Starting phenix.real_space_refine on Thu Jun 12 23:59:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pnp_17782/06_2025/8pnp_17782.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pnp_17782/06_2025/8pnp_17782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pnp_17782/06_2025/8pnp_17782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pnp_17782/06_2025/8pnp_17782.map" model { file = "/net/cci-nas-00/data/ceres_data/8pnp_17782/06_2025/8pnp_17782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pnp_17782/06_2025/8pnp_17782.cif" } resolution = 2.49 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= 0.000 sd= 0.001 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 88 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 P 31 5.49 5 S 103 5.16 5 C 8978 2.51 5 N 2494 2.21 5 O 2854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14460 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 708, 5748 Classifications: {'peptide': 708} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 675} Chain breaks: 1 Chain: "B" Number of atoms: 5850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5850 Classifications: {'peptide': 735} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 702} Chain breaks: 1 Chain: "C" Number of atoms: 2024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2024 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain: "V" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 616 Classifications: {'RNA': 29} Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 10, 'rna3p_pyr': 12} Link IDs: {'rna2p': 7, 'rna3p': 21} Chain breaks: 1 Chain: "G" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 179 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 6, 'TRANS': 16} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "V" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 9.15, per 1000 atoms: 0.63 Number of scatterers: 14460 At special positions: 0 Unit cell: (94.08, 102.48, 144.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 103 16.00 P 31 15.00 O 2854 8.00 N 2494 7.00 C 8978 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: 3.66 Conformation dependent library (CDL) restraints added in 1.8 seconds 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3244 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 16 sheets defined 53.4% alpha, 12.6% beta 5 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 4.83 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 Processing helix chain 'A' and resid 10 through 24 removed outlier: 3.712A pdb=" N TYR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 50 Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 126 through 139 removed outlier: 3.538A pdb=" N TYR A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 164 through 185 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.923A pdb=" N PHE A 314 " --> pdb=" O CYS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 350 removed outlier: 3.676A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.503A pdb=" N SER A 409 " --> pdb=" O CYS A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 452 removed outlier: 3.765A pdb=" N HIS A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 529 through 538 Proline residue: A 534 - end of helix removed outlier: 3.860A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 580 Processing helix chain 'A' and resid 582 through 601 removed outlier: 4.129A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 4.002A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 697 through 715 removed outlier: 3.547A pdb=" N LEU A 715 " --> pdb=" O LEU A 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 14 through 22 removed outlier: 5.690A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 removed outlier: 3.537A pdb=" N GLN B 115 " --> pdb=" O MET B 111 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 124 removed outlier: 3.538A pdb=" N GLN B 124 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 156 through 161 removed outlier: 3.532A pdb=" N GLU B 159 " --> pdb=" O THR B 156 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER B 160 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 175 removed outlier: 3.639A pdb=" N ASP B 175 " --> pdb=" O MET B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 245 through 265 removed outlier: 3.751A pdb=" N ARG B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 294 removed outlier: 3.582A pdb=" N ASN B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER B 293 " --> pdb=" O MET B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.511A pdb=" N GLN B 313 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.447A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 369 through 376 removed outlier: 