Starting phenix.real_space_refine on Thu Aug 6 03:03:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s3t_54551/08_2026/9s3t_54551.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s3t_54551/08_2026/9s3t_54551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9s3t_54551/08_2026/9s3t_54551.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s3t_54551/08_2026/9s3t_54551.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9s3t_54551/08_2026/9s3t_54551.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s3t_54551/08_2026/9s3t_54551.map" } resolution = 3.48 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= 1.000 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: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 8028 2.51 5 N 2212 2.21 5 O 2428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 12748 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3187 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 385} Chain: "B" Number of atoms: 3187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3187 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 385} Chain: "C" Number of atoms: 3187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3187 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 385} Chain: "D" Number of atoms: 3187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3187 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 385} Time building chain proxies: 3.28, per 1000 atoms: 0.26 Number of scatterers: 12748 At special positions: 0 Unit cell: (73.216, 87.296, 230.912, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2428 8.00 N 2212 7.00 C 8028 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: 0.85 Conformation dependent library (CDL) restraints added in 513.6 milliseconds 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3048 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 26 sheets defined 21.5% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 322 through 337 removed outlier: 4.033A pdb=" N ALA A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N THR A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 488 Processing helix chain 'A' and resid 525 through 537 removed outlier: 3.612A pdb=" N HIS A 537 " --> pdb=" O THR A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 565 removed outlier: 3.789A pdb=" N ASN A 556 " --> pdb=" O ASP A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 588 Processing helix chain 'A' and resid 627 through 638 removed outlier: 3.531A pdb=" N VAL A 633 " --> pdb=" O VAL A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 648 Processing helix chain 'B' and resid 326 through 337 removed outlier: 3.584A pdb=" N PHE B 330 " --> pdb=" O MET B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 351 removed outlier: 3.795A pdb=" N MET B 351 " --> pdb=" O ARG B 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 348 through 351' Processing helix chain 'B' and resid 478 through 489 removed outlier: 3.559A pdb=" N ILE B 482 " --> pdb=" O GLY B 478 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY B 483 " --> pdb=" O PRO B 479 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 537 Processing helix chain 'B' and resid 550 through 565 removed outlier: 3.655A pdb=" N ASN B 556 " --> pdb=" O ASP B 552 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B 560 " --> pdb=" O ASN B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 588 Processing helix chain 'B' and resid 627 through 638 Processing helix chain 'B' and resid 638 through 648 Processing helix chain 'C' and resid 323 through 337 removed outlier: 3.981A pdb=" N ALA C 329 " --> pdb=" O SER C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 351 removed outlier: 4.171A pdb=" N MET C 351 " --> pdb=" O ARG C 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 348 through 351' Processing helix chain 'C' and resid 478 through 489 Processing helix chain 'C' and resid 525 through 538 Processing helix chain 'C' and resid 550 through 565 removed outlier: 3.526A pdb=" N ASN C 556 " --> pdb=" O ASP C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 589 Processing helix chain 'C' and resid 627 through 638 removed outlier: 3.598A pdb=" N VAL C 632 " --> pdb=" O PRO C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 648 Processing helix chain 'D' and resid 322 through 337 removed outlier: 3.682A pdb=" N LYS D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N THR D 332 " --> pdb=" O LYS D 328 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL D 333 " --> pdb=" O ALA D 329 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET D 336 " --> pdb=" O THR D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 489 removed outlier: 3.787A pdb=" N GLY D 483 " --> pdb=" O PRO D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 537 removed outlier: 3.535A pdb=" N HIS D 537 " --> pdb=" O THR D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 565 removed outlier: 3.606A pdb=" N ASN D 556 " --> pdb=" O ASP D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 588 Processing helix chain 'D' and resid 627 through 638 Processing helix chain 'D' and resid 638 through 648 Processing sheet with id=AA1, first strand: chain 'A' and resid 342 through 346 Processing sheet with id=AA2, first strand: chain 'A' and resid 392 through 393 removed outlier: 3.538A pdb=" N GLY A 375 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 547 removed outlier: 