Starting phenix.real_space_refine on Thu Jul 2 21:38:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lt3_63364/07_2026/9lt3_63364.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lt3_63364/07_2026/9lt3_63364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lt3_63364/07_2026/9lt3_63364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lt3_63364/07_2026/9lt3_63364.map" model { file = "/net/cci-nas-00/data/ceres_data/9lt3_63364/07_2026/9lt3_63364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lt3_63364/07_2026/9lt3_63364.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 7 9.91 5 Mg 1 5.21 5 S 73 5.16 5 C 6283 2.51 5 N 1699 2.21 5 O 2012 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10075 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 5698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5698 Classifications: {'peptide': 737} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 703} Chain: "B" Number of atoms: 3589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3589 Classifications: {'peptide': 465} Link IDs: {'PCIS': 3, 'PTRANS': 23, 'TRANS': 438} Chain breaks: 1 Chain: "C" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 504 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 5, 'TRANS': 62} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 2, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 28 Ad-hoc single atom residues: {' CA': 5} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 5 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 15 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' MG': 1, 'NAG': 1} Classifications: {'undetermined': 2} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.80, per 1000 atoms: 0.18 Number of scatterers: 10075 At special positions: 0 Unit cell: (91.16, 131.44, 154.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 7 19.99 S 73 16.00 Mg 1 11.99 O 2012 8.00 N 1699 7.00 C 6283 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 128 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 461 " - pdb=" SG CYS A 472 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 535 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 602 " distance=2.03 Simple disulfide: pdb=" SG CYS A 668 " - pdb=" SG CYS A 681 " distance=2.03 Simple disulfide: pdb=" SG CYS B 5 " - pdb=" SG CYS B 23 " distance=2.03 Simple disulfide: pdb=" SG CYS B 13 " - pdb=" SG CYS B 435 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 38 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 49 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 184 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS B 406 " - pdb=" SG CYS B 433 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 448 " - pdb=" SG CYS B 460 " distance=2.03 Simple disulfide: pdb=" SG CYS B 462 " - pdb=" SG CYS B 471 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 21 " distance=2.03 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS C 16 " distance=1.93 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 38 " distance=2.03 Simple disulfide: pdb=" SG CYS C 29 " - pdb=" SG CYS C 35 " distance=2.03 Simple disulfide: pdb=" SG CYS C 34 " - pdb=" SG CYS C 59 " distance=2.03 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 66 " 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 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 6 " ALPHA1-4 " BMA F 4 " - " MAN F 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " BETA1-6 " BMA F 3 " - " BMA F 4 " NAG-ASN " NAG A1206 " - " ASN A 585 " " NAG A1207 " - " ASN A 524 " " NAG B1004 " - " ASN B 99 " " NAG D 1 " - " ASN A 44 " " NAG E 1 " - " ASN A 260 " " NAG F 1 " - " ASN A 266 " " NAG G 1 " - " ASN A 458 " " NAG J 1 " - " ASN B 320 " " NAG K 1 " - " ASN B 371 " Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 246.1 milliseconds 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2340 