Starting phenix.real_space_refine on Fri Feb 14 10:37:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9a_37362/02_2025/8w9a_37362_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9a_37362/02_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_37362/02_2025/8w9a_37362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9a_37362/02_2025/8w9a_37362.map" model { file = "/net/cci-nas-00/data/ceres_data/8w9a_37362/02_2025/8w9a_37362_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9a_37362/02_2025/8w9a_37362_trim.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.37, per 1000 atoms: 0.62 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: 2.28 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.34 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: 3.70 Time building geometry restraints manager: 2.69 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: 0.910 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: 0.490 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.890 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.780 ------------------------------------------------------------------------------- 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= 0.506 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 : 13.98 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.032 0.004 TRP A 780 HIS 0.023 0.003 HIS A 759 PHE 0.023 0.004 PHE A 937 TYR 0.032 0.004 TYR B 426 ARG 0.012 0.001 ARG A 537 *********************** 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 : 1.101 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: 1.5169 time to fit residues: 389.6451 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 : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 37 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 ** A 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4024 r_free = 0.4024 target = 0.178668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.144586 restraints weight = 10980.437| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.92 r_work: 0.3286 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10502 Z= 0.209 Angle : 0.650 9.743 14167 Z= 0.337 Chirality : 0.045 0.182 1531 Planarity : 0.005 0.050 1818 Dihedral : 5.287 21.992 1381 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.23 % Allowed : 8.41 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.22), residues: 1231 helix: -1.60 (0.20), residues: 555 sheet: -1.00 (0.38), residues: 160 loop : -1.41 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 780 HIS 0.008 0.001 HIS A 759 PHE 0.020 0.002 PHE A 744 TYR 0.026 0.002 TYR A 392 ARG 0.005 0.001 ARG A 537 *********************** 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 190 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.8411 (m-30) REVERT: A 227 LYS cc_start: 0.7691 (ttmt) cc_final: 0.7112 (tttt) REVERT: A 454 ASP cc_start: 0.8090 (m-30) cc_final: 0.7709 (m-30) REVERT: A 528 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7221 (mtmt) REVERT: A 529 GLU cc_start: 0.7567 (mp0) cc_final: 0.7152 (mp0) REVERT: A 717 ASP cc_start: 0.7759 (m-30) cc_final: 0.7422 (m-30) REVERT: A 883 ASP cc_start: 0.6760 (m-30) cc_final: 0.6372 (m-30) REVERT: A 1044 ASN cc_start: 0.8254 (OUTLIER) cc_final: 0.7995 (t0) REVERT: B 326 MET cc_start: 0.6791 (mpp) cc_final: 0.5897 (ptp) REVERT: B 342 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7036 (tm-30) REVERT: B 364 MET cc_start: 0.5280 (tmm) cc_final: 0.3223 (mtp) REVERT: B 367 ASP cc_start: 0.6027 (m-30) cc_final: 0.5421 (m-30) REVERT: B 420 LEU cc_start: 0.8562 (tp) cc_final: 0.8152 (tp) REVERT: B 468 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6557 (mm-30) REVERT: B 537 GLU cc_start: 0.6838 (tt0) cc_final: 0.6563 (tt0) REVERT: B 551 LYS cc_start: 0.8332 (tttt) cc_final: 0.7973 (tmmt) REVERT: B 582 MET cc_start: 0.5785 (tmm) cc_final: 0.5533 (mtp) outliers start: 14 outliers final: 2 residues processed: 185 average time/residue: 1.3578 time to fit residues: 268.3413 Evaluate side-chains 153 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 146 time to evaluate : 1.264 ------------------------------------------------------------------------------- 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 528 LYS Chi-restraints excluded: chain A residue 1044 ASN Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 468 GLU 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 50 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 