11.065A pdb=" N VAL A 501 " --> pdb=" O ASN A 543 " (cutoff:3.500A) removed outlier: 10.315A pdb=" N GLY A 545 " --> pdb=" O VAL A 501 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N VAL A 503 " --> pdb=" O GLY A 545 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N VAL A 547 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N SER A 505 " --> pdb=" O VAL A 547 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE A 568 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LEU A 624 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR A 570 " --> pdb=" O LEU A 624 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE A 621 " --> pdb=" O ALA A 610 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N PHE A 609 " --> pdb=" O HIS A 595 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 510 through 511 Processing sheet with id=AA5, first strand: chain 'A' and resid 656 through 661 removed outlier: 8.048A pdb=" N ALA A 689 " --> pdb=" O LYS A 658 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG A 660 " --> pdb=" O ALA A 689 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N SER A 691 " --> pdb=" O ARG A 660 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 342 through 346 Processing sheet with id=AA7, first strand: chain 'B' and resid 359 through 360 removed outlier: 4.005A pdb=" N LEU B 471 " --> pdb=" O VAL B 359 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 370 through 371 Processing sheet with id=AA9, first strand: chain 'B' and resid 409 through 411 Processing sheet with id=AB1, first strand: chain 'B' and resid 385 through 387 removed outlier: 7.308A pdb=" N GLU B 444 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ILE B 433 " --> pdb=" O GLU B 444 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 541 through 542 removed outlier: 6.246A pdb=" N VAL B 501 " --> pdb=" O ILE B 542 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE B 568 " --> pdb=" O PHE B 622 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU B 624 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR B 570 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N PHE B 609 " --> pdb=" O HIS B 595 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR B 611 " --> pdb=" O GLN B 593 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN B 593 " --> pdb=" O THR B 611 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 505 through 506 removed outlier: 5.733A pdb=" N SER B 505 " --> pdb=" O VAL B 547 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 510 through 511 Processing sheet with id=AB5, first strand: chain 'B' and resid 656 through 660 Processing sheet with id=AB6, first strand: chain 'B' and resid 672 through 676 removed outlier: 3.555A pdb=" N CYS B 676 " --> pdb=" O GLY B 708 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 342 through 346 Processing sheet with id=AB8, first strand: chain 'C' and resid 370 through 371 Processing sheet with id=AB9, first strand: chain 'C' and resid 423 through 426 removed outlier: 3.718A pdb=" N MET C 409 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N VAL C 408 " --> pdb=" O ASP C 386 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N PHE C 388 " --> pdb=" O VAL C 408 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ARG C 410 " --> pdb=" O PHE C 388 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ILE C 390 " --> pdb=" O ARG C 410 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 541 through 547 removed outlier: 10.537A pdb=" N VAL C 501 " --> pdb=" O ASN C 543 " (cutoff:3.500A) removed outlier: 9.633A pdb=" N GLY C 545 " --> pdb=" O VAL C 501 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL C 503 " --> pdb=" O GLY C 545 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL C 547 " --> pdb=" O VAL C 503 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N SER C 505 " --> pdb=" O VAL C 547 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE C 568 " --> pdb=" O PHE C 622 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N LEU C 624 " --> pdb=" O ILE C 568 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR C 570 " --> pdb=" O LEU C 624 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N THR C 611 " --> pdb=" O ILE C 594 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ILE C 594 " --> pdb=" O THR C 611 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 510 through 511 Processing sheet with id=AC3, first strand: chain 'C' and resid 656 through 660 Processing sheet with id=AC4, first strand: chain 'C' and resid 665 through 666 Processing sheet with id=AC5, first strand: chain 'D' and resid 343 through 346 Processing sheet with id=AC6, first strand: chain 'D' and resid 377 through 378 Processing sheet with id=AC7, first strand: chain 'D' and resid 541 through 547 removed outlier: 6.417A pdb=" N VAL D 501 " --> pdb=" O ILE D 542 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU D 544 " --> pdb=" O VAL D 501 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N VAL D 503 " --> pdb=" O LEU D 544 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE D 546 " --> pdb=" O VAL D 503 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N SER D 505 " --> pdb=" O ILE D 546 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA D 502 " --> pdb=" O ILE D 569 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N SER D 571 " --> pdb=" O ALA D 502 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N