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 24 sheets defined 13.5% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 188 through 194 Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.602A pdb=" N LYS A 369 " --> pdb=" O GLY A 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 9 Processing helix chain 'B' and resid 12 through 20 removed outlier: 4.193A pdb=" N SER B 20 " --> pdb=" O CYS B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 47 Processing helix chain 'B' and resid 50 through 52 No H-bonds generated for 'chain 'B' and resid 50 through 52' Processing helix chain 'B' and resid 121 through 126 removed outlier: 4.294A pdb=" N ASP B 126 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 146 Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 175 through 179 removed outlier: 4.211A pdb=" N ASP B 179 " --> pdb=" O PRO B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 209 Processing helix chain 'B' and resid 221 through 232 removed outlier: 3.684A pdb=" N ALA B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 258 through 262 removed outlier: 3.707A pdb=" N ARG B 261 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 262 " --> pdb=" O ASP B 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 258 through 262' Processing helix chain 'B' and resid 291 through 303 Processing helix chain 'B' and resid 314 through 325 Processing helix chain 'B' and resid 337 through 350 Processing helix chain 'B' and resid 435 through 441 removed outlier: 3.574A pdb=" N ALA B 439 " --> pdb=" O ALA B 436 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 4.071A pdb=" N SER A 407 " --> pdb=" O GLY A 425 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 26 removed outlier: 3.651A pdb=" N ALA A 22 " --> pdb=" O GLY A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.748A pdb=" N ASP A 84 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA5, first strand: chain 'A' and resid 98 through 100 Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 163 Processing sheet with id=AA7, first strand: chain 'A' and resid 225 through 229 removed outlier: 3.914A pdb=" N SER A 225 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL A 253 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASN A 266 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE A 255 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 280 through 283 Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AB1, first strand: chain 'A' and resid 343 through 348 removed outlier: 6.293A pdb=" N ILE A 344 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ALA A 361 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ALA A 359 " --> pdb=" O PRO A 346 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY A 348 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN A 389 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 378 through 379 Processing sheet with id=AB3, first strand: chain 'A' and resid 511 through 513 Processing sheet with id=AB4, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB5, first strand: chain 'A' and resid 606 through 611 removed outlier: 3.886A pdb=" N ILE A 628 " --> pdb=" O ASP A 611 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN A 623 " --> pdb=" O VAL A 701 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 701 " --> pdb=" O ASN A 623 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR A 691 " --> pdb=" O ASN A 633 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY A 655 " --> pdb=" O ARG A 698 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER A 700 " --> pdb=" O PHE A 653 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N PHE A 653 " --> pdb=" O SER A 700 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 616 through 618 removed outlier: 6.107A pdb=" N ILE A 617 " --> pdb=" O ALA