Starting phenix.real_space_refine on Thu Sep 26 21:33:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9atp_43832/09_2024/9atp_43832.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9atp_43832/09_2024/9atp_43832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9atp_43832/09_2024/9atp_43832.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9atp_43832/09_2024/9atp_43832.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9atp_43832/09_2024/9atp_43832.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9atp_43832/09_2024/9atp_43832.cif" } resolution = 3.5 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= 0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1380 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 8379 2.51 5 N 2153 2.21 5 O 2420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13004 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3513 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 26, 'TRANS': 411} Chain breaks: 5 Chain: "B" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3498 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 25, 'TRANS': 410} Chain breaks: 5 Chain: "C" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3356 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 24, 'TRANS': 392} Chain breaks: 6 Chain: "D" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 879 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "E" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 879 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "L" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 879 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Time building chain proxies: 9.03, per 1000 atoms: 0.69 Number of scatterers: 13004 At special positions: 0 Unit cell: (138.112, 140.768, 126.603, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 2420 8.00 N 2153 7.00 C 8379 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 162 " distance=2.04 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 297 " distance=2.03 Simple disulfide: pdb=" SG CYS A 332 " - pdb=" SG CYS A 357 " distance=2.03 Simple disulfide: pdb=" SG CYS A 375 " - pdb=" SG CYS A 428 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 521 " distance=2.04 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 162 " distance=2.04 Simple disulfide: pdb=" SG CYS B 287 " - pdb=" SG CYS B 297 " distance=2.03 Simple disulfide: pdb=" SG CYS B 332 " - pdb=" SG CYS B 357 " distance=2.03 Simple disulfide: pdb=" SG CYS B 375 " - pdb=" SG CYS B 428 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 162 " distance=2.04 Simple disulfide: pdb=" SG CYS C 287 " - pdb=" SG CYS C 297 " distance=2.03 Simple disulfide: pdb=" SG CYS C 332 " - pdb=" SG CYS C 357 " distance=2.03 Simple disulfide: pdb=" SG CYS C 375 " - pdb=" SG CYS C 428 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 521 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.06 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 95 " distance=2.03 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: 3.20 Conformation dependent library (CDL) restraints added in 1.6 seconds 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3068 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 26 sheets defined 9.0% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 290 through 300 Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.568A pdb=" N PHE A 367 " --> pdb=" O ILE A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 removed outlier: 3.846A pdb=" N LEU A 383 " --> pdb=" O PRO A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 406 Processing helix chain 'A' and resid 412 through 417 Processing helix chain 'B' and resid 290 through 300 Processing helix chain 'B' and resid 333 through 338 Processing helix chain 'B' and resid 345 through 349 removed outlier: 3.614A pdb=" N TRP B 349 " --> pdb=" O VAL B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 368 removed outlier: 4.030A pdb=" N TYR B 365 " --> pdb=" O TYR B 361 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA B 368 " --> pdb=" O ILE B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 386 removed outlier: 4.096A pdb=" N LEU B 383 " --> pdb=" O PRO B 380 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASN B 384 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP B 385 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU B 386 " --> pdb=" O LEU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 406 removed outlier: 4.495A pdb=" N SER B 404 " --> pdb=" O ASN B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 418 Processing helix chain 'C' and resid 290 through 300 Processing helix chain 'C' and