4.159A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN B 375 " --> pdb=" O MET B 372 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE B 376 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 removed outlier: 4.069A pdb=" N TYR B 380 " --> pdb=" O ASP B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 426 removed outlier: 3.519A pdb=" N THR B 417 " --> pdb=" O ASN B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 455 through 473 Processing helix chain 'B' and resid 505 through 512 Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 518 through 537 Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 613 through 616 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 636 through 640 Processing helix chain 'B' and resid 672 through 678 removed outlier: 6.388A pdb=" N SER B 678 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 700 removed outlier: 4.150A pdb=" N LEU B 683 " --> pdb=" O GLN B 679 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE B 699 " --> pdb=" O LEU B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 705 removed outlier: 3.818A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 732 removed outlier: 3.535A pdb=" N ALA B 717 " --> pdb=" O SER B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 756 removed outlier: 3.696A pdb=" N ARG B 755 " --> pdb=" O GLU B 751 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN B 756 " --> pdb=" O GLU B 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 13 removed outlier: 3.958A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 24 through 32 removed outlier: 4.142A pdb=" N ALA C 29 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 62 through 67 Processing helix chain 'C' and resid 92 through 103 removed outlier: 4.102A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 168 Processing helix chain 'C' and resid 169 through 172 removed outlier: 3.522A pdb=" N VAL C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 172' Processing helix chain 'C' and resid 179 through 193 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 231 through 236 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.321A pdb=" N PHE A 117 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N HIS A 146 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N GLU A 119 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N PHE A 148 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLY A 121 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 259 removed outlier: 3.682A pdb=" N TYR B 483 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE B 447 " --> pdb=" O GLY B 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 293 removed outlier: 7.334A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N VAL A 557 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU A 549 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL A 542 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN A 321 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLY A 546 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N GLU A 319 " --> pdb=" O GLY A 546 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N MET A 548 " --> pdb=" O TRP A 317 " (cutoff:3.500A) removed outlier: 9.766A pdb=" N TRP A 317 " --> pdb=" O MET A 548 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 293 removed outlier: 5.338A pdb=" N THR A 498 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N CYS A 489 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 378 removed outlier: 5.908A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N GLN B 367 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 628 through 631 removed outlier: 6.725A pdb=" N GLU A 629 " --> pdb=" O ILE A 621 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 183 Processing sheet with id=AB2, first strand: chain 'B' and resid 240 through 244 removed outlier: 3.986A pdb=" N THR B 226 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 489 through 492 Processing sheet with id=AB4, first strand: chain 'B' and resid 642 through 645 Processing sheet with id=AB5, first strand: chain 'B' and resid 667 through 668 removed outlier: 4.514A pdb=" N ILE B 667 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N MET C 90 " --> pdb=" O SER C 79 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 129 through 135 removed outlier: 4.721A pdb=" N MET C 243 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL C 133 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLU C 241 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 141 through 145 708 hydrogen bonds defined for protein. 1938 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 5.08 Time building geometry restraints manager: 4.