A 737 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 668 through 671 removed outlier: 3.600A pdb=" N CYS A 681 " --> pdb=" O LEU A 643 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ALA A 641 " --> pdb=" O LEU A 683 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 38 through 39 removed outlier: 3.589A pdb=" N TRP B 25 " --> pdb=" O GLU B 55 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 60 through 65 removed outlier: 3.583A pdb=" N GLU B 60 " --> pdb=" O ARG B 91 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG B 91 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ARG B 87 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE B 88 " --> pdb=" O GLN B 428 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N THR B 430 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU B 90 " --> pdb=" O THR B 430 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR B 415 " --> pdb=" O ARG B 360 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL B 355 " --> pdb=" O MET B 387 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N MET B 387 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU B 357 " --> pdb=" O SER B 385 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N SER B 385 " --> pdb=" O LEU B 357 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 84 removed outlier: 3.617A pdb=" N SER B 396 " --> pdb=" O THR B 373 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 190 through 197 removed outlier: 6.948A pdb=" N VAL B 193 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N ALA B 155 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N THR B 195 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N PHE B 153 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N LEU B 245 " --> pdb=" O PRO B 111 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP B 113 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL B 247 " --> pdb=" O ASP B 113 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TYR B 115 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N THR B 249 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU B 117 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR B 250 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 8.881A pdb=" N THR B 329 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B 306 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLY B 331 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N PHE B 308 " --> pdb=" O GLY B 331 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 454 through 456 Processing sheet with id=AC4, first strand: chain 'C' and resid 16 through 17 Processing sheet with id=AC5, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AC6, first strand: chain 'C' and resid 46 through 48 removed outlier: 3.581A pdb=" N ARG C 48 " --> pdb=" O ASP C 57 " (cutoff:3.500A) 308 hydrogen bonds defined for protein. 798 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: 1.62 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2817 1.33 - 1.45: 1797 1.45 - 1.58: 5544 1.58 - 1.70: 0 1.70 - 1.82: 98 Bond restraints: 10256 Sorted by residual: bond pdb=" CA ASN C 69 " pdb=" C ASN C 69 " ideal model delta sigma weight residual 1.523 1.474 0.048 1.23e-02 6.61e+03 1.54e+01 bond pdb=" C LYS C 43 " pdb=" N ARG C 44 " ideal model delta sigma weight residual 1.332 1.386 -0.054 1.38e-02 5.25e+03 1.54e+01 bond pdb=" C ASN B 99 " pdb=" N PHE B 100 " ideal model delta sigma weight residual 1.331 1.378 -0.047 1.51e-02 4.39e+03 9.78e+00 bond pdb=" C CYS C 47 " pdb=" N ARG C 48 " ideal model delta sigma weight residual 1.332 1.296 0.036 1.26e-02 6.30e+03 8.06e+00 bond pdb=" CA LEU A 593 " pdb=" C LEU A 593 " ideal model delta sigma weight residual 1.524 1.490 0.034 1.29e-02 6.01e+03 6.93e+00 ... (remaining 10251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 13355 1.55 - 