Starting phenix.real_space_refine on Wed Feb 4 06:26:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9och_70315/02_2026/9och_70315.cif Found real_map, /net/cci-nas-00/data/ceres_data/9och_70315/02_2026/9och_70315.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9och_70315/02_2026/9och_70315.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9och_70315/02_2026/9och_70315.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9och_70315/02_2026/9och_70315.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9och_70315/02_2026/9och_70315.map" } resolution = 3.3 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= 0.039 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 P 5 5.49 5 Mg 2 5.21 5 S 44 5.16 5 C 5642 2.51 5 N 1545 2.21 5 O 1657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8895 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 4288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4288 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 20, 'TRANS': 527} Chain: "D" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 279 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "A" Number of atoms: 4268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4268 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 21, 'TRANS': 529} Chain breaks: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.02, per 1000 atoms: 0.23 Number of scatterers: 8895 At special positions: 0 Unit cell: (73.08, 90.48, 141.52, 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) S 44 16.00 P 5 15.00 Mg 2 11.99 O 1657 8.00 N 1545 7.00 C 5642 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 359.5 milliseconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2094 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 7 sheets defined 69.0% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'B' and resid 134 through 146 removed outlier: 3.703A pdb=" N MET B 138 " --> pdb=" O ASN B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 167 Processing helix chain 'B' and resid 168 through 182 removed outlier: 3.798A pdb=" N TYR B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 234 removed outlier: 3.601A pdb=" N SER B 206 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N CYS B 213 " --> pdb=" O CYS B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 244 removed outlier: 3.504A pdb=" N GLU B 243 " --> pdb=" O GLY B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 262 removed outlier: 4.569A pdb=" N THR B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 284 removed outlier: 4.879A pdb=" N ASN B 269 " --> pdb=" O PRO B 265 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 281 " --> pdb=" O LYS B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 288 through 338 removed outlier: 4.198A pdb=" N LEU B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR B 293 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU B 294 " --> pdb=" O PRO B 290 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET B 300 " --> pdb=" O SER B 296 " (cutoff:3.500A) Proline residue: B 301 - end of helix removed outlier: 3.639A pdb=" N ALA B 306 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG B 313 " --> pdb=" O VAL B 309 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU B 316 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG B 327 " --> pdb=" O ASP B 323 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B 331 " --> pdb=" O ARG B 327 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL B 332 " --> pdb=" O ALA B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 346 Processing helix chain 'B' and resid 347 through 399 removed outlier: 3.619A pdb=" N LEU B 365 " --> pdb=" O GLN B 361 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET B 399 " --> pdb=" O GLY B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 440 removed outlier: 3.643A pdb=" N LEU B 410 " --> pdb=" O GLN B 406 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR B 415 " --> pdb=" O SER B 411 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR B 428 " --> pdb=" O GLN B 424 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA B 440 " --> pdb=" O ASN B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 448 removed outlier: 4.172A pdb=" N PHE B 444 " --> pdb=" O ALA B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 517 Processing helix chain 'B' and resid 535 through 537 No H-bonds generated for 'chain 'B' and resid 535 through 537' Processing helix chain 'B' and resid 538 through 545 removed outlier: 3.519A pdb=" N SER B 544 " --> pdb=" O CYS B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 