Starting phenix.real_space_refine on Sat Aug 23 05:52:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9a_37362/08_2025/8w9a_37362_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9a_37362/08_2025/8w9a_37362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w9a_37362/08_2025/8w9a_37362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9a_37362/08_2025/8w9a_37362.map" model { file = "/net/cci-nas-00/data/ceres_data/8w9a_37362/08_2025/8w9a_37362_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9a_37362/08_2025/8w9a_37362_trim.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 72 5.16 5 Cl 1 4.86 5 C 6548 2.51 5 N 1778 2.21 5 O 1890 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10289 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 969, 7922 Classifications: {'peptide': 969} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 923} Chain breaks: 5 Chain: "B" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2330 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 271} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'UEX': 1} Classifications: {'undetermined': 1, 'water': 2} Link IDs: {None: 2} Time building chain proxies: 2.66, per 1000 atoms: 0.26 Number of scatterers: 10289 At special positions: 0 Unit cell: (88.06, 125.06, 117.66, 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) Cl 1 17.00 S 72 16.00 O 1890 8.00 N 1778 7.00 C 6548 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: 1.01 Conformation dependent library (CDL) restraints added in 412.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2386 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 9 sheets defined 48.5% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 41 through 53 removed outlier: 3.626A pdb=" N PHE A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS A 51 " --> pdb=" O HIS A 47 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 52 " --> pdb=" O GLU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 122 removed outlier: 3.672A pdb=" N LEU A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 4.017A pdb=" N ASP A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET A 130 " --> pdb=" O CYS A 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 125 through 130' Processing helix chain 'A' and resid 133 through 143 removed outlier: 3.711A pdb=" N ARG A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 152 removed outlier: 3.541A pdb=" N VAL A 151 " --> pdb=" O CYS A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 167 Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 216 through 229 removed outlier: 3.540A pdb=" N ALA A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU A 223 " --> pdb=" O GLN A 219 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 269 Processing helix chain 'A' and resid 270 through 278 removed outlier: 4.003A pdb=" N MET A 278 " --> pdb=" O ARG A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.994A pdb=" N ARG A 309 " --> pdb=" O PRO A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 488 through 497 removed outlier: 3.578A pdb=" N ASN A 497 " --> pdb=" O GLU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 536 removed outlier: 3.943A pdb=" N LEU A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 554 Processing helix chain 'A' and resid 557 through 563 Proline residue: A 562 - end of helix Processing helix chain 'A' and resid 564 through 570 removed outlier: 3.835A pdb=" N LEU A 570 " --> pdb=" O PRO A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 588 removed outlier: 3.541A pdb=" N GLN A 582 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 600 through 603 removed outlier: 3.534A pdb=" N ASP A 603 " --> pdb=" O GLU A 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 600 through 603' Processing helix chain 'A' and resid 608 through 623 removed outlier: 3.583A pdb=" N PHE A 614 " --> pdb=" O MET A 610 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 621 " --> pdb=" O ARG A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 631 Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 639 through 641 No H-bonds generated for 'chain 'A' and resid 639 through 641' Processing helix chain 'A' and resid 647 through 658 Processing helix chain 'A' and resid 660 through 673 removed outlier: 3.775A pdb=" N