3.10: 409 3.10 - 4.65: 88 4.65 - 6.20: 23 6.20 - 7.75: 9 Bond angle restraints: 13884 Sorted by residual: angle pdb=" C ASN B 449 " pdb=" CA ASN B 449 " pdb=" CB ASN B 449 " ideal model delta sigma weight residual 115.79 109.96 5.83 1.19e+00 7.06e-01 2.40e+01 angle pdb=" C SER B 445 " pdb=" CA SER B 445 " pdb=" CB SER B 445 " ideal model delta sigma weight residual 116.34 110.07 6.27 1.40e+00 5.10e-01 2.01e+01 angle pdb=" CA ARG A 566 " pdb=" CB ARG A 566 " pdb=" CG ARG A 566 " ideal model delta sigma weight residual 114.10 121.85 -7.75 2.00e+00 2.50e-01 1.50e+01 angle pdb=" O ASN B 99 " pdb=" C ASN B 99 " pdb=" N PHE B 100 " ideal model delta sigma weight residual 123.21 127.42 -4.21 1.27e+00 6.20e-01 1.10e+01 angle pdb=" C ASP C 65 " pdb=" N CYS C 66 " pdb=" CA CYS C 66 " ideal model delta sigma weight residual 121.61 126.16 -4.55 1.39e+00 5.18e-01 1.07e+01 ... (remaining 13879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.55: 5784 21.55 - 43.10: 584 43.10 - 64.65: 113 64.65 - 86.20: 43 86.20 - 107.75: 32 Dihedral angle restraints: 6556 sinusoidal: 2909 harmonic: 3647 Sorted by residual: dihedral pdb=" CB CYS C 29 " pdb=" SG CYS C 29 " pdb=" SG CYS C 35 " pdb=" CB CYS C 35 " ideal model delta sinusoidal sigma weight residual -86.00 -23.83 -62.17 1 1.00e+01 1.00e-02 5.12e+01 dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 38 " pdb=" CB CYS C 38 " ideal model delta sinusoidal sigma weight residual -86.00 -134.50 48.50 1 1.00e+01 1.00e-02 3.24e+01 dihedral pdb=" CA TYR A 450 " pdb=" C TYR A 450 " pdb=" N PRO A 451 " pdb=" CA PRO A 451 " ideal model delta harmonic sigma weight residual -180.00 -153.01 -26.99 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 6553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1289 0.058 - 0.115: 261 0.115 - 0.173: 31 0.173 - 0.231: 6 0.231 - 0.288: 4 Chirality restraints: 1591 Sorted by residual: chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB ILE A 147 " pdb=" CA ILE A 147 " pdb=" CG1 ILE A 147 " pdb=" CG2 ILE A 147 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 1588 not shown) Planarity restraints: 1819 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 438 " -0.023 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C ARG A 438 " 0.079 2.00e-02 2.50e+03 pdb=" O ARG A 438 " -0.030 2.00e-02 2.50e+03 pdb=" N PRO A 439 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 68 " -0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C ARG C 68 " 0.066 2.00e-02 2.50e+03 pdb=" O ARG C 68 " -0.026 2.00e-02 2.50e+03 pdb=" N ASN C 69 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 438 " 0.049 5.00e-02 4.00e+02 7.54e-02 9.09e+00 pdb=" N PRO A 439 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 439 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 439 " 0.041 5.00e-02 4.00e+02 ... (remaining 1816 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 2 1.99 - 2.72: 468 2.72 - 3.45: 13834 3.45 - 4.17: 25395 4.17 - 4.90: 44761 Nonbonded interactions: 84460 Sorted by model distance: nonbonded pdb=" OG SER B 123 " pdb="MG MG B1001 " model vdw 1.263 2.170 nonbonded pdb=" OD1 ASP C 53 " pdb="MG MG B1001 " model vdw 1.838 2.170 nonbonded pdb=" OD1 ASN A 232 " pdb="CA CA A1202 " model vdw 2.066 3.250 nonbonded pdb=" ND2 ASN B 215 " pdb="CA CA B1003 " model vdw 2.079 3.330 nonbonded pdb=" OH TYR A 275 " pdb=" OD1 ASP B 259 " model vdw 2.167 3.040 ... (remaining 84455 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 'D' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'K' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.560 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.580 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 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 0.105 10301 Z= 0.231 Angle : 0.728 22.832 13995 Z= 0.369 Chirality : 0.049 0.288 1591 Planarity : 0.004 0.075 1810 Dihedral : 19.583 107.753 4144 Min Nonbonded Distance : 1.263 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.20 % Allowed : 24.63 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.23), residues: 1262 helix: 0.42 (0.49), residues: 127 sheet: 0.23 (0.25), residues: 428 loop : -1.20 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 562 TYR 0.016 0.001 TYR A 275 PHE 0.018 0.002 PHE A 154 TRP 0.012 0.002 TRP A 179 HIS 0.005 0.001 HIS B 446 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.23 (10256) covalent geometry : angle 0.69460 / 0.36 (13884) SS BOND : bond 0.02152 / 1.03 ( 24) SS BOND : angle 3.35705 / 2.01 ( 48) hydrogen bonds : bond 0.21164 / 13.29 ( 308) hydrogen bonds : angle 9.36190 / 6.60 ( 798) link_ALPHA1-3 : bond 0.00442 / 0.23 ( 1) link_ALPHA1-3 : angle 1.57775 / 1.31 ( 3) link_ALPHA1-4 : bond 0.00517 / 0.27 ( 1) link_ALPHA1-4 : angle 2.31737 / 1.43 ( 3) link_BETA1-4 : bond 0.00446 / 0.22 ( 9) link_BETA1-4 : angle 1.61405 / 1.08 ( 27) link_BETA1-6 : bond 0.01013 / 0.53 ( 1) link_BETA1-6 : angle 0.74166 / 0.50 ( 3) link_NAG-ASN : bond 0.00447 / 0.21 ( 9) link_NAG-ASN : angle 1.75671 / 1.20 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7401 (mmm-85) cc_final: 0.6930 (mtp-110) REVERT: A 248 ARG cc_start: 0.7612 (mtm-85) cc_final: 0.6421 (pmt170) REVERT: A 416 LYS cc_start: 0.7594 (mmtm) cc_final: 0.7292 (mmpt) REVERT: A 444 ASN cc_start: 0.7647 (m110) cc_final: 0.6992 (m-40) REVERT: A 529 ARG cc_start: 0.7222 (mtp85) cc_final: 0.6494 (mtm-85) REVERT: A 559 MET cc_start: 0.6679 (ttp) cc_final: 0.6240 (ttt) REVERT: A 687 MET cc_start: 0.6211 (ttt) cc_final: 0.5646 (ttp) REVERT: B 86 GLN cc_start: 0.5815 (OUTLIER) cc_final: 0.5347 (tm-30) REVERT: B 207 VAL cc_start: 0.8635 (t) cc_final: 0.8353 (t) outliers start: 13 outliers final: 4 residues processed: 149 average time/residue: 0.4631 time to fit residues: 74.1919 Evaluate side-chains 104 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 357 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.4980 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 GLN A 394 GLN A 494 GLN A 589 GLN A 623 ASN A 692 GLN B 141 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.224875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.146453 restraints weight = 10413.710| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.76 r_work: 0.3575 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 10301 Z= 0.307 Angle : 0.797 11.268 13995 Z= 0.398 Chirality : 0.053 0.255 1591 Planarity : 0.005 0.056 1810 Dihedral : 11.683 84.856 1809 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 4.81 % Allowed : 22.13 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.23), residues: 1262 helix: 0.10 (0.48), residues: 127 sheet: 0.18 (0.24), residues: 421 loop : -1.21 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 66 TYR 0.020 0.002 TYR B 318 PHE 0.037 0.003 PHE A 154 TRP 0.018 0.003 TRP B 238 HIS 0.006 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00738 / 0.31 (10256) covalent geometry : angle 0.78279 / 0.40 (13884) SS BOND : bond 0.00311 / 0.18 ( 24) SS BOND : angle 0.93104 / 0.63 ( 48) hydrogen bonds : bond 0.05293 / 3.42 ( 308) hydrogen bonds : angle 7.20000 / 5.02 ( 798) link_ALPHA1-3 : bond 0.00616 / 0.32 ( 1) link_ALPHA1-3 : angle 2.29433 / 1.58 ( 3) link_ALPHA1-4 : bond 0.00798 / 0.42 ( 1) link_ALPHA1-4 : angle 2.98112 / 2.06 ( 3) link_BETA1-4 : bond 0.00457 / 0.23 ( 9) link_BETA1-4 : angle 2.59600 / 1.82 ( 27) link_BETA1-6 : bond 0.00391 / 0.21 ( 1) link_BETA1-6 : angle 2.30330 / 1.84 ( 3) link_NAG-ASN : bond 0.00538 / 0.25 ( 9) link_NAG-ASN : angle 1.84611 / 1.18 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 101 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7796 (mmm-85) cc_final: 0.7382 (mtp-110) REVERT: A 46 THR cc_start: 0.7388 (OUTLIER) cc_final: 0.7008 (p) REVERT: A 186 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.7811 (t70) REVERT: A 248 ARG cc_start: 0.8088 (mtm-85) cc_final: 0.7353 (ptt90) REVERT: A 249 THR cc_start: 0.9122 (t) cc_final: 0.8598 (m) REVERT: A 275 TYR cc_start: 0.8845 (OUTLIER) cc_final: 0.7942 (m-80) REVERT: A 331 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8570 (tt) REVERT: A 416 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8023 (mmpt) REVERT: A 444 ASN cc_start: 0.7694 (m110) cc_final: 0.7407 (m-40) REVERT: B 62 ARG cc_start: 0.5346 (OUTLIER) cc_final: 0.5016 (pmt170) REVERT: B 191 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8073 (ttmm) REVERT: B 207 VAL cc_start: 0.8693 (OUTLIER) cc_final: 0.8458 (t) REVERT: B 387 MET cc_start: 0.7172 (tpt) cc_final: 0.6964 (tpp) outliers start: 52 outliers final: 19 residues processed: 138 average time/residue: 0.4950 time to fit residues: 73.4839 Evaluate side-chains 115 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 357 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 122 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 80 optimal weight: 0.0370 chunk 74 optimal weight: 20.0000 chunk 115 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 0 optimal weight: 0.8980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 HIS A 152 GLN A 692 GLN ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.227176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.153667 restraints weight = 10421.605| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.67 r_work: 0.3665 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3565 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10301 Z= 0.163 Angle : 0.638 9.683 13995 Z= 0.318 Chirality : 0.047 0.246 1591 Planarity : 0.004 0.036 1810 Dihedral : 8.961 75.851 1804 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.98 % Allowed : 22.96 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.23), residues: 1262 helix: 0.44 (0.49), residues: 121 sheet: 0.37 (0.25), residues: 409 loop : -1.06 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 62 TYR 0.013 0.001 TYR B 318 PHE 0.024 0.002 PHE A 154 TRP 0.012 0.002 TRP A 179 HIS 0.003 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (10256) covalent geometry : angle 0.62540 / 0.32 (13884) SS BOND : bond 0.00160 / 0.11 ( 24) SS BOND : angle 0.62668 / 0.43 ( 48) hydrogen bonds : bond 0.03942 / 2.57 ( 308) hydrogen bonds : angle 6.58937 / 4.60 ( 798) link_ALPHA1-3 : bond 0.00776 / 0.41 ( 1) link_ALPHA1-3 : angle 1.90126 / 1.28 ( 3) link_ALPHA1-4 : bond 0.00044 / 0.02 ( 1) link_ALPHA1-4 : angle 2.65182 / 1.67 ( 3) link_BETA1-4 : bond 0.00374 / 0.20 ( 9) link_BETA1-4 : angle 2.28996 / 1.60 ( 27) link_BETA1-6 : bond 0.00119 / 0.06 ( 1) link_BETA1-6 : angle 1.71709 / 1.16 ( 3) link_NAG-ASN : bond 0.00342 / 0.16 ( 9) link_NAG-ASN : angle 1.46455 / 0.92 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 96 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7769 (mmm-85) cc_final: 0.7347 (mtp-110) REVERT: A 46 THR cc_start: 0.7442 (m) cc_final: 0.7200 (p) REVERT: A 118 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7018 (mtp) REVERT: A 259 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8377 (mtpp) REVERT: A 327 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8205 (mm-40) REVERT: A 444 ASN cc_start: 0.7801 (m110) cc_final: 0.7465 (m110) REVERT: A 510 ARG cc_start: 0.4986 (OUTLIER) cc_final: 0.4722 (mtt180) REVERT: A 571 THR cc_start: 0.6217 (p) cc_final: 0.5950 (t) REVERT: B 62 ARG cc_start: 0.5156 (ptt-90) cc_final: 0.4747 (pmt170) REVERT: B 180 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8392 (ptp) outliers start: 43 outliers final: 19 residues processed: 126 average time/residue: 0.5102 time to fit residues: 68.9706 Evaluate side-chains 117 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 