A1048 HIS B 417 ASN B 527 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.176537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.142510 restraints weight = 11253.352| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.35 r_work: 0.3207 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10502 Z= 0.289 Angle : 0.656 9.729 14167 Z= 0.338 Chirality : 0.047 0.175 1531 Planarity : 0.005 0.046 1818 Dihedral : 5.128 20.664 1381 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.89 % Allowed : 9.11 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.23), residues: 1231 helix: -0.71 (0.21), residues: 566 sheet: -0.70 (0.38), residues: 160 loop : -1.27 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 597 HIS 0.010 0.002 HIS A 759 PHE 0.022 0.002 PHE A 667 TYR 0.023 0.002 TYR A 392 ARG 0.006 0.001 ARG A 537 *********************** 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 189 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 1.246 Fit side-chains revert: symmetry clash REVERT: A 138 ASP cc_start: 0.8833 (OUTLIER) cc_final: 0.8507 (m-30) REVERT: A 162 ARG cc_start: 0.7772 (mtm-85) cc_final: 0.7512 (mtm-85) REVERT: A 186 ASP cc_start: 0.8115 (p0) cc_final: 0.7652 (p0) REVERT: A 227 LYS cc_start: 0.7777 (ttmt) cc_final: 0.7239 (tttt) REVERT: A 454 ASP cc_start: 0.8133 (m-30) cc_final: 0.7754 (m-30) REVERT: A 883 ASP cc_start: 0.6873 (m-30) cc_final: 0.6524 (m-30) REVERT: B 326 MET cc_start: 0.6768 (mpp) cc_final: 0.6465 (mmt) REVERT: B 342 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7108 (tm-30) REVERT: B 364 MET cc_start: 0.5122 (tmm) cc_final: 0.3088 (mtp) REVERT: B 367 ASP cc_start: 0.6275 (m-30) cc_final: 0.5621 (m-30) REVERT: B 465 ARG cc_start: 0.7196 (ttp80) cc_final: 0.6822 (ptm-80) REVERT: B 469 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7248 (tt0) REVERT: B 478 GLN cc_start: 0.7970 (tp-100) cc_final: 0.7542 (tm-30) REVERT: B 495 GLU cc_start: 0.7298 (mt-10) cc_final: 0.7008 (mm-30) REVERT: B 537 GLU cc_start: 0.6816 (tt0) cc_final: 0.6559 (tt0) REVERT: B 551 LYS cc_start: 0.8292 (tttt) cc_final: 0.7933 (tmmt) outliers start: 33 outliers final: 12 residues processed: 177 average time/residue: 1.3447 time to fit residues: 254.3421 Evaluate side-chains 164 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 282 MET Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 382 ARG 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 957 THR Chi-restraints excluded: chain B residue 341 GLU 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 Chi-restraints excluded: chain B residue 525 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 40 optimal weight: 0.0980 chunk 112 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 93 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 96 optimal weight: 20.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 796 ASN A 936 HIS A1048 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.181585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.147077 restraints weight = 11103.454| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.11 r_work: 0.3321 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10502 Z= 0.133 Angle : 0.523 10.045 14167 Z= 0.267 Chirality : 0.041 0.161 1531 Planarity : 0.004 0.046 1818 Dihedral : 4.558 21.863 1381 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.01 % Allowed : 10.68 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.24), residues: 1231 helix: 0.25 (0.23), residues: 556 sheet: -0.50 (0.37), residues: 170 loop : -1.04 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 597 HIS 0.007 0.001 HIS A 213 PHE 0.014 0.001 PHE A 734 TYR 0.018 0.001 TYR A 392 ARG 0.002 0.000 ARG A 108 *********************** 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 190 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 1.152 Fit side-chains revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7316 (mtm180) cc_final: 0.7053 (mtp180) REVERT: A 162 ARG cc_start: 0.7773 (mtm-85) cc_final: 0.7561 (mtm-85) REVERT: A 186 ASP cc_start: 0.8014 (p0) cc_final: 0.7587 (p0) REVERT: A 227 LYS cc_start: 0.7784 (ttmt) cc_final: 0.7346 (tttt) REVERT: A 529 GLU cc_start: 0.7489 (mp0) cc_final: 0.7033 (mp0) REVERT: A 766 LEU cc_start: 0.8903 (mm) cc_final: 0.8564 (mm) REVERT: A 787 ASP cc_start: 0.7943 (t0) cc_final: 0.7675 (t0) REVERT: B 326 MET cc_start: 0.6704 (mpp) cc_final: 0.6458 (mmt) REVERT: B 342 