565 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 590 removed outlier: 3.675A pdb=" N GLN B 590 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 597 Processing helix chain 'B' and resid 601 through 605 Processing helix chain 'B' and resid 608 through 622 Processing helix chain 'B' and resid 638 through 645 Processing helix chain 'B' and resid 663 through 667 removed outlier: 3.523A pdb=" N GLN B 667 " --> pdb=" O GLN B 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 119 Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 129 through 135 Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 185 through 203 Processing helix chain 'A' and resid 203 through 209 removed outlier: 3.848A pdb=" N PHE A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 269 removed outlier: 4.065A pdb=" N MET A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE A 265 " --> pdb=" O GLN A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 279 removed outlier: 3.560A pdb=" N GLN A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 324 removed outlier: 3.703A pdb=" N SER A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR A 292 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER A 293 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER A 304 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU A 305 " --> pdb=" O GLU A 301 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 339 through 373 removed outlier: 5.065A pdb=" N LYS A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N TRP A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TYR A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 381 Processing helix chain 'A' and resid 382 through 434 removed outlier: 3.724A pdb=" N LYS A 393 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 402 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS A 403 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS A 423 " --> pdb=" O GLY A 419 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 475 removed outlier: 3.830A pdb=" N PHE A 447 " --> pdb=" O ASN A 443 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN A 456 " --> pdb=" O MET A 452 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Proline residue: A 466 - end of helix Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 543 through 552 Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 573 through 580 Processing helix chain 'A' and resid 594 through 600 Processing helix chain 'A' and resid 608 through 619 removed outlier: 3.560A pdb=" N ILE A 612 " --> pdb=" O THR A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.551A pdb=" N SER A 626 " --> pdb=" O HIS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 644 through 658 removed outlier: 3.753A pdb=" N ARG A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN A 649 " --> pdb=" O GLY A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 687 Processing helix chain 'A' and resid 688 through 694 removed outlier: 3.980A pdb=" N TYR A 692 " --> pdb=" O PRO A 689 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 693 " --> pdb=" O GLU A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 732 removed outlier: 3.856A pdb=" N LYS A 732 " --> pdb=" O GLN A 728 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 486 through 489 removed outlier: 5.685A pdb=" N LYS B 487 " --> pdb=" O PHE B 475 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N PHE B 475 " --> pdb=" O LYS B 487 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL B 468 " --> pdb=" O LEU B 493 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 486 through 489 removed outlier: 5.685A pdb=" N LYS B 487 " --> pdb=" O PHE B 475 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N PHE B 475 " --> pdb=" O LYS B 487 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL B 473 " --> pdb=" O GLY B 524 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY B 524 " --> pdb=" O VAL B 473 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 546 through 549 removed outlier: 6.364A pdb=" N ALA B 500 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU B 675 " --> pdb=" O ALA B 500 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL B 502 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 558 through 559 Processing sheet with id=AA5, first strand: chain 'A' and resid 527 through 528 Processing sheet with id=AA6, first strand: chain 'A' and resid 508 through 510 removed outlier: 7.828A pdb=" N PHE A 510 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N GLN A 522 " --> pdb=" O PHE A 510 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 581 through 584 removed outlier: 6.731A pdb=" N LEU A 664 " --> pdb=" O LEU A 697 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ILE A 699 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU A 666 " --> pdb=" O ILE A 699 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS A 711 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE A 712 " --> pdb=" O GLY A 723 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY A 723 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N PHE A 714 " --> pdb=" O ARG A 721 " (cutoff:3.500A) 564 hydrogen bonds defined for protein. 