510 ARG Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 357 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 40 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 120 optimal weight: 20.0000 chunk 55 optimal weight: 0.9980 chunk 121 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 63 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN B 342 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.225355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.150041 restraints weight = 10510.259| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.72 r_work: 0.3522 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10301 Z= 0.203 Angle : 0.664 9.953 13995 Z= 0.330 Chirality : 0.048 0.258 1591 Planarity : 0.004 0.033 1810 Dihedral : 7.790 62.340 1804 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 4.07 % Allowed : 24.17 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.23), residues: 1262 helix: 0.54 (0.49), residues: 121 sheet: 0.29 (0.25), residues: 409 loop : -1.10 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 476 TYR 0.017 0.002 TYR B 318 PHE 0.027 0.002 PHE A 154 TRP 0.014 0.002 TRP A 179 HIS 0.003 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.20 (10256) covalent geometry : angle 0.65237 / 0.33 (13884) SS BOND : bond 0.00169 / 0.11 ( 24) SS BOND : angle 0.62413 / 0.43 ( 48) hydrogen bonds : bond 0.03943 / 2.59 ( 308) hydrogen bonds : angle 6.46530 / 4.51 ( 798) link_ALPHA1-3 : bond 0.00646 / 0.34 ( 1) link_ALPHA1-3 : angle 2.06865 / 1.41 ( 3) link_ALPHA1-4 : bond 0.00344 / 0.18 ( 1) link_ALPHA1-4 : angle 2.88367 / 1.92 ( 3) link_BETA1-4 : bond 0.00406 / 0.20 ( 9) link_BETA1-4 : angle 2.15967 / 1.46 ( 27) link_BETA1-6 : bond 0.00131 / 0.07 ( 1) link_BETA1-6 : angle 1.92907 / 1.19 ( 3) link_NAG-ASN : bond 0.00422 / 0.20 ( 9) link_NAG-ASN : angle 1.60505 / 1.02 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 89 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7876 (mmm-85) cc_final: 0.7305 (mtp-110) REVERT: A 118 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.6989 (mtp) REVERT: A 327 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8261 (mm-40) REVERT: A 444 ASN cc_start: 0.7788 (m110) cc_final: 0.7532 (m110) REVERT: A 510 ARG cc_start: 0.5037 (OUTLIER) cc_final: 0.4829 (mtt180) REVERT: A 522 SER cc_start: 0.8257 (OUTLIER) cc_final: 0.7850 (m) REVERT: B 62 ARG cc_start: 0.5097 (ptt-90) cc_final: 0.4724 (pmt170) REVERT: B 356 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6252 (tp30) REVERT: B 366 LEU cc_start: 0.4321 (OUTLIER) cc_final: 0.4091 (pp) REVERT: B 387 MET cc_start: 0.7402 (tpt) cc_final: 0.7145 (tmm) outliers start: 44 outliers final: 22 residues processed: 119 average time/residue: 0.5372 time to fit residues: 68.5913 Evaluate side-chains 116 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 510 ARG Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 366 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 4 optimal weight: 0.9980 chunk 36 optimal weight: 0.1980 chunk 10 optimal weight: 0.1980 chunk 35 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.226355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.148223 restraints weight = 10508.937| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.69 r_work: 0.3625 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10301 Z= 0.162 Angle : 0.619 9.890 13995 Z= 0.310 Chirality : 0.047 0.253 1591 Planarity : 0.004 0.031 1810 Dihedral : 7.125 57.545 1802 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.52 % Allowed : 24.63 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.23), residues: 1262 helix: 0.60 (0.49), residues: 121 sheet: 0.32 (0.25), residues: 410 loop : -1.04 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 476 TYR 0.015 0.001 TYR B 318 PHE 0.023 0.002 PHE A 154 TRP 0.013 