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7133 (tm-30) REVERT: B 364 MET cc_start: 0.5016 (tmm) cc_final: 0.3076 (mtp) REVERT: B 367 ASP cc_start: 0.6201 (m-30) cc_final: 0.5567 (m-30) REVERT: B 495 GLU cc_start: 0.7297 (mt-10) cc_final: 0.7000 (mm-30) REVERT: B 525 MET cc_start: 0.6644 (OUTLIER) cc_final: 0.6238 (mpp) REVERT: B 537 GLU cc_start: 0.6707 (tt0) cc_final: 0.6411 (tt0) REVERT: B 551 LYS cc_start: 0.8184 (tttt) cc_final: 0.7867 (tmmt) outliers start: 23 outliers final: 5 residues processed: 178 average time/residue: 1.4105 time to fit residues: 268.7437 Evaluate side-chains 161 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 154 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 655 LYS Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 525 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 738 GLN ** A 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS B 415 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.174508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.130713 restraints weight = 11031.193| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.54 r_work: 0.3197 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 10502 Z= 0.407 Angle : 0.716 9.578 14167 Z= 0.368 Chirality : 0.051 0.173 1531 Planarity : 0.005 0.040 1818 Dihedral : 5.097 22.694 1381 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.50 % Allowed : 11.38 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.24), residues: 1231 helix: -0.17 (0.22), residues: 567 sheet: -0.32 (0.39), residues: 162 loop : -1.14 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 479 HIS 0.011 0.002 HIS A 759 PHE 0.019 0.003 PHE A 667 TYR 0.022 0.003 TYR A 56 ARG 0.006 0.001 ARG A 335 *********************** 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 196 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 1.205 Fit side-chains REVERT: A 85 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7843 (mp0) REVERT: A 162 ARG cc_start: 0.7752 (mtm-85) cc_final: 0.7515 (mtm-85) REVERT: A 186 ASP cc_start: 0.8092 (p0) cc_final: 0.7637 (p0) REVERT: A 227 LYS cc_start: 0.7760 (ttmt) cc_final: 0.7283 (tttt) REVERT: A 454 ASP cc_start: 0.8129 (m-30) cc_final: 0.7766 (m-30) REVERT: A 768 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7388 (mt-10) REVERT: A 883 ASP cc_start: 0.6936 (m-30) cc_final: 0.6649 (m-30) REVERT: B 326 MET cc_start: 0.6838 (mpp) cc_final: 0.6630 (mmt) REVERT: B 342 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7207 (tm-30) REVERT: B 364 MET cc_start: 0.5008 (tmm) cc_final: 0.3048 (mtp) REVERT: B 367 ASP cc_start: 0.6270 (m-30) cc_final: 0.5568 (m-30) REVERT: B 478 GLN cc_start: 0.7888 (tp-100) cc_final: 0.7397 (tp-100) REVERT: B 525 MET cc_start: 0.6667 (OUTLIER) cc_final: 0.6276 (mpp) REVERT: B 537 GLU cc_start: 0.6803 (tt0) cc_final: 0.6537 (tt0) REVERT: B 561 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8230 (mttt) outliers start: 40 outliers final: 16 residues processed: 182 average time/residue: 1.3152 time to fit residues: 256.9888 Evaluate side-chains 168 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 1.262 ------------------------------------------------------------------------------- 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 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 633 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 449 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 525 MET Chi-restraints excluded: chain B residue 561 LYS Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 109 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 738 GLN A 936 HIS A1048 HIS ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4009 r_free = 0.4009 target = 0.177107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.142726 restraints weight = 11131.918| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.38 r_work: 0.3255 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10502 Z= 0.217 Angle : 0.592 9.941 14167 Z= 0.304 Chirality : 0.045 0.165 1531 Planarity : 0.004 0.043 1818 Dihedral : 4.802 21.402 1381 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.36 % Allowed : 13.05 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.24), residues: 1231 helix: 0.17 (0.22), residues: 566 sheet: -0.12 (0.39), residues: 161 loop : -1.05 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 597 HIS 0.008 0.001 HIS A 213 PHE 0.018 0.002 PHE A 667 TYR 0.018 0.002 TYR A 392 ARG 0.002 