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4412 1.33 - 1.46: 2337 1.46 - 1.58: 7783 1.58 - 1.70: 64 1.70 - 1.82: 177 Bond restraints: 14773 Sorted by residual: bond pdb=" N TYR G 1 " pdb=" CA TYR G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.83e+00 bond pdb=" N MET C 1 " pdb=" CA MET C 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.82e+00 bond pdb=" CB GLU C 158 " pdb=" CG GLU C 158 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.29e-01 bond pdb=" CD LYS A 361 " pdb=" CE LYS A 361 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.10e-01 ... (remaining 14768 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 19805 1.76 - 3.52: 225 3.52 - 5.28: 37 5.28 - 7.04: 3 7.04 - 8.79: 1 Bond angle restraints: 20071 Sorted by residual: angle pdb=" CB MET C 1 " pdb=" CG MET C 1 " pdb=" SD MET C 1 " ideal model delta sigma weight residual 112.70 121.49 -8.79 3.00e+00 1.11e-01 8.59e+00 angle pdb=" CG LYS A 361 " pdb=" CD LYS A 361 " pdb=" CE LYS A 361 " ideal model delta sigma weight residual 111.30 117.88 -6.58 2.30e+00 1.89e-01 8.19e+00 angle pdb=" C2' A V 4 " pdb=" C1' A V 4 " pdb=" N9 A V 4 " ideal model delta sigma weight residual 112.00 115.46 -3.46 1.50e+00 4.44e-01 5.33e+00 angle pdb=" CB MET B 744 " pdb=" CG MET B 744 " pdb=" SD MET B 744 " ideal model delta sigma weight residual 112.70 119.51 -6.81 3.00e+00 1.11e-01 5.16e+00 angle pdb=" CA GLU C 158 " pdb=" CB GLU C 158 " pdb=" CG GLU C 158 " ideal model delta sigma weight residual 114.10 118.58 -4.48 2.00e+00 2.50e-01 5.01e+00 ... (remaining 20066 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 7700 17.77 - 35.54: 945 35.54 - 53.32: 300 53.32 - 71.09: 113 71.09 - 88.86: 30 Dihedral angle restraints: 9088 sinusoidal: 4079 harmonic: 5009 Sorted by residual: dihedral pdb=" CA ASP C 161 " pdb=" CB ASP C 161 " pdb=" CG ASP C 161 " pdb=" OD1 ASP C 161 " ideal model delta sinusoidal sigma weight residual -30.00 -88.13 58.13 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA VAL A 517 " pdb=" C VAL A 517 " pdb=" N VAL A 518 " pdb=" CA VAL A 518 " ideal model delta harmonic sigma weight residual 180.00 163.53 16.47 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CB GLU B 78 " pdb=" CG GLU B 78 " pdb=" CD GLU B 78 " pdb=" OE1 GLU B 78 " ideal model delta sinusoidal sigma weight residual 0.00 -88.86 88.86 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 9085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1744 0.041 - 0.081: 358 0.081 - 0.122: 100 0.122 - 0.163: 11 0.163 - 0.204: 1 Chirality restraints: 2214 Sorted by residual: chirality pdb=" CB VAL B 719 " pdb=" CA VAL B 719 " pdb=" CG1 VAL B 719 " pdb=" CG2 VAL B 719 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C1' A V 4 " pdb=" O4' A V 4 " pdb=" C2' A V 4 " pdb=" N9 A V 4 " both_signs ideal model delta sigma weight residual False 2.46 2.31 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA VAL B 368 " pdb=" N VAL B 368 " pdb=" C VAL B 368 " pdb=" CB VAL B 368 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 2211 not shown) Planarity restraints: 2479 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A V 4 " -0.028 2.00e-02 2.50e+03 1.27e-02 4.41e+00 pdb=" N9 A V 4 " 0.029 2.00e-02 2.50e+03 pdb=" C8 A V 4 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A V 4 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A V 4 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A V 4 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A V 4 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A V 4 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A V 4 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A V 4 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 495 " 0.173 9.50e-02 1.11e+02 7.77e-02 4.27e+00 pdb=" NE ARG A 495 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 495 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 495 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 495 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 587 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.96e+00 pdb=" C GLN A 587 " -0.030 2.00e-02 2.50e+03 pdb=" O GLN A 587 " 0.011 2.00e-02 2.50e+03 pdb=" N SER A 588 " 0.010 2.00e-02 2.50e+03 ... (remaining 2476 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 154 2.60 - 3.17: 12369 3.17 - 3.75: 23475 3.75 - 4.32: 33810 4.32 - 4.90: 54368 Nonbonded interactions: 124176 Sorted by model distance: nonbonded pdb=" OD2 ASP B 522 " pdb=" OH TYR B 559 " model vdw 2.019 3.040 nonbonded pdb=" OP1 A V 6 " pdb=" O HOH V 101 " model vdw 2.085 3.040 nonbonded pdb=" OE1 GLU A 524 " pdb=" O HOH A 801 " model vdw 2.097 3.040 nonbonded pdb=" OE1 GLU A 610 " pdb=" ND2 ASN A 614 " model vdw 2.137 3.120 nonbonded pdb=" O MET C 11 " pdb=" NH1 ARG C 17 " model vdw 2.160 3.120 ... (remaining 124171 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: 2.920 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: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 38.440 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 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:13.