Starting phenix.real_space_refine on Sun Dec 29 09:55:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wsr_37822/12_2024/8wsr_37822.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wsr_37822/12_2024/8wsr_37822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wsr_37822/12_2024/8wsr_37822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wsr_37822/12_2024/8wsr_37822.map" model { file = "/net/cci-nas-00/data/ceres_data/8wsr_37822/12_2024/8wsr_37822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wsr_37822/12_2024/8wsr_37822.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4891 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4135 2.51 5 N 1065 2.21 5 O 1237 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6475 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1514 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 12, 'TRANS': 180} Chain: "A" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "B" 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: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.71, per 1000 atoms: 0.73 Number of scatterers: 6475 At special positions: 0 Unit cell: (75.9, 84.18, 120.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 1237 8.00 N 1065 7.00 C 4135 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.03 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " 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 BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A 901 " - " ASN A 103 " " NAG A 902 " - " ASN A 53 " " NAG A 903 " - " ASN A 90 " " NAG A 905 " - " ASN A 432 " " NAG A 906 " - " ASN A 322 " " NAG B 1 " - " ASN A 546 " Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 908.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 904 " pdb="ZN ZN A 904 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 904 " - pdb=" NE2 HIS A 378 " 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1486 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 6 sheets defined 59.4% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'C' and resid 324 through 329 Processing helix chain 'C' and resid 336 through 340 removed outlier: 3.518A pdb=" N TRP C 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 356 removed outlier: 3.967A pdb=" N VAL C 354 " --> pdb=" O ASP C 351 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR C 356 " --> pdb=" O SER C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 376 removed outlier: 3.754A pdb=" N LEU C 374 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN C 375 " --> pdb=" O THR C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 397 Processing helix chain 'C' and resid 403 through 409 Processing helix chain 'C' and resid 425 through 430 Processing helix chain 'C' and resid 488 through 492 removed outlier: 4.009A pdb=" N GLN C 492 " --> pdb=" O VAL C 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.896A pdb=" N THR A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.771A pdb=" N GLN A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.758A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE A 88 " --> pdb=" O LEU A 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 84 through 88' Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.721A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 146 through 155 removed outlier: 3.817A pdb=" N GLU A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.598A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 176 through 193 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 232 removed outlier: 4.121A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.535A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 282 removed outlier: 4.236A pdb=" N SER A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.816A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.698A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.901A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.578A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.597A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.584A pdb=" N THR A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 527 " --> pdb=" O PHE A 523 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.567A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 538 through 542' Processing helix chain 'A' and resid 547 through 561 removed outlier: 3.802A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU A 560 " --> pdb=" O ASN A 556 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLY A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.838A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 