0.000 ARG A 335 *********************** 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 181 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 1.209 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7917 (mp0) REVERT: A 115 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8307 (tmm160) REVERT: A 162 ARG cc_start: 0.7759 (mtm-85) cc_final: 0.7551 (mtm-85) REVERT: A 186 ASP cc_start: 0.8104 (p0) cc_final: 0.7658 (p0) REVERT: A 227 LYS cc_start: 0.7790 (ttmt) cc_final: 0.7323 (tttt) REVERT: A 738 GLN cc_start: 0.7972 (mm110) cc_final: 0.7712 (mm-40) REVERT: A 766 LEU cc_start: 0.8942 (mm) cc_final: 0.8583 (mm) REVERT: A 768 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7430 (mt-10) REVERT: A 787 ASP cc_start: 0.8059 (t0) cc_final: 0.7847 (t0) REVERT: B 326 MET cc_start: 0.6793 (mpp) cc_final: 0.6579 (mmt) REVERT: B 341 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7382 (mp0) REVERT: B 342 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7301 (tm-30) REVERT: B 364 MET cc_start: 0.5019 (tmm) cc_final: 0.3026 (mtp) REVERT: B 367 ASP cc_start: 0.6160 (m-30) cc_final: 0.5469 (m-30) REVERT: B 525 MET cc_start: 0.6675 (OUTLIER) cc_final: 0.6287 (mpp) REVERT: B 537 GLU cc_start: 0.6732 (tt0) cc_final: 0.6448 (tt0) outliers start: 27 outliers final: 15 residues processed: 171 average time/residue: 1.3941 time to fit residues: 254.3821 Evaluate side-chains 165 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 1.280 ------------------------------------------------------------------------------- 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 198 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 655 LYS 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 B residue 341 GLU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 525 MET Chi-restraints excluded: chain B residue 561 LYS Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 68 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4008 r_free = 0.4008 target = 0.176886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.142229 restraints weight = 11118.213| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.27 r_work: 0.3222 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10502 Z= 0.232 Angle : 0.600 9.920 14167 Z= 0.307 Chirality : 0.045 0.164 1531 Planarity : 0.004 0.037 1818 Dihedral : 4.740 21.316 1381 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.54 % Allowed : 13.22 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.24), residues: 1231 helix: 0.31 (0.22), residues: 566 sheet: 0.01 (0.40), residues: 156 loop : -1.03 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 479 HIS 0.007 0.001 HIS A 213 PHE 0.019 0.002 PHE A 667 TYR 0.018 0.002 TYR A 392 ARG 0.003 0.000 ARG A 335 *********************** 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 180 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 1.239 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7899 (mp0) REVERT: A 115 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8278 (tmm160) REVERT: A 155 ASP cc_start: 0.7914 (t0) cc_final: 0.7664 (m-30) REVERT: A 162 ARG cc_start: 0.7745 (mtm-85) cc_final: 0.7423 (mtm-85) REVERT: A 186 ASP cc_start: 0.8097 (p0) cc_final: 0.7653 (p0) REVERT: A 227 LYS cc_start: 0.7795 (ttmt) cc_final: 0.7341 (tttt) REVERT: A 738 GLN cc_start: 0.7865 (mm110) cc_final: 0.7644 (mm-40) REVERT: A 766 LEU cc_start: 0.8938 (mm) cc_final: 0.8576 (mm) REVERT: A 768 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7439 (mt-10) REVERT: B 326 MET cc_start: 0.6783 (mpp) cc_final: 0.5867 (ptp) REVERT: B 341 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7336 (mp0) REVERT: B 342 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7270 (tm-30) REVERT: B 364 MET cc_start: 0.4910 (tmm) cc_final: 0.2966 (mtp) REVERT: B 367 ASP cc_start: 0.6099 (m-30) cc_final: 0.5390 (m-30) REVERT: B 525 MET cc_start: 0.6652 (OUTLIER) cc_final: 0.6204 (mpp) outliers start: 29 outliers final: 14 residues processed: 167 average time/residue: 1.3383 time to fit residues: 239.5079 Evaluate side-chains 164 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 1.302 ------------------------------------------------------------------------------- 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 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 B residue 341 GLU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 525 MET Chi-restraints excluded: chain B residue 561 