resid 333 through 338 removed outlier: 3.760A pdb=" N VAL C 337 " --> pdb=" O PRO C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 368 removed outlier: 3.729A pdb=" N TYR C 365 " --> pdb=" O TYR C 361 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA C 368 " --> pdb=" O ILE C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 383 removed outlier: 3.811A pdb=" N LEU C 383 " --> pdb=" O PRO C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 406 removed outlier: 4.464A pdb=" N SER C 404 " --> pdb=" O ASN C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 418 Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'L' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 34 removed outlier: 6.769A pdb=" N VAL A 33 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N LEU A 219 " --> pdb=" O HIS A 203 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N HIS A 203 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N SER A 201 " --> pdb=" O PRO A 221 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR A 261 " --> pdb=" O PHE A 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 52 removed outlier: 3.558A pdb=" N VAL A 44 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP A 283 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 165 through 168 Processing sheet with id=AA4, first strand: chain 'A' and resid 350 through 354 removed outlier: 3.889A pdb=" N ASN A 350 " --> pdb=" O SER A 395 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 395 " --> pdb=" O ASN A 350 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASN A 390 " --> pdb=" O GLU A 512 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU A 512 " --> pdb=" O ASN A 390 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 448 through 450 Processing sheet with id=AA6, first strand: chain 'A' and resid 469 through 470 removed outlier: 3.561A pdb=" N TYR A 485 " --> pdb=" O TYR A 469 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 23 through 27 removed outlier: 3.583A pdb=" N THR B 26 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N ASN B 58 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR B 265 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N SER B 201 " --> pdb=" O PRO B 221 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N HIS B 203 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 9.650A pdb=" N LEU B 219 " --> pdb=" O HIS B 203 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL B 33 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 45 through 52 removed outlier: 3.805A pdb=" N ASP B 283 " --> pdb=" O LYS B 274 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 165 through 168 removed outlier: 6.352A pdb=" N ASN B 118 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG B 99 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLY B 100 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU B 237 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 350 through 354 removed outlier: 3.670A pdb=" N ASN B 350 " --> pdb=" O SER B 395 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER B 395 " --> pdb=" O ASN B 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 448 through 449 Processing sheet with id=AB3, first strand: chain 'C' and resid 24 through 27 removed outlier: 8.018A pdb=" N ASN C 58 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N TYR C 265 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N PHE C 197 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP C 224 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE C 199 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU C 220 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N HIS C 203 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N ALA C 218 " --> pdb=" O HIS C 203 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL C 33 " --> pdb=" O LEU C 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 45 through 52 removed outlier: 3.828A pdb=" N ASP C 283 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 102 through 104 Processing sheet with id=AB6, first strand: chain 'C' and resid 131 through 132 removed outlier: 6.543A pdb=" N GLN C 131 " --> pdb=" O SER C 157 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 350 through 354 Processing sheet with id=AB8, first strand: chain 'C' and resid 448 through 450 Processing sheet with id=AB9, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AC1, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.444A pdb=" N GLY D 10 " --> pdb=" O THR D 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.359A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N PHE D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N