MET D 504 " --> pdb=" O SER D 571 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE D 568 " --> pdb=" O PHE D 622 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU D 624 " --> pdb=" O ILE D 568 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR D 570 " --> pdb=" O LEU D 624 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N PHE D 609 " --> pdb=" O HIS D 595 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN D 593 " --> pdb=" O THR D 611 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 657 through 661 removed outlier: 7.745A pdb=" N ALA D 689 " --> pdb=" O LYS D 658 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ARG D 660 " --> pdb=" O ALA D 689 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N SER D 691 " --> pdb=" O ARG D 660 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN D 690 " --> pdb=" O ILE D 677 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE D 677 " --> pdb=" O GLN D 690 " (cutoff:3.500A) 357 hydrogen bonds defined for protein. 978 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: 2.08 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4347 1.34 - 1.46: 2287 1.46 - 1.58: 6218 1.58 - 1.70: 0 1.70 - 1.82: 140 Bond restraints: 12992 Sorted by residual: bond pdb=" CA SER C 691 " pdb=" CB SER C 691 " ideal model delta sigma weight residual 1.529 1.473 0.056 1.64e-02 3.72e+03 1.15e+01 bond pdb=" CA SER B 705 " pdb=" CB SER B 705 " ideal model delta sigma weight residual 1.527 1.484 0.043 1.38e-02 5.25e+03 9.56e+00 bond pdb=" N MET B 696 " pdb=" CA MET B 696 " ideal model delta sigma weight residual 1.456 1.492 -0.037 1.23e-02 6.61e+03 8.93e+00 bond pdb=" N SER A 698 " pdb=" CA SER A 698 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.27e-02 6.20e+03 8.47e+00 bond pdb=" N MET D 703 " pdb=" CA MET D 703 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 7.97e+00 ... (remaining 12987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 17156 1.93 - 3.85: 466 3.85 - 5.78: 44 5.78 - 7.70: 7 7.70 - 9.63: 3 Bond angle restraints: 17676 Sorted by residual: angle pdb=" N THR D 692 " pdb=" CA THR D 692 " pdb=" C THR D 692 " ideal model delta sigma weight residual 111.28 102.28 9.00 1.09e+00 8.42e-01 6.82e+01 angle pdb=" N MET C 703 " pdb=" CA MET C 703 " pdb=" C MET C 703 " ideal model delta sigma weight residual 113.72 104.09 9.63 1.52e+00 4.33e-01 4.01e+01 angle pdb=" N MET C 696 " pdb=" CA MET C 696 " pdb=" C MET C 696 " ideal model delta sigma weight residual 112.92 105.13 7.79 1.23e+00 6.61e-01 4.01e+01 angle pdb=" N ASN A 694 " pdb=" CA ASN A 694 " pdb=" C ASN A 694 " ideal model delta sigma weight residual 111.28 105.27 6.01 1.09e+00 8.42e-01 3.04e+01 angle pdb=" N ASN D 694 " pdb=" CA ASN D 694 " pdb=" C ASN D 694 " ideal model delta sigma weight residual 111.28 105.74 5.54 1.09e+00 8.42e-01 2.59e+01 ... (remaining 17671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.72: 6801 16.72 - 33.45: 849 33.45 - 50.17: 236 50.17 - 66.90: 74 66.90 - 83.62: 24 Dihedral angle restraints: 7984 sinusoidal: 3240 harmonic: 4744 Sorted by residual: dihedral pdb=" CD ARG B 704 " pdb=" NE ARG B 704 " pdb=" CZ ARG B 704 " pdb=" NH1 ARG B 704 " ideal model delta sinusoidal sigma weight residual 0.00 41.17 -41.17 1 1.00e+01 1.00e-02 2.37e+01 dihedral pdb=" CA LYS D 602 " pdb=" C LYS D 602 " pdb=" N PRO D 603 " pdb=" CA PRO D 603 " ideal model delta harmonic sigma weight residual 180.00 -156.92 -23.08 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA GLY D 604 " pdb=" C GLY D 604 " pdb=" N LEU D 605 " pdb=" CA LEU D 605 " ideal model delta harmonic sigma weight residual -180.00 -157.02 -22.98 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 7981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1525 0.041 - 0.083: 298 0.083 - 0.124: 204 0.124 - 0.166: 24 0.166 - 0.207: 9 Chirality restraints: 2060 Sorted by residual: chirality pdb=" CA LEU A 700 " pdb=" N LEU A 700 " pdb=" C LEU A 700 " pdb=" CB LEU A 700 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA LEU C 700 " pdb=" N LEU C 700 " pdb=" C LEU C 700 " pdb=" CB LEU C 700 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA GLN D 690 " pdb=" N GLN D 690 " pdb=" C GLN D 690 " pdb=" CB GLN D 690 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.84e-01 ... (remaining 2057 not shown) Planarity restraints: 2336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 704 " 0.704 9.50e-02 1.11e+02 3.16e-01 6.07e+01 pdb=" NE ARG B 704 " -0.043 2.00e-02 2.50e+03 pdb=" CZ ARG B 704 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 704 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 704 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 699 " -0.498 9.50e-02 1.11e+02 2.23e-01 3.05e+01 pdb=" NE ARG A 699 " 0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A 699 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 699 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 699 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 699 " -0.370 9.50e-02 1.11e+02 1.66e-01 1.69e+01 pdb=" NE ARG D 699 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG D 699 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG D 699 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 699 " -0.012 2.00e-02 2.50e+03 ... (remaining 2333 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 170 2.68 - 3.23: 12785 3.23 - 3.79: 20029 3.79 - 4.34: 26517 4.34 - 4.90: 43197 Nonbonded interactions: 102698 