PHE A 666 " --> pdb=" O ARG A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 693 Processing helix chain 'A' and resid 697 through 722 removed outlier: 4.340A pdb=" N HIS A 701 " --> pdb=" O MET A 697 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 718 " --> pdb=" O ASN A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 741 removed outlier: 3.633A pdb=" N VAL A 736 " --> pdb=" O MET A 732 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 748 Processing helix chain 'A' and resid 807 through 826 removed outlier: 3.578A pdb=" N ARG A 818 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN A 822 " --> pdb=" O ARG A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 864 Processing helix chain 'A' and resid 875 through 884 Processing helix chain 'A' and resid 886 through 888 No H-bonds generated for 'chain 'A' and resid 886 through 888' Processing helix chain 'A' and resid 889 through 911 removed outlier: 3.600A pdb=" N ALA A 893 " --> pdb=" O ILE A 889 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 897 " --> pdb=" O ALA A 893 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY A 903 " --> pdb=" O ARG A 899 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 909 " --> pdb=" O CYS A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 965 removed outlier: 3.591A pdb=" N ILE A 962 " --> pdb=" O GLN A 958 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 973 removed outlier: 3.849A pdb=" N LYS A 973 " --> pdb=" O GLU A 970 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 970 through 973' Processing helix chain 'A' and resid 974 through 992 removed outlier: 3.531A pdb=" N ILE A 991 " --> pdb=" O ALA A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1004 removed outlier: 3.776A pdb=" N PHE A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A1002 " --> pdb=" O PHE A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1026 removed outlier: 3.961A pdb=" N ARG A1023 " --> pdb=" O ILE A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1045 removed outlier: 3.640A pdb=" N LEU A1036 " --> pdb=" O GLU A1032 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A1037 " --> pdb=" O GLN A1033 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP A1045 " --> pdb=" O LYS A1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 344 Processing helix chain 'B' and resid 400 through 409 removed outlier: 3.549A pdb=" N TYR B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 416 Processing helix chain 'B' and resid 417 through 421 removed outlier: 3.852A pdb=" N ASP B 421 " --> pdb=" O PRO B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 437 removed outlier: 3.682A pdb=" N VAL B 437 " --> pdb=" O ASP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 504 removed outlier: 3.805A pdb=" N VAL B 445 " --> pdb=" O ASN B 441 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY B 446 " --> pdb=" O ILE B 442 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR B 452 " --> pdb=" O LYS B 448 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN B 457 " --> pdb=" O ASN B 453 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG B 465 " --> pdb=" O ARG B 461 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR B 471 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE B 493 " --> pdb=" O GLU B 489 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU B 496 " --> pdb=" O LYS B 492 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR B 500 " --> pdb=" O GLU B 496 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU B 502 " --> pdb=" O CYS B 498 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG B 503 " --> pdb=" O GLN B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 524 removed outlier: 4.248A pdb=" N GLN B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 553 removed outlier: 3.525A pdb=" N GLU B 537 " --> pdb=" O SER B 533 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 539 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 541 " --> pdb=" O GLU B 537 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 544 " --> pdb=" O ASP B 540 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP B 548 " --> pdb=" O ARG B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 582 removed outlier: 3.642A pdb=" N ASP B 560 " --> pdb=" O TYR B 556 