MET D 34 " --> pdb=" O PHE D 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AC4, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.181A pdb=" N GLY E 10 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N SER E 114 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL E 12 " --> pdb=" O SER E 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.564A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N PHE E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N MET E 34 " --> pdb=" O PHE E 50 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 3 through 7 Processing sheet with id=AC7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.205A pdb=" N GLY L 10 " --> pdb=" O THR L 112 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N SER L 114 " --> pdb=" O GLY L 10 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL L 12 " --> pdb=" O SER L 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'L' and resid 57 through 59 removed outlier: 6.605A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N PHE L 50 " --> pdb=" O MET L 34 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N MET L 34 " --> pdb=" O PHE L 50 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 963 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.99 Time building geometry restraints manager: 3.79 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: 4093 1.34 - 1.47: 3549 1.47 - 1.59: 5642 1.59 - 1.71: 0 1.71 - 1.83: 61 Bond restraints: 13345 Sorted by residual: bond pdb=" CB ASP A 194 " pdb=" CG ASP A 194 " ideal model delta sigma weight residual 1.516 1.554 -0.038 2.50e-02 1.60e+03 2.37e+00 bond pdb=" CA LEU B 272 " pdb=" CB LEU B 272 " ideal model delta sigma weight residual 1.528 1.507 0.021 1.51e-02 4.39e+03 1.98e+00 bond pdb=" CA ASP A 194 " pdb=" CB ASP A 194 " ideal model delta sigma weight residual 1.529 1.551 -0.022 1.62e-02 3.81e+03 1.87e+00 bond pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " ideal model delta sigma weight residual 1.808 1.768 0.040 3.30e-02 9.18e+02 1.45e+00 bond pdb=" CD LYS L 64 " pdb=" CE LYS L 64 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.32e+00 ... (remaining 13340 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 17779 2.28 - 4.55: 313 4.55 - 6.83: 37 6.83 - 9.10: 5 9.10 - 11.38: 1 Bond angle restraints: 18135 Sorted by residual: angle pdb=" N GLY L 10 " pdb=" CA GLY L 10 " pdb=" C GLY L 10 " ideal model delta sigma weight residual 110.43 116.02 -5.59 1.35e+00 5.49e-01 1.71e+01 angle pdb=" CB MET L 82 " pdb=" CG MET L 82 " pdb=" SD MET L 82 " ideal model delta sigma weight residual 112.70 124.08 -11.38 3.00e+00 1.11e-01 1.44e+01 angle pdb=" N GLY E 10 " pdb=" CA GLY E 10 " pdb=" C GLY E 10 " ideal model delta sigma weight residual 110.43 115.44 -5.01 1.35e+00 5.49e-01 1.38e+01 angle pdb=" CA GLU A 129 " pdb=" CB GLU A 129 " pdb=" CG GLU A 129 " ideal model delta sigma weight residual 114.10 121.50 -7.40 2.00e+00 2.50e-01 1.37e+01 angle pdb=" N GLY A 100 " pdb=" CA GLY A 100 " pdb=" C GLY A 100 " ideal model delta sigma weight residual 110.56 115.28 -4.72 1.36e+00 5.41e-01 1.20e+01 ... (remaining 18130 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 6867 17.95 - 35.90: 818 35.90 - 53.86: 143 53.86 - 71.81: 14 71.81 - 89.76: 12 Dihedral angle restraints: 7854 sinusoidal: 3078 harmonic: 4776 Sorted by residual: dihedral pdb=" CA LYS A 94 " pdb=" C LYS A 94 " pdb=" N SER A 95 " pdb=" CA SER A 95 " ideal model delta harmonic sigma weight residual 180.00 155.40 24.60 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CB CYS B 476 " pdb=" SG CYS B 476 " pdb=" SG CYS B 484 " pdb=" CB CYS B 484 " ideal model delta sinusoidal sigma weight residual 93.00 53.81 39.19 1 1.00e+01 1.00e-02 2.16e+01 dihedral pdb=" CA ALA B 516 " pdb=" C ALA B 516 " pdb=" N PRO B 517 " pdb=" CA PRO B 517 " ideal model delta harmonic sigma weight residual 180.00 -157.63 -22.37 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 7851 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1726 0.074 - 0.148: 247 0.148 - 0.222: 10 0.222 - 0.295: 1 0.295 - 0.369: 3 Chirality restraints: 1987 Sorted by residual: chirality pdb=" CB VAL L 63 " pdb=" CA VAL L 63 " pdb=" CG1 VAL L 63 " pdb=" CG2 VAL L 63 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CB THR C 30 " pdb=" CA THR C 30 " pdb=" OG1 THR C 30 " pdb=" CG2 THR C 30 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CB ILE E 28 " pdb=" CA ILE E 28 " pdb=" CG1 ILE E 28 " pdb=" CG2 ILE E 28 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 1984 not shown) Planarity restraints: 2326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 101 " 0.026 2.00e-02 2.50e+03 