removed outlier: 3.621A pdb=" N LEU A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Proline residue: A 590 - end of helix Processing sheet with id=AA1, first strand: chain 'C' and resid 341 through 344 removed outlier: 3.667A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN C 381 " --> pdb=" O GLU C 502 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.177A pdb=" N CYS C 348 " --> pdb=" O CYS C 511 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL C 510 " --> pdb=" O PHE C 379 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AA4, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA5, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.346A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 347 through 350 301 hydrogen bonds defined for protein. 840 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: 1.88 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2062 1.34 - 1.46: 1722 1.46 - 1.59: 2813 1.59 - 1.71: 0 1.71 - 1.84: 58 Bond restraints: 6655 Sorted by residual: bond pdb=" N PRO A 135 " pdb=" CD PRO A 135 " ideal model delta sigma weight residual 1.473 1.393 0.080 1.40e-02 5.10e+03 3.24e+01 bond pdb=" CA TYR A 83 " pdb=" C TYR A 83 " ideal model delta sigma weight residual 1.524 1.588 -0.064 1.26e-02 6.30e+03 2.58e+01 bond pdb=" C TYR A 83 " pdb=" N PRO A 84 " ideal model delta sigma weight residual 1.332 1.388 -0.057 1.30e-02 5.92e+03 1.90e+01 bond pdb=" CA ASN A 322 " pdb=" C ASN A 322 " ideal model delta sigma weight residual 1.528 1.480 0.049 1.28e-02 6.10e+03 1.46e+01 bond pdb=" C ILE A 468 " pdb=" N PRO A 469 " ideal model delta sigma weight residual 1.330 1.372 -0.042 1.25e-02 6.40e+03 1.14e+01 ... (remaining 6650 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 8824 2.32 - 4.65: 190 4.65 - 6.97: 28 6.97 - 9.29: 3 9.29 - 11.62: 6 Bond angle restraints: 9051 Sorted by residual: angle pdb=" N GLY C 463 " pdb=" CA GLY C 463 " pdb=" C GLY C 463 " ideal model delta sigma weight residual 112.37 100.84 11.53 1.40e+00 5.10e-01 6.78e+01 angle pdb=" N TYR C 460 " pdb=" CA TYR C 460 " pdb=" C TYR C 460 " ideal model delta sigma weight residual 111.24 122.11 -10.87 1.38e+00 5.25e-01 6.20e+01 angle pdb=" N ILE C 459 " pdb=" CA ILE C 459 " pdb=" C ILE C 459 " ideal model delta sigma weight residual 112.17 118.43 -6.26 9.50e-01 1.11e+00 4.35e+01 angle pdb=" C ILE A 468 " pdb=" N PRO A 469 " pdb=" CA PRO A 469 " ideal model delta sigma weight residual 120.21 114.43 5.78 9.60e-01 1.09e+00 3.63e+01 angle pdb=" N GLU A 402 " pdb=" CA GLU A 402 " pdb=" C GLU A 402 " ideal model delta sigma weight residual 111.82 118.50 -6.68 1.16e+00 7.43e-01 3.32e+01 ... (remaining 9046 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 3438 17.86 - 35.73: 415 35.73 - 53.59: 126 53.59 - 71.46: 30 71.46 - 89.32: 11 Dihedral angle restraints: 4020 sinusoidal: 1704 harmonic: 2316 Sorted by residual: dihedral pdb=" CB CYS C 323 " pdb=" SG CYS C 323 " pdb=" SG CYS C 348 " pdb=" CB CYS C 348 " ideal model delta sinusoidal sigma weight residual -86.00 -174.14 88.14 1 1.00e+01 1.00e-02 9.29e+01 dihedral pdb=" N TYR C 460 " pdb=" C TYR C 460 " pdb=" CA TYR C 460 " pdb=" CB TYR C 460 " ideal model delta harmonic sigma weight residual 122.80 142.12 -19.32 0 2.50e+00 1.60e-01 5.97e+01 dihedral pdb=" C TYR C 460 " pdb=" N TYR C 460 " pdb=" CA TYR C 460 " pdb=" CB TYR C 460 " ideal model delta harmonic sigma weight residual -122.60 -139.37 16.77 0 2.50e+00 1.60e-01 4.50e+01 ... (remaining 4017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.172: 950 0.172 - 0.343: 16 0.343 - 0.515: 2 0.515 - 0.686: 0 0.686 - 0.858: 1 Chirality restraints: 969 Sorted by residual: chirality pdb=" CA TYR C 460 " pdb=" N TYR C 460 " pdb=" C TYR C 460 " pdb=" CB TYR C 460 " both_signs ideal model delta sigma weight residual False 2.51 1.65 0.86 2.00e-01 2.50e+01 1.84e+01 chirality pdb=" CA GLU A 402 " pdb=" N GLU A 402 " pdb=" C GLU A 402 " pdb=" CB GLU A 402 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 103 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.83e+00 ... (remaining 966 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 901 " -0.356 2.00e-02 2.50e+03 3.05e-01 1.17e+03 pdb=" C7 NAG A 901 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG A 901 " -0.139 2.00e-02 2.50e+03 pdb=" N2 NAG A 901 " 0.543 2.00e-02 2.50e+03 pdb=" O7 NAG A 901 " -0.135 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 906 " 0.263 2.00e-02 2.50e+03 2.25e-01 6.33e+02 pdb=" C7 NAG A 906 " -0.064 2.00e-02 2.50e+03 pdb=" C8 NAG A 906 " 0.165 2.00e-02 2.50e+03 pdb=" N2 NAG A 906 " -0.390 2.00e-02 2.50e+03 pdb=" O7 NAG A 906 