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET B 563 " --> pdb=" O ILE B 559 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN B 564 " --> pdb=" O ASP B 560 " (cutoff:3.500A) Proline residue: B 568 - end of helix removed outlier: 3.543A pdb=" N ILE B 571 " --> pdb=" O LYS B 567 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN B 572 " --> pdb=" O PRO B 568 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 573 " --> pdb=" O ASP B 569 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG B 574 " --> pdb=" O LEU B 570 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR B 580 " --> pdb=" O THR B 576 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 581 " --> pdb=" O ARG B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 598 removed outlier: 3.711A pdb=" N LEU B 598 " --> pdb=" O LEU B 594 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 36 removed outlier: 7.815A pdb=" N LEU A 99 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLU A 23 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL A 101 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU A 25 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N PHE A 98 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL A 73 " --> pdb=" O PHE A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 204 through 212 removed outlier: 5.832A pdb=" N ILE A 197 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ALA A 289 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU A 252 " --> pdb=" O PHE A 261 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 324 through 326 removed outlier: 6.558A pdb=" N LYS A 325 " --> pdb=" O LYS A 485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 382 through 392 removed outlier: 7.000A pdb=" N TRP A 383 " --> pdb=" O CYS A 340 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N CYS A 340 " --> pdb=" O TRP A 383 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU A 334 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ILE A 338 " --> pdb=" O GLU A 476 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLU A 476 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N CYS A 340 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 366 removed outlier: 3.910A pdb=" N GLU A 365 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 371 through 372 removed outlier: 6.601A pdb=" N LEU A 402 " --> pdb=" O ASN A 426 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN A 426 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU A 404 " --> pdb=" O TRP A 424 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N TRP A 424 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE A 406 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 770 through 771 removed outlier: 6.819A pdb=" N VAL A 845 " --> pdb=" O ILE A 841 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 854 through 856 Processing sheet with id=AA9, first strand: chain 'B' and resid 377 through 381 removed outlier: 4.132A pdb=" N THR B 354 " --> pdb=" O ARG B 373 " (cutoff:3.500A) 413 hydrogen bonds defined for protein. 1182 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: 1.67 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1725 1.30 - 1.43: 2679 1.43 - 1.56: 5984 1.56 - 1.69: 1 1.69 - 1.82: 113 Bond restraints: 10502 Sorted by residual: bond pdb=" C25 UEX A1101 " pdb=" N35 UEX A1101 " ideal model delta sigma weight residual 1.291 1.455 -0.164 2.00e-02 2.50e+03 6.74e+01 bond pdb=" C15 UEX A1101 " pdb=" N35 UEX A1101 " ideal model delta sigma weight residual 1.364 1.479 -0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" C04 UEX A1101 " pdb=" N03 UEX A1101 " ideal model delta sigma weight residual 1.359 1.456 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C25 UEX A1101 " pdb=" N26 UEX A1101 " ideal model delta sigma weight residual 1.367 1.449 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C25 UEX A1101 " pdb=" N23 UEX A1101 " ideal model delta sigma weight residual 1.379 1.452 -0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 10497 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 13772 2.05 - 4.11: 348 4.11 - 6.16: 33 6.16 - 8.22: 10 8.22 - 10.27: 4 Bond angle restraints: 14167 Sorted by residual: angle pdb=" N ILE B 509 " pdb=" CA ILE B 509 " pdb=" C ILE B 509 " ideal model delta sigma weight residual 113.71 108.94 4.77 9.50e-01 1.11e+00 2.52e+01 angle pdb=" C25 UEX A1101 " pdb=" N26 UEX A1101 " pdb=" C27 UEX A1101 " ideal model delta sigma weight residual 121.93 132.20 -10.27 3.00e+00 1.11e-01 1.17e+01 angle pdb=" C ARG B 386 " pdb=" N ASP B 387 " pdb=" CA ASP B 387 " ideal model delta sigma weight residual 121.54 127.95 -6.41 1.91e+00 2.74e-01 1.13e+01 angle pdb=" N23 UEX A1101 " pdb=" C25 UEX A1101 " pdb=" N26 UEX A1101 " ideal model delta sigma weight residual 118.03 127.92 -9.89 3.00e+00 1.11e-01 1.09e+01 angle pdb=" CA TYR A 392 " pdb=" CB TYR A 392 " pdb=" CG TYR A 392 " ideal model delta sigma weight residual 113.90 119.11 -5.21 1.80e+00 3.09e-01 8.37e+00 ... (remaining 14162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.59: 6090 15.59 - 31.18: 271 31.18 - 46.77: 55 46.77 - 62.35: 3 62.35 - 77.94: 10 Dihedral angle restraints: 6429 sinusoidal: 2754 harmonic: 3675 Sorted by residual: dihedral pdb=" CA ARG A1047 " pdb=" C ARG A1047 " pdb=" N HIS A1048 " pdb=" CA HIS A1048 " ideal model delta harmonic sigma weight residual -180.00 -153.04 -26.96 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA LYS B 506 " pdb=" C LYS B 506 " pdb=" N GLU B 507 " pdb=" CA GLU B 507 " ideal model delta harmonic sigma weight residual 180.00 156.74 23.26 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA TRP B 597 " pdb=" C TRP B 597 " pdb=" N LEU B 598 " pdb=" CA LEU B 598 " ideal model delta harmonic sigma weight residual -180.00 -159.04 -20.96 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 6426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1174 0.062 - 0.123: 327 0.123 - 0.185: 28 0.185 - 0.246: 1 0.246 - 0.308: 1 Chirality restraints: 1531 Sorted by residual: chirality pdb=" CG LEU A 456 " pdb=" CB LEU A 456 " pdb=" CD1 LEU A 456 " pdb=" CD2 LEU A 456 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA ASP A 258 " pdb=" N ASP A 258 " pdb=" C ASP A 258 " pdb=" CB ASP A 258 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.59e-01 chirality pdb=" CB ILE A 391 " pdb=" CA ILE A 391 " pdb=" CG1 ILE A 391 " pdb=" CG2 ILE A 391 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.79e-01 ... (remaining 1528 not shown) Planarity restraints: 1818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 759 " -0.014 2.00e-02 2.50e+03 1.86e-02 5.20e+00 pdb=" CG HIS A 759 " 0.039 2.00e-02 2.50e+03 pdb=" ND1 HIS A 759 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 HIS A 759 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 HIS A 759 " 0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS A 759 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 780 " -0.007 2.00e-02 2.50e+03 1.35e-02 4.58e+00 pdb=" CG TRP A 780 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A 780 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 780 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 780 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 780 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 780 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 780 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 780 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 780 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 174 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO A 175 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 175 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 175 " 0.028 5.00e-02 4.00e+02 ... (remaining 1815 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 302 2.70 - 3.25: 9967 3.25 - 3.80: 14712 3.80 - 4.35: 21567 4.35 - 4.90: 34523 Nonbonded interactions: 81071 Sorted by model distance: nonbonded pdb=" OG1 THR A 358 " pdb=" OH TYR A 389 " model vdw 2.156 3.040 nonbonded pdb=" N ARG A 19 " pdb=" O CYS A 36 " model vdw 2.170 3.120 nonbonded pdb=" OE1 GLU A 768 " pdb=" ND2 ASN A 782 " model vdw 2.212 3.120 nonbonded pdb=" O SER A 66 " pdb=" OG SER A 67 " model vdw 2.228 3.040 nonbonded pdb=" NZ LYS A 733 " pdb=" OE2 GLU A 737 " model vdw 2.229 3.120 ... (remaining 81066 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.440 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 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 : 0.008 0.164 10502 Z= 0.342 Angle : 0.803 10.272 14167 Z= 0.429 