Starting phenix.real_space_refine on Wed Aug 5 13:44:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9a_37362/08_2026/8w9a_37362_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9a_37362/08_2026/8w9a_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 { model { file = "/net/cci-nas-00/data/ceres_data/8w9a_37362/08_2026/8w9a_37362_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9a_37362/08_2026/8w9a_37362_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w9a_37362/08_2026/8w9a_37362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9a_37362/08_2026/8w9a_37362.map" } 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-2.2rc3-6140/lib/python3.11/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: 2.20, per 1000 atoms: 0.21 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: 0.72 Conformation dependent library (CDL) restraints added in 255.3 milliseconds 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: 0.34 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: 1.98 Time building geometry restraints manager: 0.93 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 10.590 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:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 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 are 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/Z covalent geometry : bond 0.00790 / 0.34 (10502) covalent geometry : angle 0.80266 / 0.43 (14167) hydrogen bonds : bond 0.32266 / 20.76 ( 413) hydrogen bonds : angle 9.46925 / 6.34 ( 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 : 0.378 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: 0.5419 (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: 0.5971 time to fit residues: 153.6949 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 : 0.374 ------------------------------------------------------------------------------- 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... 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: 0.8707 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 are 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/Z covalent geometry : bond 0.00434 / 0.19 (10502) covalent geometry : angle 0.69737 / 0.36 (14167) hydrogen bonds : bond 0.07507 / 4.78 ( 413) hydrogen bonds : angle 4.87241 / 3.29 ( 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 : 0.303 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: 0.8001 (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: 0.5765 time to fit residues: 114.2858 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 : 0.426 ------------------------------------------------------------------------------- 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... 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: 0.8683 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 are 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/Z covalent geometry : bond 0.00306 / 0.14 (10502) covalent geometry : angle 0.58896 / 0.30 (14167) hydrogen bonds : bond 0.06056 / 3.87 ( 413) hydrogen bonds : angle 4.34550 / 2.95 ( 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 : 0.334 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: 0.8107 (ttp-170) REVERT: A 529 GLU cc_start: 0.7605 (mp0) cc_final: 0.7113 (mp0) REVERT: A 787 ASP cc_start: 0.8024 (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: 0.6494 time to fit residues: 123.0097 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 : 0.420 ------------------------------------------------------------------------------- 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 ************** Weight determination summary: number of chunks: 123 random chunks: chunk 64 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 14 optimal weight: 0.3980 chunk 47 optimal weight: 7.9990 chunk 1 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 71.0064 > 50:) chunk 92 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS A 738 GLN ** A 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS B 415 GLN ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.175997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.135987 restraints weight = 11191.280| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.68 r_work: 0.3198 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10502 Z= 0.201 Angle : 0.655 10.166 14167 Z= 0.336 Chirality : 0.047 0.174 1531 Planarity : 0.005 0.044 1818 Dihedral : 5.028 21.483 1381 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.33 % Allowed : 10.16 % Favored : 86.51 % 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 are not related in a simple way. whole: -1.08 (0.24), residues: 1231 helix: -0.25 (0.22), residues: 562 sheet: -0.47 (0.39), residues: 162 loop : -1.20 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 335 TYR 0.021 0.002 TYR A 392 PHE 0.021 0.002 PHE A 667 TRP 0.012 0.002 TRP A 479 