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 78 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.86e+00 pdb=" C THR A 78 " 0.052 2.00e-02 2.50e+03 pdb=" O THR A 78 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU A 79 " -0.017 2.00e-02 2.50e+03 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 1.12 - 1.88: 4 1.88 - 2.63: 59 2.63 - 3.39: 8244 3.39 - 4.14: 13890 4.14 - 4.90: 26230 Nonbonded interactions: 48427 Sorted by model distance: nonbonded pdb=" ND2 ASN A 137 " pdb=" OE2 GLU A 140 " model vdw 1.124 3.120 nonbonded pdb=" O PRO A 135 " pdb=" OD1 ASP A 136 " model vdw 1.291 3.040 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 904 " model vdw 1.453 2.230 nonbonded pdb=" ND2 ASN A 137 " pdb=" CD GLU A 140 " model vdw 1.735 3.350 nonbonded pdb=" OD1 ASN A 134 " pdb=" CD PRO A 135 " model vdw 2.046 3.440 ... (remaining 48422 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.450 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:13.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 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 0.080 6655 Z= 0.334 Angle : 0.822 11.615 9051 Z= 0.497 Chirality : 0.063 0.858 969 Planarity : 0.012 0.305 1164 Dihedral : 17.386 89.319 2513 Min Nonbonded Distance : 1.124 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.45 % Allowed : 22.83 % Favored : 75.72 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.29), residues: 785 helix: 0.66 (0.28), residues: 383 sheet: 1.16 (0.68), residues: 44 loop : -1.20 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 478 HIS 0.006 0.001 HIS A 374 PHE 0.017 0.001 PHE A 308 TYR 0.020 0.002 TYR A 183 ARG 0.007 0.001 ARG A 582 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 0.825 Fit side-chains revert: symmetry clash REVERT: A 129 THR cc_start: 0.8785 (t) cc_final: 0.8570 (p) outliers start: 10 outliers final: 6 residues processed: 160 average time/residue: 1.3575 time to fit residues: 227.1267 Evaluate side-chains 140 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 134 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 391 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 396 GLN C 437 ASN C 492 GLN A 34 HIS A 42 GLN A 86 GLN A 102 GLN A 121 ASN A 194 ASN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN A 340 GLN A 531 GLN A 535 HIS A 601 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6655 Z= 0.223 Angle : 0.576 8.846 9051 Z= 0.302 Chirality : 0.044 0.204 969 Planarity : 0.005 0.058 1164 Dihedral : 6.758 55.184 1012 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.47 % Allowed : 22.40 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.29), residues: 785 helix: 1.36 (0.27), residues: 385 sheet: 1.22 (0.68), residues: 44 loop : -1.28 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 477 HIS 0.005 0.001 HIS A 374 PHE 0.011 0.001 PHE A 308 TYR 0.017 0.001 TYR A 50 ARG 0.006 0.001 ARG A 582 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 THR cc_start: 0.8753 (t) cc_final: 0.8489 (p) REVERT: A 184 VAL cc_start: 0.8311 (t) cc_final: 0.7989 (t) REVERT: A 287 GLN cc_start: 0.8332 (mm-40) cc_final: 0.8119 (mm110) REVERT: A 574 VAL cc_start: 0.8577 (m) cc_final: 0.8272 (t) outliers start: 24 outliers final: 10 residues processed: 156 average time/residue: 1.2637 time to fit residues: 206.8653 Evaluate side-chains 143 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 409 ASN Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 134 ASN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN A 531 GLN A 601 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6655 Z= 0.227 Angle : 0.547 8.062 9051 Z= 0.286 Chirality : 0.043 0.310 969 Planarity : 0.004 0.053 1164 Dihedral : 6.161 57.469 1007 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.61 % Allowed : 23.70 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.29), residues: 785 helix: 1.57 (0.27), residues: 385 sheet: 1.18 (0.67), residues: 44 loop : -1.30 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 477 HIS 0.005 0.001 HIS A 374 PHE 0.013 0.001 PHE A 308 TYR 0.015 0.001 TYR A 50 ARG 0.007 0.001 ARG C 445 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 THR cc_start: 0.8759 (t) cc_final: 0.8509 (p) REVERT: A 184 VAL cc_start: 0.8273 (t) cc_final: 0.7993 (t) REVERT: A 574 VAL cc_start: 0.8605 (m) cc_final: 0.8305 (t) outliers start: 25 outliers final: 12 residues processed: 152 average time/residue: 1.3115 time to fit residues: 208.8739 Evaluate side-chains 141 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 401 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 71 optimal weight: 0.0570 