Chirality : 0.053 0.308 1531 Planarity : 0.006 0.051 1818 Dihedral : 10.206 77.942 4043 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.18 % Allowed : 1.31 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.40 (0.20), residues: 1231 helix: -3.79 (0.14), residues: 563 sheet: -1.75 (0.35), residues: 166 loop : -1.98 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 537 TYR 0.032 0.004 TYR B 426 PHE 0.023 0.004 PHE A 937 TRP 0.032 0.004 TRP A 780 HIS 0.023 0.003 HIS A 759 Details of bonding type rmsd covalent geometry : bond 0.00790 (10502) covalent geometry : angle 0.80266 (14167) hydrogen bonds : bond 0.32266 ( 413) hydrogen bonds : angle 9.46925 ( 1182) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 240 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 ASP cc_start: 0.7485 (m-30) cc_final: 0.7239 (m-30) REVERT: B 364 MET cc_start: 0.5882 (tmm) cc_final: 0.3614 (mtp) REVERT: B 367 ASP cc_start: 0.5420 (m-30) cc_final: 0.4975 (m-30) REVERT: B 420 LEU cc_start: 0.8383 (tp) cc_final: 0.8122 (tp) REVERT: B 465 ARG cc_start: 0.6916 (ttp80) cc_final: 0.6703 (ttm-80) REVERT: B 478 GLN cc_start: 0.7819 (tp-100) cc_final: 0.7435 (tp-100) REVERT: B 528 TYR cc_start: 0.8020 (t80) cc_final: 0.7747 (t80) outliers start: 2 outliers final: 0 residues processed: 242 average time/residue: 0.7357 time to fit residues: 188.5454 Evaluate side-chains 169 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 157 ASN A 213 HIS A 370 ASN A 380 ASN A 384 ASN A 419 HIS A 630 GLN A 738 GLN A 795 GLN A 917 HIS A1048 HIS B 499 GLN ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.176056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.141336 restraints weight = 11093.257| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.14 r_work: 0.3248 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10502 Z= 0.187 Angle : 0.697 10.698 14167 Z= 0.362 Chirality : 0.047 0.184 1531 Planarity : 0.006 0.050 1818 Dihedral : 5.417 22.683 1381 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.84 % Allowed : 7.97 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.37 (0.22), residues: 1231 helix: -1.67 (0.19), residues: 559 sheet: -0.99 (0.38), residues: 160 loop : -1.44 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 537 TYR 0.027 0.002 TYR A 392 PHE 0.022 0.003 PHE A 667 TRP 0.015 0.002 TRP B 583 HIS 0.010 0.002 HIS A 759 Details of bonding type rmsd covalent geometry : bond 0.00434 (10502) covalent geometry : angle 0.69737 (14167) hydrogen bonds : bond 0.07507 ( 413) hydrogen bonds : angle 4.87241 ( 1182) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.8461 (m-30) REVERT: A 227 LYS cc_start: 0.7710 (ttmt) cc_final: 0.7114 (tttt) REVERT: A 454 ASP cc_start: 0.8119 (m-30) cc_final: 0.7743 (m-30) REVERT: A 459 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8638 (mp) REVERT: A 528 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7139 (mtmt) REVERT: A 827 GLN cc_start: 0.8118 (mm-40) cc_final: 0.7914 (mm-40) REVERT: A 883 ASP cc_start: 0.6822 (m-30) cc_final: 0.6487 (m-30) REVERT: B 326 MET cc_start: 0.6814 (mpp) cc_final: 0.6576 (mmt) REVERT: B 342 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7063 (tm-30) REVERT: B 364 MET cc_start: 0.5181 (tmm) cc_final: 0.3131 (mtp) REVERT: B 367 ASP cc_start: 0.6084 (m-30) cc_final: 0.5474 (m-30) REVERT: B 420 LEU cc_start: 0.8535 (tp) cc_final: 0.8129 (tp) REVERT: B 465 ARG cc_start: 0.7252 (ttp80) cc_final: 0.6951 (ptm-80) REVERT: B 469 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7246 (tt0) REVERT: B 478 GLN cc_start: 0.8000 (tp-100) cc_final: 0.7547 (tp-100) REVERT: B 492 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8216 (ttmm) REVERT: B 537 GLU cc_start: 0.6900 (tt0) cc_final: 0.6640 (tt0) REVERT: B 551 LYS cc_start: 0.8345 (tttt) cc_final: 0.7989 (tmmt) REVERT: B 582 MET cc_start: 0.5779 (tmm) cc_final: 0.5549 (mtp) outliers start: 21 outliers final: 2 residues processed: 186 average time/residue: 0.6843 time to fit residues: 135.5951 Evaluate side-chains 156 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 148 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 469 GLU Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 69 optimal weight: 0.1980 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 31 optimal weight: 0.5980 chunk 16 optimal weight: 20.0000 chunk 108 optimal weight: 20.