2.81e-02 1.97e+01 pdb=" CG TRP B 101 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 TRP B 101 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP B 101 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 101 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 101 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 101 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 101 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 101 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 101 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 516 " -0.056 5.00e-02 4.00e+02 8.48e-02 1.15e+01 pdb=" N PRO B 517 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO B 517 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 517 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 225 " 0.039 5.00e-02 4.00e+02 5.89e-02 5.55e+00 pdb=" N PRO C 226 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 226 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 226 " 0.032 5.00e-02 4.00e+02 ... (remaining 2323 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 186 2.61 - 3.19: 11356 3.19 - 3.76: 19072 3.76 - 4.33: 26290 4.33 - 4.90: 43357 Nonbonded interactions: 100261 Sorted by model distance: nonbonded pdb=" OD1 ASP L 99 " pdb=" N LYS L 100 " model vdw 2.043 3.120 nonbonded pdb=" NH2 ARG L 66 " pdb=" O SER L 84 " model vdw 2.133 3.120 nonbonded pdb=" NH2 ARG B 31 " pdb=" O PRO B 213 " model vdw 2.169 3.120 nonbonded pdb=" OE1 GLN C 49 " pdb=" OG1 THR C 270 " model vdw 2.177 3.040 nonbonded pdb=" OH TYR A 88 " pdb=" OE1 GLU A 187 " model vdw 2.209 3.040 ... (remaining 100256 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 62 or resid 83 through 173 or resid 184 through \ 466 or resid 486 through 525)) selection = (chain 'B' and (resid 22 through 62 or resid 83 through 173 or resid 184 through \ 466 or resid 486 through 525)) selection = (chain 'C' and (resid 22 through 62 or resid 83 through 525)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 32.090 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 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 : 0.005 0.040 13345 Z= 0.314 Angle : 0.730 11.381 18135 Z= 0.396 Chirality : 0.050 0.369 1987 Planarity : 0.005 0.085 2326 Dihedral : 15.179 89.758 4726 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.22 % Favored : 93.47 % Rotamer: Outliers : 0.21 % Allowed : 21.50 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.20), residues: 1592 helix: -2.04 (0.48), residues: 103 sheet: 0.37 (0.22), residues: 540 loop : -1.64 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP B 101 HIS 0.020 0.001 HIS A 501 PHE 0.038 0.002 PHE L 67 TYR 0.016 0.002 TYR B 166 ARG 0.008 0.001 ARG B 462 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 98 VAL cc_start: 0.4089 (t) cc_final: 0.3527 (t) REVERT: D 103 ASP cc_start: 0.4834 (m-30) cc_final: 0.4162 (m-30) outliers start: 3 outliers final: 2 residues processed: 97 average time/residue: 0.2440 time to fit residues: 35.9703 Evaluate side-chains 83 residues out of total 1437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 81 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 474 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 125 optimal weight: 50.0000 chunk 48 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 145 optimal weight: 0.0170 overall best weight: 1.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13345 Z= 0.271 Angle : 0.617 6.900 18135 Z= 0.330 Chirality : 0.047 0.217 1987 Planarity : 0.005 0.059 2326 Dihedral : 4.569 33.969 1780 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.28 % Favored : 93.47 % Rotamer: Outliers : 2.23 % Allowed : 19.14 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.21), residues: 1592 helix: -1.84 (0.44), residues: 117 sheet: 0.54 (0.23), residues: 529 loop : -1.59 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 101 HIS 0.006 0.001 HIS A 501 PHE 0.017 0.002 PHE L 67 TYR 0.014 0.001 TYR B 417 ARG 0.006 0.001 ARG D 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 87 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 ILE cc_start: 0.6921 (OUTLIER) cc_final: 0.6699 (tp) REVERT: B 101 TRP cc_start: 0.7948 (m-90) cc_final: 0.7720 (m-90) REVERT: B 467 GLU cc_start: 0.8920 (tp30) cc_final: 0.8383 (pp20) REVERT: B 515 HIS cc_start: 0.5830 (t-90) cc_final: 0.5628 (t-90) REVERT: D 46 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7508 (mm-30) REVERT: L 75 LYS cc_start: 0.9200 (mmmt) cc_final: 0.8875 (mmmm) outliers start: 32 outliers final: 17 residues processed: 111 average time/residue: 0.2411 time to fit residues: 40.1555 Evaluate side-chains 95 residues out of total 