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 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 0.035 14773 Z= 0.121 Angle : 0.497 8.794 20071 Z= 0.255 Chirality : 0.037 0.204 2214 Planarity : 0.004 0.078 2479 Dihedral : 18.516 88.860 5844 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.24 % Favored : 97.70 % Rotamer: Outliers : 1.24 % Allowed : 22.64 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: 0.87 (0.21), residues: 1697 helix: 1.64 (0.19), residues: 807 sheet: -0.13 (0.38), residues: 190 loop : -0.42 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 88 HIS 0.002 0.001 HIS A 128 PHE 0.010 0.001 PHE B 551 TYR 0.016 0.001 TYR A 305 ARG 0.013 0.000 ARG A 495 Details of bonding type rmsd hydrogen bonds : bond 0.13634 ( 717) hydrogen bonds : angle 6.04576 ( 1964) covalent geometry : bond 0.00273 (14773) covalent geometry : angle 0.49655 (20071) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 189 time to evaluate : 1.579 Fit side-chains revert: symmetry clash REVERT: A 116 ARG cc_start: 0.6162 (ppt90) cc_final: 0.5523 (ppt90) REVERT: A 222 ASN cc_start: 0.8401 (p0) cc_final: 0.8171 (p0) REVERT: B 135 ARG cc_start: 0.8199 (ptp-110) cc_final: 0.7947 (ptt90) REVERT: B 653 LYS cc_start: 0.8365 (mtmm) cc_final: 0.7958 (mmtm) REVERT: C 146 ASP cc_start: 0.7066 (p0) cc_final: 0.6617 (p0) outliers start: 19 outliers final: 15 residues processed: 203 average time/residue: 1.5880 time to fit residues: 348.9605 Evaluate side-chains 200 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 21 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 0.2980 chunk 134 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 99 optimal weight: 0.1980 chunk 155 optimal weight: 0.3980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 388 ASN A 466 ASN A 513 ASN A 556 GLN A 670 GLN B 312 ASN B 485 ASN C 82 ASN C 242 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.136042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.099933 restraints weight = 17535.337| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.63 r_work: 0.3020 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.0813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14773 Z= 0.118 Angle : 0.509 6.540 20071 Z= 0.267 Chirality : 0.039 0.171 2214 Planarity : 0.004 0.045 2479 Dihedral : 10.689 73.606 2343 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.12 % Favored : 97.82 % Rotamer: Outliers : 2.42 % Allowed : 20.03 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.20), residues: 1697 helix: 1.78 (0.19), residues: 814 sheet: 0.22 (0.39), residues: 178 loop : -0.49 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 309 HIS 0.003 0.001 HIS A 510 PHE 0.009 0.001 PHE A 611 TYR 0.012 0.001 TYR B 555 ARG 0.008 0.000 ARG A 495 Details of bonding type rmsd hydrogen bonds : bond 0.04433 ( 717) hydrogen bonds : angle 4.70882 ( 1964) covalent geometry : bond 0.00255 (14773) covalent geometry : angle 0.50919 (20071) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 196 time to evaluate : 1.687 Fit side-chains REVERT: A 222 ASN cc_start: 0.8408 (p0) cc_final: 0.8121 (p0) REVERT: B 331 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7487 (tm-30) outliers start: 37 outliers final: 15 residues processed: 219 average time/residue: 1.5895 time to fit residues: 376.5554 Evaluate side-chains 200 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 79 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 388 ASN A 513 ASN A 556 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.131383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.094638 restraints weight = 17409.904| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.63 r_work: 0.2931 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14773 Z= 0.224 Angle : 0.585 8.379 20071 Z= 0.307 Chirality : 0.044 0.193 2214 Planarity : 0.005 0.048 2479 Dihedral : 10.746 73.672 2327 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.59 % Favored : 97.35 % Rotamer: Outliers : 3.27 % Allowed : 19.37 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: 0.72 (0.20), residues: 1697 helix: 1.52 (0.18), residues: 822 sheet: 0.13 (0.39), residues: 178 loop : -0.65 (0.21), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 438 HIS 0.005 0.001 HIS A 128 PHE 0.016 0.002 PHE A 611 TYR 0.019 0.002 TYR A 305 ARG 0.005 0.001 ARG B 560 Details of bonding type rmsd hydrogen bonds : bond 0.05666 ( 717) hydrogen bonds : angle 4.75803 ( 1964) covalent geometry : bond 0.00528 (14773) covalent geometry : angle 0.58539 (20071) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 189 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASN cc_start: 0.8440 (p0) cc_final: 0.8177 (p0) REVERT: B 75 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8249 (mm-30) REVERT: B 156 THR cc_start: 0.8930 (p) cc_final: 0.8593 (p) REVERT: B 331 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7596 (tm-30) REVERT: B 353 LYS cc_start: 0.9128 (mtpt) cc_final: 0.8874 (mtmm) REVERT: B 744 MET cc_start: 0.7076 (mmm) cc_final: 0.6868 (mmt) REVERT: C 90 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8148 (mmt) REVERT: C 146 ASP cc_start: 0.8686 (p0) cc_final: 0.8107 (p0) REVERT: C 158 GLU cc_start: 0.6941 (mp0) cc_final: 0.6739 (mp0) outliers start: 50 outliers final: 18 residues processed: 221 average time/residue: 1.9473 time to fit residues: 464.0089 Evaluate side-chains 203 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain G residue 21 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 24 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 159 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 388 ASN A 556 GLN B 184 HIS C 82 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.130484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.093532 restraints weight = 17401.225| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.68 r_work: 0.2914 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 14773 Z= 0.247 Angle : 0.603 10.052 20071 Z= 0.317 Chirality : 0.045 0.203 2214 Planarity : 0.005 0.053 2479 Dihedral : 10.896 73.446 2325 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.53 % Favored : 97.41 % Rotamer: Outliers : 3.53 % Allowed : 20.16 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: 0.51 (0.20), residues: 1697 helix: 1.32 (0.18), residues: 821 sheet: -0.17 (0.36), residues: 196 loop : -0.67 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 368 HIS 0.005 0.001 HIS B 47 PHE 0.015 0.002 PHE A 520 TYR 0.025 0.002 TYR A 305 ARG 0.005 0.001 ARG B 560 Details of bonding type rmsd hydrogen bonds : bond 0.05768 ( 717) hydrogen bonds : angle 4.73872 ( 1964) covalent geometry : bond 0.00585 (14773) covalent geometry : angle 0.60266 (20071) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 186 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 HIS cc_start: 0.7257 (OUTLIER) cc_final: 0.6672 (t-90) REVERT: A 222 ASN cc_start: 0.8447 (p0) cc_final: 0.8148 (p0) REVERT: A 256 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.8070 (ttm170) REVERT: B 75 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8255 (mm-30) REVERT: B 135 ARG cc_start: 0.8542 (ptp-110) cc_final: 0.8142 (ptm-80) REVERT: B 156 THR cc_start: 0.8979 (p) cc_final: 0.8735 (p) REVERT: B 331 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7610 (tm-30) REVERT: B 375 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8534 (p0) REVERT: C 90 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8104 (mmt) REVERT: C 146 ASP cc_start: 0.8651 (p0) cc_final: 0.8063 (p0) REVERT: C 213 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7768 (ttm170) outliers start: 54 outliers final: 26 residues processed: 219 average time/residue: 1.7010 time to fit residues: 403.1297 Evaluate side-chains 214 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain G residue 21 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 56 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN B 184 HIS C 82 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.133601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.098089 restraints weight = 17622.352| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.54 r_work: 0.2968 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14773 Z= 0.135 Angle : 0.532 9.832 20071 Z= 0.278 Chirality : 0.040 0.188 2214 Planarity : 0.004 0.054 2479 Dihedral : 10.780 73.560 2325 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.95 % Allowed : 20.68 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: 0.69 (0.20), residues: 1697 helix: 1.52 (0.18), residues: 817 sheet: -0.05 (0.38), residues: 185 loop : -0.64 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 368 HIS 0.010 0.001 HIS A 74 PHE 0.011 0.001 PHE A 520 TYR 0.025 0.001 TYR A 305 ARG 0.004 0.000 ARG A 124 Details of bonding type rmsd hydrogen bonds : bond 0.04645 ( 717) hydrogen bonds : angle 4.57401 ( 1964) covalent geometry : bond 0.00306 (14773) covalent geometry : angle 0.53232 (20071) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 187 time to evaluate : 1.790 Fit side-chains revert: symmetry clash REVERT: A 74 HIS cc_start: 0.7401 (OUTLIER) cc_final: 0.6701 (t-90) REVERT: A 136 ASN cc_start: 0.5811 (OUTLIER) cc_final: 0.4365 (m110) REVERT: A 222 ASN cc_start: 0.8421 (p0) cc_final: 0.8125 (p0) REVERT: B 75 