HIS 0.008 0.002 HIS A 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 (10502) covalent geometry : angle 0.65546 / 0.34 (14167) hydrogen bonds : bond 0.06802 / 4.36 ( 413) hydrogen bonds : angle 4.36681 / 2.98 ( 1182) *********************** REFINEMENT MACRO_CYCLE 4 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 197 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7849 (mp0) REVERT: A 138 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8458 (m-30) REVERT: A 162 ARG cc_start: 0.7755 (mtm-85) cc_final: 0.7526 (mtm-85) REVERT: A 186 ASP cc_start: 0.8076 (p0) cc_final: 0.7598 (p0) REVERT: A 227 LYS cc_start: 0.7779 (ttmt) cc_final: 0.7328 (tttt) REVERT: A 291 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7327 (mm-30) REVERT: A 382 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.8076 (ttp-170) REVERT: A 454 ASP cc_start: 0.8091 (m-30) cc_final: 0.7725 (m-30) REVERT: A 768 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7374 (mt-10) REVERT: A 883 ASP cc_start: 0.6882 (m-30) cc_final: 0.6530 (m-30) REVERT: B 326 MET cc_start: 0.6768 (mpp) cc_final: 0.6515 (mmt) REVERT: B 342 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7121 (tm-30) REVERT: B 364 MET cc_start: 0.5036 (tmm) cc_final: 0.3008 (mtp) REVERT: B 367 ASP cc_start: 0.6172 (m-30) cc_final: 0.5489 (m-30) REVERT: B 465 ARG cc_start: 0.7082 (ttp80) cc_final: 0.6785 (ptm-80) REVERT: B 469 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.7138 (tt0) REVERT: B 495 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6954 (mm-30) REVERT: B 537 GLU cc_start: 0.6798 (tt0) cc_final: 0.6516 (tt0) outliers start: 38 outliers final: 13 residues processed: 185 average time/residue: 0.5546 time to fit residues: 109.9525 Evaluate side-chains 167 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 291 GLU 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 768 GLU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 469 GLU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 502 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 64 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 33 optimal weight: 0.1980 chunk 28 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS A 219 GLN A 738 GLN ** A 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS B 415 GLN ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.176635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.133021 restraints weight = 11119.975| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.55 r_work: 0.3221 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10502 Z= 0.172 Angle : 0.615 9.837 14167 Z= 0.316 Chirality : 0.046 0.169 1531 Planarity : 0.004 0.045 1818 Dihedral : 4.914 21.560 1381 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.06 % Allowed : 11.12 % Favored : 85.81 % 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 are not related in a simple way. whole: -0.81 (0.24), residues: 1231 helix: -0.02 (0.22), residues: 561 sheet: -0.27 (0.39), residues: 162 loop : -1.10 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 335 TYR 0.019 0.002 TYR A 392 PHE 0.020 0.002 PHE A 667 TRP 0.011 0.002 TRP A 669 HIS 0.007 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (10502) covalent geometry : angle 0.61505 / 0.32 (14167) hydrogen bonds : bond 0.06312 / 4.04 ( 413) hydrogen bonds : angle 4.23278 / 2.89 ( 1182) *********************** REFINEMENT MACRO_CYCLE 5 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 190 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7838 (mp0) REVERT: A 138 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.8396 (m-30) REVERT: A 162 ARG cc_start: 0.7748 (mtm-85) cc_final: 0.7513 (mtm-85) REVERT: A 186 ASP cc_start: 0.8039 (p0) cc_final: 0.7597 (p0) REVERT: A 227 LYS cc_start: 0.7751 (ttmt) cc_final: 0.7273 (tttm) REVERT: A 291 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7317 (mm-30) REVERT: A 745 MET cc_start: 0.8575 (tpt) cc_final: 0.8346 (tpt) REVERT: A 768 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7341 (mt-10) REVERT: B 326 MET cc_start: 0.6748 (mpp) cc_final: 0.6529 (mmt) REVERT: B 342 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7179 (tm-30) REVERT: B 364 MET cc_start: 0.4992 (tmm) cc_final: 0.2997 (mtp) REVERT: B 367 ASP cc_start: 0.5994 (m-30) cc_final: 0.5306 (m-30) REVERT: B 465 ARG cc_start: 0.6969 (ttp80) cc_final: 0.6645 (ptm-80) REVERT: B 495 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6912 (mm-30) REVERT: B 537 GLU cc_start: 0.6779 (tt0) cc_final: 0.6500 (tt0) outliers start: 35 outliers final: 15 residues processed: 175 average time/residue: 0.5358 time to fit residues: 100.5560 Evaluate side-chains 167 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 502 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 63 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 95 optimal weight: 0.7980 chunk 107 optimal weight: 0.0870 chunk 98 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 overall best weight: 2.