0.002 TRP A 179 HIS 0.003 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (10256) covalent geometry : angle 0.60821 / 0.31 (13884) SS BOND : bond 0.00149 / 0.09 ( 24) SS BOND : angle 0.53652 / 0.37 ( 48) hydrogen bonds : bond 0.03504 / 2.29 ( 308) hydrogen bonds : angle 6.23869 / 4.35 ( 798) link_ALPHA1-3 : bond 0.00704 / 0.37 ( 1) link_ALPHA1-3 : angle 1.89987 / 1.32 ( 3) link_ALPHA1-4 : bond 0.00052 / 0.03 ( 1) link_ALPHA1-4 : angle 2.65210 / 1.72 ( 3) link_BETA1-4 : bond 0.00386 / 0.20 ( 9) link_BETA1-4 : angle 1.99610 / 1.33 ( 27) link_BETA1-6 : bond 0.00048 / 0.03 ( 1) link_BETA1-6 : angle 1.96009 / 1.15 ( 3) link_NAG-ASN : bond 0.00339 / 0.16 ( 9) link_NAG-ASN : angle 1.50335 / 0.96 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 91 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7721 (mmm-85) cc_final: 0.7288 (mtp-110) REVERT: A 249 THR cc_start: 0.9086 (t) cc_final: 0.8687 (m) REVERT: A 259 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8387 (mtpp) REVERT: A 327 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8157 (mm-40) REVERT: A 444 ASN cc_start: 0.7745 (m110) cc_final: 0.7495 (m110) REVERT: A 510 ARG cc_start: 0.5118 (OUTLIER) cc_final: 0.4864 (mtt180) REVERT: A 522 SER cc_start: 0.8141 (OUTLIER) cc_final: 0.7922 (m) REVERT: A 580 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7732 (mt0) REVERT: B 14 GLN cc_start: 0.6354 (OUTLIER) cc_final: 0.6091 (pp30) REVERT: B 62 ARG cc_start: 0.5410 (ptt-90) cc_final: 0.5023 (pmt170) REVERT: B 387 MET cc_start: 0.7338 (tpt) cc_final: 0.7035 (mmm) outliers start: 38 outliers final: 21 residues processed: 119 average time/residue: 0.5501 time to fit residues: 70.5119 Evaluate side-chains 114 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 510 ARG Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 454 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.6386 > 50: distance: 18 - 22: 29.226 distance: 19 - 33: 26.854 distance: 22 - 23: 28.382 distance: 23 - 24: 41.520 distance: 23 - 26: 8.341 distance: 24 - 25: 46.158 distance: 24 - 27: 13.216 distance: 27 - 28: 30.142 distance: 28 - 29: 30.873 distance: 28 - 31: 55.151 distance: 29 - 30: 26.929 distance: 29 - 33: 8.638 distance: 30 - 47: 20.174 distance: 31 - 32: 50.279 distance: 32 - 154: 22.048 distance: 33 - 34: 45.240 distance: 34 - 35: 40.839 distance: 34 - 37: 44.862 distance: 35 - 36: 41.277 distance: 35 - 42: 42.765 distance: 36 - 56: 39.060 distance: 37 - 38: 21.711 distance: 38 - 39: 41.767 distance: 39 - 40: 38.761 distance: 39 - 41: 28.306 distance: 42 - 43: 32.681 distance: 43 - 44: 50.000 distance: 43 - 46: 54.238 distance: 44 - 45: 43.131 distance: 44 - 47: 57.142 distance: 47 - 48: 43.028 distance: 48 - 49: 16.624 distance: 48 - 51: 11.686 distance: 49 - 50: 8.165 distance: 49 - 56: 9.586 distance: 51 - 52: 20.690 distance: 52 - 53: 5.608 distance: 53 - 54: 10.016 distance: 53 - 55: 8.560 distance: 56 - 57: 55.679 distance: 57 - 58: 23.715 distance: 57 - 60: 49.087 distance: 58 - 59: 29.208 distance: 58 - 61: 45.224 distance: 61 - 62: 43.083 distance: 62 - 63: 23.393 distance: 62 - 65: 26.162 distance: 63 - 64: 39.065 distance: 63 - 70: 39.955 distance: 65 - 66: 42.247 distance: 66 - 67: 22.600 distance: 67 - 68: 31.839 distance: 67 - 69: 20.676 distance: 70 - 71: 43.283 distance: 70 - 76: 29.277 distance: 71 - 72: 35.214 distance: 71 - 74: 52.410 distance: 72 - 73: 55.293 distance: 72 - 77: 26.394 distance: 74 - 75: 33.705 distance: 75 - 76: 45.941 distance: 77 - 78: 38.107 distance: 78 - 79: 39.801 distance: 78 - 81: 24.600 distance: 79 - 80: 53.534 distance: 79 - 85: 39.968 distance: 81 - 82: 38.889 distance: 82 - 83: 24.715 distance: 82 - 84: 23.026 distance: 85 - 86: 67.625 distance: 86 - 87: 39.758 distance: 86 - 89: 3.089 distance: 87 - 88: 57.168 distance: 87 - 91: 27.898 distance: 89 - 90: 33.631