1437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 77 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 111 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 0.0870 chunk 45 optimal weight: 1.9990 chunk 120 optimal weight: 30.0000 chunk 98 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 145 optimal weight: 30.0000 chunk 157 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 144 optimal weight: 50.0000 chunk 49 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN A 501 HIS ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN D 5 GLN D 32 ASN L 76 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 13345 Z= 0.513 Angle : 0.734 8.863 18135 Z= 0.392 Chirality : 0.050 0.199 1987 Planarity : 0.005 0.052 2326 Dihedral : 5.170 26.783 1774 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.66 % Favored : 92.02 % Rotamer: Outliers : 3.48 % Allowed : 20.53 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.20), residues: 1592 helix: -1.99 (0.42), residues: 122 sheet: 0.20 (0.23), residues: 506 loop : -1.74 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 101 HIS 0.005 0.001 HIS C 203 PHE 0.024 0.003 PHE A 132 TYR 0.024 0.002 TYR B 166 ARG 0.005 0.001 ARG C 154 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 74 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 430 ILE cc_start: 0.7243 (OUTLIER) cc_final: 0.6782 (tp) REVERT: B 101 TRP cc_start: 0.8050 (m-90) cc_final: 0.7830 (m-90) REVERT: B 211 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8027 (m-30) REVERT: B 410 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8649 (mt0) REVERT: B 467 GLU cc_start: 0.8955 (tp30) cc_final: 0.8288 (pp20) REVERT: D 46 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8258 (mm-30) REVERT: L 75 LYS cc_start: 0.9220 (mmmt) cc_final: 0.8999 (mmmm) outliers start: 50 outliers final: 29 residues processed: 118 average time/residue: 0.2246 time to fit residues: 40.5894 Evaluate side-chains 97 residues out of total 1437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 65 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 132 PHE Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 111 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-dev-5461/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-dev-5461/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: 69.7975 > 50: distance: 76 - 199: 34.433 distance: 79 - 196: 36.492 distance: 90 - 184: 36.145 distance: 93 - 181: 32.649 distance: 125 - 127: 19.680 distance: 127 - 128: 31.919 distance: 128 - 129: 17.408 distance: 128 - 131: 15.840 distance: 129 - 130: 20.631 distance: 129 - 138: 5.817 distance: 131 - 132: 7.283 distance: 132 - 133: 33.584 distance: 132 - 134: 9.136 distance: 133 - 135: 39.534 distance: 134 - 136: 44.151 distance: 135 - 137: 20.565 distance: 136 - 137: 27.395 distance: 138 - 139: 44.507 distance: 139 - 140: 16.906 distance: 139 - 142: 38.019 distance: 140 - 141: 17.312 distance: 140 - 144: 32.859 distance: 142 - 143: 31.571 distance: 144 - 145: 31.759 distance: 145 - 146: 28.346 distance: 145 - 148: 40.916 distance: 146 - 147: 10.175 distance: 146 - 149: 15.207 distance: 149 - 150: 21.144 distance: 150 - 151: 17.768 distance: 150 - 153: 18.998 distance: 151 - 152: 36.110 distance: 151 - 157: 28.641 distance: 153 - 154: 41.128 distance: 154 - 155: 11.457 distance: 154 - 156: 7.283 distance: 157 - 158: 17.776 distance: 158 - 159: 12.682 distance: 158 - 161: 44.603 distance: 159 - 160: 10.017 distance: 159 - 166: 20.490 distance: 161 - 162: 43.363 distance: 162 - 163: 40.153 distance: 163 - 164: 24.095 distance: 163 - 165: 42.769 distance: 166 - 167: 11.221 distance: 166 - 172: 54.926 distance: 167 - 168: 41.308 distance: 167 - 170: 38.720 distance: 168 - 169: 55.367 distance: 168 - 173: 21.409 distance: 170 - 171: 56.693 distance: 171 - 172: 34.111 distance: 173 - 174: 30.485 distance: 174 - 175: 22.290 distance: 174 - 177: 25.596 distance: 175 - 176: 5.169 distance: 175 - 181: 21.731 distance: 177 - 178: 21.467 distance: 178 - 179: 25.219 distance: 178 - 180: 32.824 distance: 181 - 182: 45.446 distance: 182 - 183: 11.243 distance: 182 - 185: 22.735 distance: 183 - 184: 6.797 distance: 183 - 188: 3.778 distance: 185 - 187: 39.661 distance: 188 - 189: 49.056 distance: 189 - 190: 14.133 distance: 189 - 192: 39.884 distance: 190 - 191: 16.394 distance: 190 - 196: 61.591 distance: 192 - 193: 30.228 distance: 193 - 194: 30.315 distance: 193 - 195: 16.288 distance: 196 - 197: 40.156 distance: 197 - 198: 39.475 distance: 197 - 200: 51.777 distance: 198 - 199: 58.021 distance: 198 - 204: 28.163 distance: 200 - 201: 31.413 distance: 201 - 202: 50.601 distance: 201 - 203: 26.403