chunk 75 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN A 601 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6655 Z= 0.196 Angle : 0.516 6.469 9051 Z= 0.271 Chirality : 0.043 0.352 969 Planarity : 0.004 0.052 1164 Dihedral : 6.076 59.068 1007 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.75 % Allowed : 24.42 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.29), residues: 785 helix: 1.63 (0.27), residues: 386 sheet: 1.24 (0.67), residues: 44 loop : -1.18 (0.29), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 477 HIS 0.005 0.001 HIS A 374 PHE 0.011 0.001 PHE A 308 TYR 0.015 0.001 TYR A 50 ARG 0.006 0.000 ARG C 445 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 THR cc_start: 0.8736 (t) cc_final: 0.8480 (p) REVERT: A 184 VAL cc_start: 0.8205 (t) cc_final: 0.7943 (t) REVERT: A 574 VAL cc_start: 0.8612 (m) cc_final: 0.8369 (t) outliers start: 19 outliers final: 13 residues processed: 141 average time/residue: 1.3247 time to fit residues: 195.4971 Evaluate side-chains 137 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 608 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 4.9990 chunk 56 optimal weight: 0.0970 chunk 31 optimal weight: 0.9980 chunk 64 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 0.4980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6655 Z= 0.145 Angle : 0.467 5.171 9051 Z= 0.248 Chirality : 0.041 0.310 969 Planarity : 0.004 0.050 1164 Dihedral : 5.499 53.588 1005 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.46 % Allowed : 25.14 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.30), residues: 785 helix: 1.65 (0.27), residues: 393 sheet: 1.44 (0.66), residues: 43 loop : -1.09 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 477 HIS 0.004 0.001 HIS A 374 PHE 0.008 0.001 PHE A 308 TYR 0.015 0.001 TYR A 50 ARG 0.004 0.000 ARG C 445 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: A 129 THR cc_start: 0.8678 (t) cc_final: 0.8383 (p) REVERT: A 401 HIS cc_start: 0.7884 (OUTLIER) cc_final: 0.7422 (m-70) REVERT: A 574 VAL cc_start: 0.8561 (m) cc_final: 0.8346 (t) outliers start: 17 outliers final: 6 residues processed: 139 average time/residue: 1.2656 time to fit residues: 184.2305 Evaluate side-chains 133 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 401 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.5535 > 50: distance: 19 - 38: 4.235 distance: 24 - 46: 6.468 distance: 34 - 38: 3.497 distance: 35 - 62: 18.298 distance: 39 - 40: 5.964 distance: 39 - 42: 6.548 distance: 40 - 41: 6.330 distance: 40 - 46: 3.567 distance: 41 - 67: 9.974 distance: 42 - 43: 14.363 distance: 43 - 44: 9.429 distance: 43 - 45: 7.408 distance: 46 - 47: 4.217 distance: 47 - 48: 5.563 distance: 47 - 50: 11.842 distance: 48 - 49: 8.323 distance: 48 - 54: 9.133 distance: 50 - 51: 8.181 distance: 51 - 52: 13.221 distance: 52 - 53: 14.165 distance: 54 - 55: 11.486 distance: 55 - 56: 14.936 distance: 55 - 58: 9.334 distance: 56 - 57: 11.582 distance: 56 - 62: 7.013 distance: 58 - 59: 9.755 distance: 59 - 60: 7.649 distance: 59 - 61: 5.282 distance: 62 - 63: 4.142 distance: 63 - 64: 12.319 distance: 63 - 66: 17.456 distance: 64 - 65: 6.756 distance: 64 - 67: 19.383 distance: 67 - 68: 12.247 distance: 68 - 69: 22.061 distance: 68 - 71: 8.807 distance: 69 - 70: 17.280 distance: 69 - 79: 30.573 distance: 71 - 72: 7.835 distance: 72 - 73: 10.092 distance: 72 - 74: 9.042 distance: 73 - 75: 15.424 distance: 74 - 76: 4.961 distance: 75 - 77: 3.548 distance: 76 - 77: 7.407 distance: 77 - 78: 11.960 distance: 79 - 80: 36.153 distance: 79 - 85: 46.214 distance: 80 - 81: 16.941 distance: 80 - 83: 10.458 distance: 81 - 82: 8.269 distance: 81 - 86: 10.961 distance: 83 - 84: 39.211 distance: 84 - 85: 3.852 distance: 86 - 87: 10.436 distance: 87 - 88: 14.938 distance: 87 - 90: 6.216 distance: 88 - 89: 5.511 distance: 88 - 92: 5.597 distance: 90 - 91: 11.282 distance: 92 - 93: 7.931 distance: 93 - 94: 5.686 distance: 93 - 96: 9.018 distance: 94 - 95: 13.379 distance: 94 - 104: 9.719 distance: 96 - 97: 9.841 distance: 97 - 98: 3.789 distance: 97 - 99: 4.354 distance: 98 - 100: 6.775 distance: 99 - 101: 4.641 distance: 100 - 102: 6.882 distance: 101 - 102: 7.180 distance: 102 - 103: 4.941 distance: 104 - 105: 8.880 distance: 105 - 106: 6.808 distance: 105 - 108: 5.691 distance: 106 - 107: 9.717 distance: 106 - 112: 4.942 distance: 108 - 109: 25.766 distance: 108 - 110: 30.441 distance: 109 - 111: 10.974 distance: 112 - 113: 6.348 distance: 113 - 114: 8.080 distance: 113 - 116: 6.134 distance: 114 - 115: 8.835 distance: 114 - 118: 15.289 distance: 116 - 117: 12.476