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 97 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 219 GLN A 826 ASN A 936 HIS A1048 HIS B 407 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 = 0.4016 r_free = 0.4016 target = 0.177761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.143298 restraints weight = 11130.719| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.50 r_work: 0.3237 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10502 Z= 0.206 Angle : 0.581 9.980 14167 Z= 0.296 Chirality : 0.044 0.162 1531 Planarity : 0.004 0.038 1818 Dihedral : 4.626 20.790 1381 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.45 % Allowed : 13.31 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.24), residues: 1231 helix: 0.50 (0.22), residues: 564 sheet: 0.13 (0.40), residues: 156 loop : -1.01 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 479 HIS 0.007 0.001 HIS A 213 PHE 0.017 0.002 PHE A 667 TYR 0.017 0.001 TYR A 392 ARG 0.003 0.000 ARG A 88 *********************** 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 177 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 1.241 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7885 (mp0) REVERT: A 115 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8275 (tmm160) REVERT: A 155 ASP cc_start: 0.7917 (t0) cc_final: 0.7683 (m-30) REVERT: A 162 ARG cc_start: 0.7736 (mtm-85) cc_final: 0.7427 (mtm-85) REVERT: A 186 ASP cc_start: 0.8077 (p0) cc_final: 0.7612 (p0) REVERT: A 227 LYS cc_start: 0.7807 (ttmt) cc_final: 0.7357 (tttt) REVERT: A 529 GLU cc_start: 0.7463 (mp0) cc_final: 0.6967 (mp0) REVERT: A 768 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7450 (mt-10) REVERT: B 326 MET cc_start: 0.6793 (mpp) cc_final: 0.5825 (ptp) REVERT: B 341 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: B 342 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7332 (tm-30) REVERT: B 364 MET cc_start: 0.4839 (tmm) cc_final: 0.2952 (mtp) REVERT: B 367 ASP cc_start: 0.6163 (m-30) cc_final: 0.5461 (m-30) REVERT: B 476 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7778 (mt-10) REVERT: B 525 MET cc_start: 0.6592 (OUTLIER) cc_final: 0.6131 (mpp) outliers start: 28 outliers final: 12 residues processed: 165 average time/residue: 1.4481 time to fit residues: 255.3772 Evaluate side-chains 163 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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 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 B residue 341 GLU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 122 optimal weight: 20.0000 chunk 106 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3996 r_free = 0.3996 target = 0.175840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.133982 restraints weight = 11122.463| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.70 r_work: 0.3241 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10502 Z= 0.340 Angle : 0.675 9.787 14167 Z= 0.346 Chirality : 0.049 0.165 1531 Planarity : 0.005 0.037 1818 Dihedral : 4.907 22.364 1381 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.54 % Allowed : 13.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.24), residues: 1231 helix: 0.17 (0.22), residues: 569 sheet: 0.10 (0.40), residues: 158 loop : -1.08 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 479 HIS 0.007 0.002 HIS A 213 PHE 0.018 0.002 PHE A 667 TYR 0.020 0.002 TYR A 392 ARG 0.005 0.001 ARG A 335 *********************** 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 172 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7874 (mp0) REVERT: A 162 ARG cc_start: 0.7728 (mtm-85) cc_final: 0.7394 (mtm-85) REVERT: A 186 ASP cc_start: 0.8098 (p0) cc_final: 0.7648 (p0) REVERT: A 227 LYS cc_start: 0.7777 (ttmt) cc_final: 0.7306 (tttt) REVERT: A 454 ASP cc_start: 0.8144 (m-30) cc_final: 0.7783 (m-30) REVERT: A 459 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8673 (mp) REVERT: A 766 LEU cc_start: 0.8942 (mm) cc_final: 0.8574 (mm) REVERT: A 768 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7405 (mt-10) REVERT: A 883 ASP cc_start: 0.6947 (m-30) cc_final: 0.6655 (m-30) REVERT: B 326 MET cc_start: 0.6735 (mpp) cc_final: 0.5844 (ptp) REVERT: B 342 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7340 (tm-30) REVERT: B 364 MET cc_start: 0.4900 (tmm) cc_final: 0.2952 (mtp) REVERT: B 367 ASP cc_start: 0.6128 (m-30) cc_final: 0.5418 (m-30) REVERT: B 476 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7750 (mt-10) REVERT: B 525 MET cc_start: 0.6697 (OUTLIER) cc_final: 0.6303 (mpp) outliers start: 29 outliers final: 18 residues processed: 161 average time/residue: 1.3819 time to fit residues: 238.2883 Evaluate side-chains 162 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 459 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 738 GLN 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 B residue 341 GLU 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 493 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 525 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 40 optimal weight: 0.0050 chunk 75 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 48 optimal weight: 0.0470 chunk 19 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 overall best weight: 1.9496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4019 r_free = 0.4019 target = 0.177976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.143896 restraints weight = 11059.952| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.09 r_work: 0.3258 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10502 Z= 0.196 Angle : 0.584 9.971 14167 Z= 0.299 Chirality : 0.044 0.162 1531 Planarity : 0.004 0.038 1818 Dihedral : 4.692 21.195 1381 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.93 % Allowed : 14.62 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.24), residues: 1231 helix: 0.50 (0.22), residues: 564 sheet: 0.23 (0.40), residues: 156 loop : -0.98 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 479 HIS 0.007 0.001 HIS A 213 PHE 0.016 0.002 PHE A 667 TYR 0.018 0.001 TYR A 392 ARG 0.002 0.000 ARG A1047 ********************** 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 167 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7884 (mp0) REVERT: A 115 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8266 (tmm160) REVERT: A 162 ARG cc_start: 0.7748 (mtm-85) cc_final: 0.7409 (mtm-85) REVERT: A 186 ASP cc_start: 0.8045 (p0) cc_final: 0.7603 (p0) REVERT: A 227 LYS cc_start: 0.7792 (ttmt) cc_final: 0.7351 (tttt) REVERT: A 529 GLU cc_start: 0.7360 (mp0) cc_final: 0.6873 (mp0) REVERT: A 768 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7356 (mt-10) REVERT: B 326 MET cc_start: 0.6797 (mpp) cc_final: 0.5869 (ptp) REVERT: B 341 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: B 342 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7300 (tm-30) REVERT: B 364 MET cc_start: 0.4935 (tmm) cc_final: 0.2999 (mtp) REVERT: B 367 ASP cc_start: 0.6139 (m-30) cc_final: 0.5610 (m-30) REVERT: B 476 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7885 (mt-10) REVERT: B 525 MET cc_start: 0.6710 (OUTLIER) cc_final: 0.6305 (mpp) outliers start: 22 outliers final: 10 residues processed: 157 average time/residue: 1.3801 time to fit residues: 231.7665 Evaluate side-chains 154 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 1.121 ------------------------------------------------------------------------------- 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 286 MET Chi-restraints excluded: chain A residue 633 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 B residue 341 GLU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 525 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 37 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 103 optimal weight: 0.4980 chunk 54 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 56 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4010 r_free = 0.4010 target = 0.177116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.135554 restraints weight = 11076.448| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.67 r_work: 0.3258 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2944 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= 0.242 Angle : 0.611 9.935 14167 Z= 0.312 Chirality : 0.045 0.161 1531 Planarity : 0.004 0.038 1818 Dihedral : 4.709 21.383 1381 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.84 % Allowed : 14.71 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.24), residues: 1231 helix: 0.49 (0.22), residues: 560 sheet: 0.28 (0.40), residues: 156 loop : -1.00 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 479 HIS 0.007 0.001 HIS A 213 PHE 0.018 0.002 PHE A 667 TYR 0.019 0.002 TYR A 392 ARG 0.004 0.000 ARG B 544 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8812.39 seconds wall clock time: 155 minutes 35.32 seconds (9335.32 seconds total)