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN A 213 HIS A 384 ASN A 796 ASN A1048 HIS B 417 ASN B 527 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.178651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.144975 restraints weight = 11112.254| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.22 r_work: 0.3282 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10502 Z= 0.136 Angle : 0.589 9.865 14167 Z= 0.302 Chirality : 0.044 0.171 1531 Planarity : 0.004 0.047 1818 Dihedral : 4.925 20.698 1381 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.10 % Allowed : 9.98 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.23), residues: 1231 helix: -0.49 (0.22), residues: 562 sheet: -0.68 (0.38), residues: 160 loop : -1.21 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 335 TYR 0.022 0.002 TYR A 392 PHE 0.018 0.002 PHE A 667 TRP 0.012 0.002 TRP B 597 HIS 0.008 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00306 (10502) covalent geometry : angle 0.58896 (14167) hydrogen bonds : bond 0.06056 ( 413) hydrogen bonds : angle 4.34550 ( 1182) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 138 ASP cc_start: 0.8809 (OUTLIER) cc_final: 0.8481 (m-30) REVERT: A 162 ARG cc_start: 0.7747 (mtm-85) cc_final: 0.7512 (mtm-85) REVERT: A 186 ASP cc_start: 0.8094 (p0) cc_final: 0.7619 (p0) REVERT: A 227 LYS cc_start: 0.7781 (ttmt) cc_final: 0.7248 (tttt) REVERT: A 382 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.8108 (ttp-170) REVERT: A 529 GLU cc_start: 0.7605 (mp0) cc_final: 0.7113 (mp0) REVERT: A 787 ASP cc_start: 0.8025 (t0) cc_final: 0.7777 (t0) REVERT: A 1044 ASN cc_start: 0.8287 (OUTLIER) cc_final: 0.8029 (t0) REVERT: B 326 MET cc_start: 0.6721 (mpp) cc_final: 0.6405 (mmt) REVERT: B 342 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7058 (tm-30) REVERT: B 364 MET cc_start: 0.4986 (tmm) cc_final: 0.3049 (mtp) REVERT: B 367 ASP cc_start: 0.6089 (m-30) cc_final: 0.5468 (m-30) REVERT: B 465 ARG cc_start: 0.7087 (ttp80) cc_final: 0.6739 (ptm-80) REVERT: B 495 GLU cc_start: 0.7283 (mt-10) cc_final: 0.6987 (mm-30) REVERT: B 537 GLU cc_start: 0.6762 (tt0) cc_final: 0.6501 (tt0) REVERT: B 551 LYS cc_start: 0.8281 (tttt) cc_final: 0.7932 (tmmt) REVERT: B 584 LEU cc_start: 0.3959 (OUTLIER) cc_final: 0.3748 (mm) outliers start: 24 outliers final: 7 residues processed: 177 average time/residue: 0.6101 time to fit residues: 115.3280 Evaluate side-chains 158 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 1044 ASN Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.0064 > 50: distance: 7 - 124: 36.316 distance: 10 - 121: 35.082 distance: 21 - 107: 33.001 distance: 24 - 104: 29.810 distance: 36 - 93: 30.946 distance: 39 - 90: 35.395 distance: 57 - 62: 33.679 distance: 62 - 63: 39.620 distance: 63 - 64: 39.551 distance: 66 - 67: 56.417 distance: 71 - 72: 40.123 distance: 72 - 73: 56.025 distance: 72 - 74: 40.892 distance: 75 - 78: 38.995 distance: 79 - 80: 45.266 distance: 80 - 81: 18.218 distance: 82 - 83: 68.418 distance: 83 - 84: 4.281 distance: 83 - 86: 38.437 distance: 84 - 85: 37.019 distance: 84 - 90: 3.607 distance: 86 - 87: 36.932 distance: 86 - 88: 56.469 distance: 87 - 89: 52.980 distance: 90 - 91: 57.019 distance: 91 - 92: 40.454 distance: 91 - 94: 68.726 distance: 92 - 93: 52.395 distance: 94 - 96: 41.119 distance: 97 - 98: 39.908 distance: 98 - 99: 40.180 distance: 98 - 101: 39.872 distance: 99 - 100: 47.841 distance: 99 - 104: 25.980 distance: 101 - 102: 42.954 distance: 101 - 103: 40.257 distance: 104 - 105: 58.283 distance: 105 - 108: 16.358 distance: 106 - 107: 39.963 distance: 108 - 109: 21.382 distance: 109 - 110: 41.302 distance: 109 - 111: 55.507 distance: 113 - 114: 45.487 distance: 113 - 116: 39.652 distance: 114 - 115: 15.430 distance: 114 - 121: 15.426 distance: 117 - 118: 56.737 distance: 121 - 122: 27.868 distance: 122 - 123: 34.527 distance: 122 - 125: 56.734 distance: 123 - 124: 43.757 distance: 123 - 127: 18.606 distance: 125 - 126: 56.405 distance: 127 - 128: 53.127 distance: 128 - 129: 55.972 distance: 129 - 130: 56.873 distance: 129 - 135: 34.465 distance: 131 - 132: 13.884 distance: 132 - 133: 49.037 distance: 132 - 134: 41.190 distance: 203 - 208: 3.071