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8192 (mm-30) REVERT: B 331 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7528 (tm-30) REVERT: C 146 ASP cc_start: 0.8578 (p0) cc_final: 0.7996 (p0) outliers start: 45 outliers final: 25 residues processed: 218 average time/residue: 1.6363 time to fit residues: 385.2379 Evaluate side-chains 216 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 92 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN B 184 HIS B 413 ASN B 485 ASN C 13 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.132266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.094910 restraints weight = 17526.677| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.77 r_work: 0.2940 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14773 Z= 0.155 Angle : 0.541 9.797 20071 Z= 0.281 Chirality : 0.040 0.191 2214 Planarity : 0.004 0.054 2479 Dihedral : 10.732 73.500 2325 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.27 % Allowed : 20.42 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: 0.66 (0.20), residues: 1697 helix: 1.49 (0.18), residues: 823 sheet: -0.08 (0.36), residues: 192 loop : -0.68 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 368 HIS 0.003 0.001 HIS B 47 PHE 0.011 0.001 PHE B 551 TYR 0.025 0.002 TYR A 305 ARG 0.004 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.04768 ( 717) hydrogen bonds : angle 4.57249 ( 1964) covalent geometry : bond 0.00359 (14773) covalent geometry : angle 0.54129 (20071) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 188 time to evaluate : 2.681 Fit side-chains revert: symmetry clash REVERT: A 74 HIS cc_start: 0.7362 (OUTLIER) cc_final: 0.6563 (t-90) REVERT: A 136 ASN cc_start: 0.5845 (OUTLIER) cc_final: 0.4374 (m110) REVERT: A 222 ASN cc_start: 0.8438 (p0) cc_final: 0.8129 (p0) REVERT: A 256 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7978 (ttm170) REVERT: B 75 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8252 (mm-30) REVERT: B 331 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7560 (tm-30) REVERT: B 744 MET cc_start: 0.7092 (mmm) cc_final: 0.6818 (mmt) REVERT: C 65 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8210 (pt0) REVERT: C 90 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8065 (mmt) REVERT: C 146 ASP cc_start: 0.8576 (p0) cc_final: 0.7971 (p0) outliers start: 50 outliers final: 25 residues processed: 222 average time/residue: 2.0703 time to fit residues: 500.3592 Evaluate side-chains 219 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 50.4841 > 50: distance: 22 - 142: 10.913 distance: 25 - 139: 4.789 distance: 77 - 83: 7.750 distance: 83 - 84: 9.324 distance: 84 - 85: 5.581 distance: 85 - 86: 23.215 distance: 85 - 91: 30.712 distance: 87 - 88: 18.063 distance: 88 - 89: 13.593 distance: 88 - 90: 13.620 distance: 91 - 92: 7.758 distance: 92 - 93: 14.273 distance: 93 - 94: 17.782 distance: 93 - 95: 22.037 distance: 95 - 96: 21.593 distance: 96 - 97: 4.381 distance: 96 - 99: 11.337 distance: 97 - 98: 3.995 distance: 97 - 104: 10.295 distance: 99 - 100: 6.120 distance: 100 - 101: 5.631 distance: 101 - 102: 12.756 distance: 102 - 103: 3.516 distance: 104 - 105: 7.138 distance: 105 - 106: 4.818 distance: 106 - 107: 12.092 distance: 106 - 108: 4.499 distance: 108 - 109: 6.581 distance: 108 - 213: 9.035 distance: 109 - 110: 4.124 distance: 109 - 112: 4.715 distance: 110 - 111: 3.403 distance: 111 - 210: 4.252 distance: 113 - 114: 5.398 distance: 114 - 116: 7.073 distance: 115 - 117: 6.582 distance: 116 - 118: 5.448 distance: 117 - 118: 4.550 distance: 118 - 119: 16.314 distance: 120 - 121: 11.680 distance: 121 - 122: 9.824 distance: 121 - 124: 7.172 distance: 122 - 123: 8.974 distance: 122 - 128: 10.281 distance: 124 - 125: 11.304 distance: 125 - 126: 5.234 distance: 126 - 127: 6.515 distance: 128 - 129: 7.130 distance: 128 - 198: 8.188 distance: 129 - 130: 3.212 distance: 129 - 132: 8.046 distance: 130 - 131: 3.420 distance: 130 - 139: 4.241 distance: 131 - 195: 7.354 distance: 132 - 133: 6.659 distance: 133 - 134: 6.226 distance: 133 - 135: 4.735 distance: 134 - 136: 5.046 distance: 135 - 137: 3.364 distance: 136 - 138: 9.599 distance: 137 - 138: 6.408 distance: 140 - 141: 9.499 distance: 140 - 143: 4.995 distance: 141 - 142: 10.768 distance: 141 - 148: 3.786 distance: 143 - 144: 12.327 distance: 144 - 145: 4.563 distance: 145 - 146: 5.056 distance: 148 - 149: 12.784 distance: 148 - 184: 13.793 distance: 149 - 150: 3.624 distance: 149 - 152: 3.726 distance: 150 - 151: 12.220 distance: 150 - 154: 7.740 distance: 151 - 181: 9.142 distance: 152 - 153: 8.382 distance: 154 - 155: 5.027 distance: 155 - 156: 5.005 distance: 155 - 158: 4.528 distance: 156 - 157: 3.065 distance: 159 - 160: 5.251 distance: 160 - 161: 7.135 distance: 161 - 162: 4.963