1623 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: 1.46 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2612 1.34 - 1.46: 1405 1.46 - 1.58: 4962 1.58 - 1.70: 8 1.70 - 1.82: 71 Bond restraints: 9058 Sorted by residual: bond pdb=" CA PHE B 302 " pdb=" C PHE B 302 " ideal model delta sigma weight residual 1.524 1.573 -0.049 1.24e-02 6.50e+03 1.58e+01 bond pdb=" CA MET D 124 " pdb=" C MET D 124 " ideal model delta sigma weight residual 1.522 1.564 -0.042 1.39e-02 5.18e+03 9.21e+00 bond pdb=" N PHE B 158 " pdb=" CA PHE B 158 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.52e+00 bond pdb=" CA PHE B 157 " pdb=" C PHE B 157 " ideal model delta sigma weight residual 1.524 1.549 -0.025 1.32e-02 5.74e+03 3.71e+00 bond pdb=" C ARG B 494 " pdb=" N PRO B 495 " ideal model delta sigma weight residual 1.332 1.355 -0.023 1.32e-02 5.74e+03 3.06e+00 ... (remaining 9053 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 12087 2.29 - 4.57: 159 4.57 - 6.86: 35 6.86 - 9.15: 8 9.15 - 11.43: 2 Bond angle restraints: 12291 Sorted by residual: angle pdb=" N THR B 303 " pdb=" CA THR B 303 " pdb=" C THR B 303 " ideal model delta sigma weight residual 111.28 122.71 -11.43 1.09e+00 8.42e-01 1.10e+02 angle pdb=" C ASN D 125 " pdb=" CA ASN D 125 " pdb=" CB ASN D 125 " ideal model delta sigma weight residual 117.23 109.79 7.44 1.36e+00 5.41e-01 2.99e+01 angle pdb=" N ASN B 436 " pdb=" CA ASN B 436 " pdb=" C ASN B 436 " ideal model delta sigma weight residual 111.07 105.59 5.48 1.07e+00 8.73e-01 2.62e+01 angle pdb=" N PHE B 302 " pdb=" CA PHE B 302 " pdb=" C PHE B 302 " ideal model delta sigma weight residual 110.97 116.45 -5.48 1.09e+00 8.42e-01 2.53e+01 angle pdb=" N THR B 303 " pdb=" CA THR B 303 " pdb=" CB THR B 303 " ideal model delta sigma weight residual 110.12 102.77 7.35 1.47e+00 4.63e-01 2.50e+01 ... (remaining 12286 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 4879 17.63 - 35.26: 436 35.26 - 52.89: 113 52.89 - 70.52: 22 70.52 - 88.15: 9 Dihedral angle restraints: 5459 sinusoidal: 2201 harmonic: 3258 Sorted by residual: dihedral pdb=" C PHE B 157 " pdb=" N PHE B 157 " pdb=" CA PHE B 157 " pdb=" CB PHE B 157 " ideal model delta harmonic sigma weight residual -122.60 -131.85 9.25 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" CA MET B 300 " pdb=" C MET B 300 " pdb=" N PRO B 301 " pdb=" CA PRO B 301 " ideal model delta harmonic sigma weight residual -180.00 -162.28 -17.72 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" C PHE B 302 " pdb=" N PHE B 302 " pdb=" CA PHE B 302 " pdb=" CB PHE B 302 " ideal model delta harmonic sigma weight residual -122.60 -131.29 8.69 0 2.50e+00 1.60e-01 1.21e+01 ... (remaining 5456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1221 0.059 - 0.117: 182 0.117 - 0.176: 10 0.176 - 0.235: 7 0.235 - 0.293: 3 Chirality restraints: 1423 Sorted by residual: chirality pdb=" CA PHE B 157 " pdb=" N PHE B 157 " pdb=" C PHE B 157 " pdb=" CB PHE B 157 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA MET D 124 " pdb=" N MET D 124 " pdb=" C MET D 124 " pdb=" CB MET D 124 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA PHE B 302 " pdb=" N PHE B 302 " pdb=" C PHE B 302 " pdb=" CB PHE B 302 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 1420 not shown) Planarity restraints: 1569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 302 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C PHE B 302 " -0.037 2.00e-02 2.50e+03 pdb=" O PHE B 302 " 0.015 2.00e-02 2.50e+03 pdb=" N THR B 303 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 428 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C TYR A 428 " 0.034 2.00e-02 2.50e+03 pdb=" O TYR A 428 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE A 429 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS D 115 " 0.026 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO D 116 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 116 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 116 " 0.022 