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS A 219 GLN A 738 GLN A 936 HIS A1048 HIS B 415 GLN ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.177206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.143597 restraints weight = 11226.343| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.35 r_work: 0.3219 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10502 Z= 0.153 Angle : 0.592 9.903 14167 Z= 0.303 Chirality : 0.045 0.165 1531 Planarity : 0.004 0.044 1818 Dihedral : 4.784 21.224 1381 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.63 % Allowed : 12.00 % Favored : 85.38 % 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 are not related in a simple way. whole: -0.61 (0.24), residues: 1231 helix: 0.17 (0.22), residues: 565 sheet: -0.06 (0.39), residues: 161 loop : -1.08 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 335 TYR 0.018 0.002 TYR A 392 PHE 0.018 0.002 PHE A 667 TRP 0.011 0.002 TRP A 669 HIS 0.008 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (10502) covalent geometry : angle 0.59233 / 0.30 (14167) hydrogen bonds : bond 0.05902 / 3.78 ( 413) hydrogen bonds : angle 4.10342 / 2.81 ( 1182) *********************** REFINEMENT MACRO_CYCLE 6 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 182 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.329 Fit side-chains REVERT: A 85 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7859 (mp0) REVERT: A 115 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8264 (tmm160) REVERT: A 162 ARG cc_start: 0.7705 (mtm-85) cc_final: 0.7376 (mtm-85) REVERT: A 186 ASP cc_start: 0.8069 (p0) cc_final: 0.7633 (p0) REVERT: A 227 LYS cc_start: 0.7761 (ttmt) cc_final: 0.7302 (tttt) REVERT: A 291 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7351 (mm-30) REVERT: A 738 GLN cc_start: 0.7942 (mm110) cc_final: 0.7672 (mm-40) REVERT: A 766 LEU cc_start: 0.8971 (mm) cc_final: 0.8657 (mm) REVERT: A 768 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7331 (mt-10) REVERT: B 326 MET cc_start: 0.6756 (mpp) cc_final: 0.6528 (mmt) REVERT: B 342 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7347 (tm-30) REVERT: B 364 MET cc_start: 0.4948 (tmm) cc_final: 0.2985 (mtp) REVERT: B 367 ASP cc_start: 0.6062 (m-30) cc_final: 0.5360 (m-30) REVERT: B 465 ARG cc_start: 0.6899 (ttp80) cc_final: 0.6613 (ptm-80) outliers start: 30 outliers final: 15 residues processed: 170 average time/residue: 0.5486 time to fit residues: 100.1130 Evaluate side-chains 163 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 502 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 90 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 67 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 114 optimal weight: 20.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS A 219 GLN ** A 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.175988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.141662 restraints weight = 11070.325| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.14 r_work: 0.3199 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10502 Z= 0.204 Angle : 0.654 9.789 14167 Z= 0.335 Chirality : 0.048 0.168 1531 Planarity : 0.005 0.041 1818 Dihedral : 4.949 22.202 1381 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.45 % Allowed : 12.87 % Favored : 84.68 % 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 are not related in a simple way. whole: -0.70 (0.24), residues: 1231 helix: 0.06 (0.22), residues: 569 sheet: -0.08 (0.39), residues: 164 loop : -1.11 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 335 TYR 0.019 0.002 TYR A 392 PHE 0.019 0.002 PHE A 667 TRP 0.011 0.002 TRP A 479 HIS 0.007 0.002 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.20 (10502) covalent geometry : angle 0.65413 / 0.33 (14167) hydrogen bonds : bond 0.06615 / 4.24 ( 413) hydrogen bonds : angle 4.20937 / 2.88 ( 1182) *********************** REFINEMENT MACRO_CYCLE 7 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 173 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7843 (mp0) REVERT: A 162 ARG cc_start: 0.7711 (mtm-85) cc_final: 0.7368 (mtm-85) REVERT: A 186 ASP cc_start: 0.8086 (p0) cc_final: 0.7631 (p0) REVERT: A 227 LYS cc_start: 0.7768 (ttmt) cc_final: 0.7314 (tttt) REVERT: A 291 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7366 (mm-30) REVERT: A 454 ASP cc_start: 0.8149 (m-30) cc_final: 0.7793 (m-30) REVERT: A 738 GLN cc_start: 0.7895 (mm110) cc_final: 0.7648 (mm-40) REVERT: A 766 LEU cc_start: 0.8947 (mm) cc_final: 0.8596 (mm) REVERT: A 768 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7395 (mt-10) REVERT: A 883 ASP cc_start: 0.6953 (m-30) cc_final: 0.6646 (m-30) REVERT: B 326 MET cc_start: 0.6790 (mpp) cc_final: 0.5888 (ptp) REVERT: B 342 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7352 (tm-30) REVERT: B 364 MET cc_start: 0.4977 (tmm) cc_final: 0.2993 (mtp) REVERT: B 367 ASP cc_start: 0.6126 (m-30) cc_final: 0.5421 (m-30) REVERT: B 465 ARG cc_start: 0.6954 (ttp80) cc_final: 0.6742 (ptm-80) REVERT: B 537 GLU cc_start: 0.6797 (tt0) cc_final: 0.6526 (tt0) outliers start: 28 outliers final: 16 residues processed: 164 average time/residue: 0.5787 time to fit residues: 101.8640 Evaluate side-chains 157 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 502 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 4 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS A 219 GLN ** A 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.176089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.141753 restraints weight = 11015.058| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.29 r_work: 0.3213 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10502 Z= 0.194 Angle : 0.645 9.817 14167 Z= 0.330 Chirality : 0.047 0.167 1531 Planarity : 0.005 0.042 1818 Dihedral : 4.941 22.149 1381 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.63 % Allowed : 13.05 % Favored : 84.33 % 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 are not related in a simple way. whole: -0.65 (0.24), residues: 1231 helix: 0.11 (0.22), residues: 568 sheet: 0.00 (0.40), residues: 157 loop : -1.10 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 335 TYR 0.019 0.002 TYR A 392 PHE 0.019 0.002 PHE A 667 TRP 0.012 0.002 TRP A 479 HIS 0.007 0.002 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.19 (10502) covalent geometry : angle 0.64483 / 0.33 (14167) hydrogen bonds : bond 0.06468 / 4.15 ( 413) hydrogen bonds : angle 4.16878 / 2.85 ( 1182) *********************** REFINEMENT MACRO_CYCLE 8 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 176 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7831 (mp0) REVERT: A 162 ARG cc_start: 0.7716 (mtm-85) cc_final: 0.7381 (mtm-85) REVERT: A 186 ASP cc_start: 0.8069 (p0) cc_final: 0.7642 (p0) REVERT: A 227 LYS cc_start: 0.7756 (ttmt) cc_final: 0.7293 (tttt) REVERT: A 291 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7331 (mm-30) REVERT: A 454 ASP cc_start: 0.8180 (m-30) cc_final: 0.7821 (m-30) REVERT: A 543 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8245 (mm) REVERT: A 768 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7348 (mt-10) REVERT: A 883 ASP cc_start: 0.6965 (m-30) cc_final: 0.6662 (m-30) REVERT: B 326 MET cc_start: 0.6797 (mpp) cc_final: 0.5860 (ptp) REVERT: B 342 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7388 (tm-30) REVERT: B 364 MET cc_start: 0.4957 (tmm) cc_final: 0.3014 (mtp) REVERT: B 367 ASP cc_start: 0.6141 (m-30) cc_final: 0.5402 (m-30) REVERT: B 465 ARG cc_start: 0.6905 (ttp80) cc_final: 0.6677 (ptm-80) outliers start: 30 outliers final: 19 residues processed: 166 average time/residue: 0.5924 time to fit residues: 105.5850 Evaluate side-chains 164 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 502 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 78 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS A 219 GLN A 738 GLN ** A 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.176606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.142785 restraints weight = 11041.949| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.29 r_work: 0.3217 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10502 Z= 0.172 Angle : 0.622 9.872 14167 Z= 0.318 Chirality : 0.046 0.165 1531 Planarity : 0.004 0.042 1818 Dihedral : 4.857 21.772 1381 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.36 % Allowed : 13.49 % Favored : 84.15 % 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 are not related in a simple way. whole: -0.53 (0.24), residues: 1231 helix: 0.25 (0.22), residues: 565 sheet: 0.09 (0.40), residues: 157 loop : -1.09 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 335 TYR 0.019 0.002 TYR A 392 PHE 0.018 0.002 PHE A 667 TRP 0.012 0.002 TRP B 597 HIS 0.007 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (10502) covalent geometry : angle 0.62163 / 0.32 (14167) hydrogen bonds : bond 0.06149 / 3.94 ( 413) hydrogen bonds : angle 4.10189 / 2.81 ( 1182) *********************** REFINEMENT MACRO_CYCLE 9 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 174 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7831 (mp0) REVERT: A 162 ARG cc_start: 0.7708 (mtm-85) cc_final: 0.7373 (mtm-85) REVERT: A 186 ASP cc_start: 0.8070 (p0) cc_final: 0.7632 (p0) REVERT: A 227 LYS cc_start: 0.7774 (ttmt) cc_final: 0.7323 (tttt) REVERT: A 454 ASP cc_start: 0.8127 (m-30) cc_final: 0.7769 (m-30) REVERT: A 543 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8247 (mm) REVERT: A 738 GLN cc_start: 0.7890 (mm110) cc_final: 0.7665 (mm-40) REVERT: A 766 LEU cc_start: 0.8948 (mm) cc_final: 0.8583 (mm) REVERT: A 768 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7323 (mt-10) REVERT: A 883 ASP cc_start: 0.6940 (m-30) cc_final: 0.6625 (m-30) REVERT: B 326 MET cc_start: 0.6834 (mpp) cc_final: 0.5875 (ptp) REVERT: B 342 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7397 (tm-30) REVERT: B 364 MET cc_start: 0.4983 (tmm) cc_final: 0.3046 (mtp) REVERT: B 367 ASP cc_start: 0.6130 (m-30) cc_final: 0.5399 (m-30) REVERT: B 465 ARG cc_start: 0.6856 (ttp80) cc_final: 0.6640 (ptm-80) REVERT: B 476 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7730 (mt-10) outliers start: 27 outliers final: 18 residues processed: 164 average time/residue: 0.5483 time to fit residues: 96.4197 Evaluate side-chains 166 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 502 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 72 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 88 optimal weight: 0.0980 chunk 51 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS A 219 GLN A 936 HIS A1048 HIS ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.178788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.144182 restraints weight = 11025.050| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.29 r_work: 0.3248 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10502 Z= 0.123 Angle : 0.573 10.071 14167 Z= 0.290 Chirality : 0.043 0.162 1531 Planarity : 0.004 0.040 1818 Dihedral : 4.616 20.583 1381 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.75 % Allowed : 14.36 % Favored : 83.89 % 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 are not related in a simple way. whole: -0.21 (0.24), residues: 1231 helix: 0.57 (0.22), residues: 563 sheet: 0.23 (0.40), residues: 155 loop : -0.98 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 765 TYR 0.018 0.001 TYR A 392 PHE 0.015 0.002 PHE A 667 TRP 0.011 0.001 TRP A 669 HIS 0.008 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (10502) covalent geometry : angle 0.57275 / 0.29 (14167) hydrogen bonds : bond 0.05215 / 3.33 ( 413) hydrogen bonds : angle 3.90820 / 2.67 ( 1182) ********************** REFINEMENT MACRO_CYCLE 10 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 173 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7824 (mp0) REVERT: A 93 ARG cc_start: 0.7282 (mtm180) cc_final: 0.7052 (mtp180) REVERT: A 115 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8231 (tmm160) REVERT: A 162 ARG cc_start: 0.7678 (mtm-85) cc_final: 0.7361 (mtm-85) REVERT: A 186 ASP cc_start: 0.8060 (p0) cc_final: 0.7610 (p0) REVERT: A 227 LYS cc_start: 0.7767 (ttmt) cc_final: 0.7321 (tttt) REVERT: A 529 GLU cc_start: 0.7316 (mp0) cc_final: 0.6816 (mp0) REVERT: A 766 LEU cc_start: 0.8897 (mm) cc_final: 0.8534 (mm) REVERT: B 326 MET cc_start: 0.6790 (mpp) cc_final: 0.5824 (ptp) REVERT: B 342 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7343 (tm-30) REVERT: B 364 MET cc_start: 0.4900 (tmm) cc_final: 0.3019 (mtp) REVERT: B 367 ASP cc_start: 0.6163 (m-30) cc_final: 0.5449 (m-30) REVERT: B 420 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8313 (tt) REVERT: B 465 ARG cc_start: 0.6726 (ttp80) cc_final: 0.6517 (ptm-80) REVERT: B 476 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7849 (mt-10) outliers start: 20 outliers final: 10 residues processed: 166 average time/residue: 0.6186 time to fit residues: 109.8494 Evaluate side-chains 154 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 502 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 74 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 70 optimal weight: 0.1980 chunk 116 optimal weight: 10.0000 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS A 219 GLN A 738 GLN A 826 ASN A 936 HIS A1048 HIS ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.179225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.145551 restraints weight = 11099.951| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.15 r_work: 0.3271 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3060 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= 0.121 Angle : 0.566 10.082 14167 Z= 0.287 Chirality : 0.043 0.161 1531 Planarity : 0.004 0.040 1818 Dihedral : 4.491 20.353 1381 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.31 % Allowed : 14.54 % Favored : 84.15 % 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 are not related in a simple way. whole: -0.01 (0.24), residues: 1231 helix: 0.72 (0.22), residues: 565 sheet: 0.31 (0.40), residues: 155 loop : -0.87 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1047 TYR 0.017 0.001 TYR A 392 PHE 0.014 0.001 PHE A 667 TRP 0.013 0.001 TRP A 479 HIS 0.007 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (10502) covalent geometry : angle 0.56577 / 0.29 (14167) hydrogen bonds : bond 0.05058 / 3.24 ( 413) hydrogen bonds : angle 3.83934 / 2.63 ( 1182) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4031.39 seconds wall clock time: 69 minutes 10.12 seconds (4150.12 seconds total)