------------------------------------------------------------- NQH flips ********* 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 456 GLN Total number of N/Q/H flips: 5 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 652 HIS Total number of N/Q/H flips: 1 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 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 15848 Z= 0.156 Angle : 0.573 7.634 21692 Z= 0.296 Chirality : 0.040 0.189 2444 Planarity : 0.005 0.044 2610 Dihedral : 16.506 140.875 2596 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer Outliers : 0.00 % 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: -0.75 (0.20), residues: 1764 helix: 1.69 (0.18), residues: 836 sheet: -1.46 (0.36), residues: 206 loop : -3.01 (0.20), residues: 722 *********************** 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 55 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 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 outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2084 time to fit residues: 13.9585 Evaluate side-chains 31 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.456 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6434 Evaluate side-chains 34 residues out of total 327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.2175 time to fit residues: 8.7991 Evaluate side-chains 22 residues out of total 327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.380 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5482 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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: 0.0139 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0048 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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: 0.0170 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 45 optimal weight: 0.0270 chunk 165 optimal weight: 8.9990 chunk 178 optimal weight: 5.9990 chunk 147 optimal weight: 0.8980 chunk 164 optimal weight: 9.9990 chunk 56 optimal weight: 30.0000 chunk 132 optimal weight: 0.9980 overall best weight: 2.7842 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 721 GLN Total number of N/Q/H flips: 1 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 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 15848 Z= 0.265 Angle : 0.736 10.626 21692 Z= 0.394 Chirality : 0.058 1.180 2444 Planarity : 0.012 0.348 2610 Dihedral : 16.688 143.301 2596 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer Outliers : 0.53 % 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: -1.19 (0.20), residues: 1764 helix: 1.06 (0.18), residues: 828 sheet: -1.10 (0.37), residues: 186 loop : -2.99 (0.19), residues: 750 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 43 average time/residue: 0.1776 time to fit residues: 9.7122 Evaluate side-chains 31 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 0.438 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0612 time to fit residues: 0.6811 Evaluate side-chains 23 residues out of total 327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1218 time to fit residues: 3.8746 Evaluate side-chains 17 residues out of total 327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.329 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4519 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0114 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0042 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. 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: 0.0138 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 675, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 771, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.0682 > 50: distance: 0 - 1: 8.483 distance: 1 - 2: 9.954 distance: 1 - 4: 8.232 distance: 2 - 3: 5.853 distance: 2 - 10: 18.222 distance: 3 - 41: 40.294 distance: 4 - 5: 8.189 distance: 5 - 6: 18.207 distance: 5 - 7: 12.910 distance: 6 - 8: 4.851 distance: 7 - 9: 19.887 distance: 8 - 9: 11.024 distance: 10 - 11: 15.200 distance: 11 - 12: 16.529 distance: 11 - 14: 19.882 distance: 12 - 13: 7.096 distance: 12 - 21: 40.436 distance: 13 - 48: 35.102 distance: 14 - 15: 9.760 distance: 15 - 16: 21.238 distance: 17 - 18: 11.718 distance: 18 - 19: 16.758 distance: 18 - 20: 15.863 distance: 21 - 22: 8.766 distance: 22 - 23: 24.804 distance: 22 - 25: 36.844 distance: 23 - 24: 16.277 distance: 23 - 32: 23.924 distance: 24 - 55: 43.919 distance: 25 - 26: 19.993 distance: 26 - 27: 6.111 distance: 27 - 28: 20.666 distance: 28 - 29: 9.442 distance: 29 - 30: 15.969 distance: 29 - 31: 6.066 distance: 32 - 33: 13.298 distance: 33 - 34: 20.690 distance: 33 - 36: 3.323 distance: 34 - 35: 41.018 distance: 34 - 41: 28.185 distance: 35 - 62: 31.711 distance: 36 - 37: 34.165 distance: 37 - 38: 33.302 distance: 38 - 39: 28.701 distance: 38 - 40: 15.625 distance: 41 - 42: 44.123 distance: 42 - 43: 16.542 distance: 42 - 45: 38.670 distance: 43 - 44: 43.728 distance: 43 - 48: 55.387 distance: 44 - 73: 42.281 distance: 45 - 46: 5.197 distance: 45 - 47: 29.283 distance: 48 - 49: 50.249 distance: 49 - 50: 14.071 distance: 49 - 52: 39.811 distance: 50 - 51: 21.569 distance: 50 - 55: 20.606 distance: 51 - 84: 34.081 distance: 52 - 53: 50.425 distance: 52 - 54: 46.890 distance: 55 - 56: 21.931 distance: 56 - 57: 13.568 distance: 56 - 59: 30.485 distance: 57 - 58: 12.627 distance: 57 - 62: 15.777 distance: 59 - 60: 44.774 distance: 59 - 61: 52.668 distance: 62 - 63: 14.043 distance: 63 - 64: 15.590 distance: 63 - 66: 23.265 distance: 64 - 65: 32.539 distance: 64 - 73: 19.729 distance: 66 - 67: 20.610 distance: 67 - 68: 29.316 distance: 68 - 69: 37.097 distance: 69 - 70: 17.003 distance: 70 - 71: 32.316 distance: 70 - 72: 25.231 distance: 73 - 74: 34.729 distance: 74 - 75: 21.325 distance: 74 - 77: 17.489 distance: 75 - 76: 5.771 distance: 75 - 84: 34.581 distance: 77 - 78: 26.682 distance: 78 - 79: 30.678 distance: 79 - 80: 15.271 distance: 80 - 81: 9.774 distance: 81 - 82: 10.492 distance: 81 - 83: 9.971 distance: 84 - 85: 40.983 distance: 85 - 86: 20.808 distance: 85 - 88: 34.636 distance: 86 - 87: 54.862 distance: 88 - 89: 44.292 distance: 88 - 90: 68.068