5.00e-02 4.00e+02 ... (remaining 1566 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 32 2.59 - 3.16: 7470 3.16 - 3.74: 13671 3.74 - 4.32: 17726 4.32 - 4.90: 30508 Nonbonded interactions: 69407 Sorted by model distance: nonbonded pdb=" O2B ADP B 701 " pdb="MG MG B 702 " model vdw 2.007 2.170 nonbonded pdb=" OG SER A 545 " pdb="MG MG A 902 " model vdw 2.012 2.170 nonbonded pdb=" OE1 GLN B 551 " pdb="MG MG B 702 " model vdw 2.029 2.170 nonbonded pdb=" O3G ATP A 901 " pdb="MG MG A 902 " model vdw 2.068 2.170 nonbonded pdb=" O2B ATP A 901 " pdb="MG MG A 902 " model vdw 2.201 2.170 ... (remaining 69402 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.110 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.240 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 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 : 0.003 0.049 9058 Z= 0.150 Angle : 0.696 11.434 12291 Z= 0.401 Chirality : 0.045 0.293 1423 Planarity : 0.004 0.040 1569 Dihedral : 15.023 88.155 3365 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 11.69 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.39 (0.26), residues: 1124 helix: 1.36 (0.20), residues: 696 sheet: 0.89 (0.68), residues: 68 loop : 0.22 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 235 TYR 0.011 0.001 TYR B 415 PHE 0.023 0.002 PHE B 157 TRP 0.016 0.001 TRP A 413 HIS 0.004 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9058) covalent geometry : angle 0.69599 (12291) hydrogen bonds : bond 0.16610 ( 562) hydrogen bonds : angle 5.53722 ( 1623) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: B 310 TYR cc_start: 0.8057 (t80) cc_final: 0.7371 (t80) REVERT: A 395 GLN cc_start: 0.7804 (tp40) cc_final: 0.7453 (tm-30) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.0785 time to fit residues: 12.6747 Evaluate side-chains 106 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.0980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.110150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.090419 restraints weight = 17573.520| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.10 r_work: 0.3090 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9058 Z= 0.126 Angle : 0.563 7.394 12291 Z= 0.279 Chirality : 0.039 0.131 1423 Planarity : 0.004 0.035 1569 Dihedral : 6.435 78.297 1275 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.45 % Allowed : 10.44 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.82 (0.26), residues: 1124 helix: 1.75 (0.20), residues: 705 sheet: 0.99 (0.69), residues: 68 loop : 0.25 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 235 TYR 0.012 0.001 TYR A 465 PHE 0.016 0.002 PHE B 157 TRP 0.007 0.001 TRP A 413 HIS 0.002 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9058) covalent geometry : angle 0.56251 (12291) hydrogen bonds : bond 0.05235 ( 562) hydrogen bonds : angle 4.07289 ( 1623) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: B 310 TYR cc_start: 0.8046 (t80) cc_final: 0.7263 (t80) REVERT: B 624 ASP cc_start: 0.8874 (t0) cc_final: 0.8672 (p0) REVERT: B 645 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8548 (mm) outliers start: 14 outliers final: 9 residues processed: 123 average time/residue: 0.0671 time to fit residues: 12.5618 Evaluate side-chains 119 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 337 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 34 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.110516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.090656 restraints weight = 17452.725| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.10 r_work: 0.3091 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9058 Z= 0.114 Angle : 0.527 6.961 12291 Z= 0.258 Chirality : 0.038 0.127 1423 Planarity : 0.003 0.032 1569 Dihedral : 6.090 73.794 1275 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.55 % Allowed : 11.27 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.18 (0.26), residues: 1124 helix: 2.10 (0.20), residues: 701 sheet: 0.86 (0.66), residues: 73 loop : 0.34 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 235 TYR 0.011 0.001 TYR A 465 PHE 0.011 0.001 PHE B 201 TRP 0.005 0.001 TRP A 413 HIS 0.003 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 9058) covalent geometry : angle 0.52743 (12291) hydrogen bonds : bond 0.04778 ( 562) hydrogen bonds : angle 3.78447 ( 1623) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: B 166 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7400 (mm-30) REVERT: B 285 MET cc_start: 0.8486 (tmm) cc_final: 0.8285 (tmm) REVERT: B 310 TYR cc_start: 0.7994 (t80) cc_final: 0.7235 (t80) REVERT: B 624 ASP cc_start: 0.8945 (t0) cc_final: 0.8579 (p0) REVERT: B 645 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8549 (mm) REVERT: A 301 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8493 (mm-30) outliers start: 15 outliers final: 9 residues processed: 128 average time/residue: 0.0674 time to fit residues: 13.0204 Evaluate side-chains 116 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 337 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 99 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 98 optimal weight: 0.0770 chunk 96 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.110171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.090168 restraints weight = 17656.401| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.13 r_work: 0.3086 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9058 Z= 0.118 Angle : 0.534 7.793 12291 Z= 0.259 Chirality : 0.038 0.154 1423 Planarity : 0.003 0.033 1569 Dihedral : 5.977 76.290 1275 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.76 % Allowed : 12.00 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.22 (0.26), residues: 1124 helix: 2.13 (0.20), residues: 708 sheet: 0.84 (0.65), residues: 75 loop : 0.31 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 235 TYR 0.010 0.001 TYR A 465 PHE 0.011 0.001 PHE A 275 TRP 0.010 0.001 TRP B 263 HIS 0.002 0.001 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9058) covalent geometry : angle 0.53429 (12291) hydrogen bonds : bond 0.04644 ( 562) hydrogen bonds : angle 3.71380 ( 1623) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: B 285 MET cc_start: 0.8439 (tmm) cc_final: 0.8116 (tmm) REVERT: B 310 TYR cc_start: 0.8015 (t80) cc_final: 0.7321 (t80) REVERT: B 624 ASP cc_start: 0.8959 (t0) cc_final: 0.8566 (p0) REVERT: B 645 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8570 (mm) REVERT: A 301 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8500 (mm-30) outliers start: 17 outliers final: 7 residues processed: 122 average time/residue: 0.0715 time to fit residues: 13.4596 Evaluate side-chains 111 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 333 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.5691 > 50: distance: 59 - 74: 21.794 distance: 63 - 79: 22.490 distance: 68 - 87: 20.129 distance: 71 - 74: 20.342 distance: 72 - 95: 13.357 distance: 74 - 75: 12.155 distance: 75 - 76: 41.638 distance: 75 - 78: 37.261 distance: 76 - 77: 44.232 distance: 76 - 79: 38.405 distance: 79 - 80: 34.994 distance: 80 - 81: 31.336 distance: 80 - 83: 19.360 distance: 81 - 82: 38.390 distance: 81 - 87: 6.652 distance: 83 - 84: 21.957 distance: 84 - 85: 16.811 distance: 84 - 86: 28.636 distance: 87 - 88: 9.296 distance: 88 - 89: 6.553 distance: 88 - 91: 20.786 distance: 89 - 90: 12.683 distance: 89 - 95: 12.863 distance: 91 - 92: 14.825 distance: 92 - 93: 25.049 distance: 92 - 94: 21.019 distance: 95 - 96: 5.308 distance: 96 - 97: 17.598 distance: 96 - 99: 22.815 distance: 97 - 98: 8.341 distance: 97 - 104: 16.708 distance: 99 - 100: 32.425 distance: 100 - 101: 15.624 distance: 101 - 102: 10.232 distance: 101 - 103: 8.412 distance: 104 - 105: 30.324 distance: 105 - 106: 45.759 distance: 105 - 108: 46.934 distance: 106 - 107: 54.376 distance: 106 - 112: 33.358 distance: 108 - 109: 20.740 distance: 109 - 110: 20.655 distance: 109 - 111: 22.995 distance: 112 - 113: 20.288 distance: 113 - 114: 11.859 distance: 113 - 116: 33.169 distance: 114 - 115: 27.333 distance: 114 - 120: 8.904 distance: 116 - 117: 50.682 distance: 117 - 118: 31.606 distance: 117 - 119: 35.171 distance: 120 - 121: 22.582 distance: 121 - 122: 19.546 distance: 121 - 124: 9.082 distance: 122 - 123: 38.487 distance: 122 - 132: 17.172 distance: 124 - 125: 13.718 distance: 125 - 126: 17.335 distance: 125 - 127: 17.983 distance: 126 - 128: 9.962 distance: 127 - 129: 9.254 distance: 128 - 130: 13.464 distance: 129 - 130: 15.093 distance: 130 - 131: 5.134 distance: 132 - 133: 19.486 distance: 133 - 134: 9.683 distance: 133 - 136: 16.046 distance: 134 - 135: 31.436 distance: 134 - 141: 32.206 distance: 136 - 137: 13.182 distance: 137 - 138: 21.760 distance: 138 - 139: 20.710 distance: 138 - 140: 25.276 distance: 141 - 142: 15.254 distance: 141 - 147: 28.415 distance: 142 - 143: 24.117 distance: 142 - 145: 34.970 distance: 143 - 144: 28.301 distance: 143 - 148: 26.726 distance: 145 - 146: 35.225 distance: 146 - 147: 7.798 distance: 148 - 149: 24.515 distance: 149 - 150: 21.350 distance: 149 - 152: 13.130 distance: 150 - 151: 3.259 distance: 150 - 155: 12.714 distance: 152 - 153: 7.372 distance: 152 - 154: 9.455