Sorted by model distance: nonbonded pdb=" NH1 ARG B 699 " pdb=" CG MET B 701 " model vdw 2.125 3.520 nonbonded pdb=" O SER D 702 " pdb=" N ARG D 704 " model vdw 2.199 3.120 nonbonded pdb=" NE2 HIS A 674 " pdb=" O ASN A 694 " model vdw 2.362 3.120 nonbonded pdb=" O VAL C 470 " pdb=" NH2 ARG D 699 " model vdw 2.393 3.120 nonbonded pdb=" N HIS A 476 " pdb=" O MET B 703 " model vdw 2.400 3.120 ... (remaining 102693 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.940 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 11.560 Find NCS groups from input model: 0.180 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 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 : 0.004 0.056 12992 Z= 0.238 Angle : 0.725 9.630 17676 Z= 0.448 Chirality : 0.047 0.207 2060 Planarity : 0.010 0.316 2336 Dihedral : 17.011 83.622 4936 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.58 % Favored : 97.30 % Rotamer: Outliers : 7.39 % Allowed : 18.87 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.39 (0.19), residues: 1664 helix: -0.28 (0.27), residues: 312 sheet: -0.10 (0.29), residues: 298 loop : -0.22 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 699 TYR 0.009 0.001 TYR D 581 PHE 0.014 0.001 PHE C 596 TRP 0.006 0.001 TRP B 680 HIS 0.004 0.001 HIS C 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.24 (12992) covalent geometry : angle 0.72516 / 0.45 (17676) hydrogen bonds : bond 0.22735 / 14.64 ( 357) hydrogen bonds : angle 8.76248 / 6.16 ( 978) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 176 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 MET cc_start: 0.6963 (OUTLIER) cc_final: 0.6501 (mmm) REVERT: A 582 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.7818 (tp) REVERT: A 682 HIS cc_start: 0.8147 (t-90) cc_final: 0.7725 (t-90) REVERT: B 336 MET cc_start: 0.7453 (mmm) cc_final: 0.6783 (mmm) REVERT: B 387 ARG cc_start: 0.7105 (mmt-90) cc_final: 0.6237 (mmt-90) REVERT: B 444 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8156 (mp0) REVERT: B 562 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7662 (mp) REVERT: B 696 MET cc_start: 0.5471 (mmm) cc_final: 0.4364 (mmt) REVERT: B 701 MET cc_start: 0.8078 (mmm) cc_final: 0.7629 (mmm) REVERT: B 704 ARG cc_start: 0.4144 (OUTLIER) cc_final: 0.3107 (mtp85) REVERT: B 720 VAL cc_start: 0.7695 (OUTLIER) cc_final: 0.7463 (m) REVERT: C 710 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7924 (tp) REVERT: D 498 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.8184 (m-10) outliers start: 105 outliers final: 79 residues processed: 257 average time/residue: 0.1039 time to fit residues: 38.9768 Evaluate side-chains 257 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 171 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 498 PHE Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 647 GLN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 676 CYS Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain B residue 711 MET Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 498 PHE Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 686 LEU Chi-restraints excluded: chain C residue 699 ARG Chi-restraints excluded: chain C residue 701 MET Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 498 PHE Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 701 MET Chi-restraints excluded: chain D residue 733 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.0070 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 593 GLN D 476 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.147993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.125339 restraints weight = 27223.732| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 2.59 r_work: 0.3835 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.0722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12992 Z= 0.142 Angle : 0.574 7.709 17676 Z= 0.298 Chirality : 0.045 0.142 2060 Planarity : 0.004 0.039 2336 Dihedral : 8.574 68.630 1938 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 5.42 % Allowed : 22.18 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.17 (0.19), residues: 1664 helix: 0.38 (0.27), residues: 328 sheet: -0.19 (0.29), residues: 296 loop : -0.17 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 699 TYR 0.012 0.001 TYR D 581 PHE 0.012 0.001 PHE D 368 TRP 0.007 0.001 TRP D 688 HIS 0.003 0.001 HIS D 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (12992) covalent geometry : angle 0.57405 / 0.30 (17676) hydrogen bonds : bond 0.05381 / 3.59 ( 357) hydrogen bonds : angle 6.16963 / 4.32 ( 978) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 171 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 TYR cc_start: 0.7188 (OUTLIER) cc_final: 0.6498 (p90) REVERT: A 582 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.7890 (tp) REVERT: A 682 HIS cc_start: 0.8021 (t-90) cc_final: 0.7708 (t-90) REVERT: B 336 MET cc_start: 0.8033 (mmm) cc_final: 0.7321 (mmm) REVERT: B 444 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8204 (mp0) REVERT: B 481 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: B 696 MET cc_start: 0.3264 (mmm) cc_final: 0.2284 (mmt) REVERT: C 491 THR cc_start: 0.7753 (OUTLIER) cc_final: 0.7492 (p) REVERT: C 590 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8463 (tp) REVERT: C 699 ARG cc_start: 0.1890 (mmp-170) cc_final: 0.1355 (mmm160) REVERT: D 498 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.8141 (m-10) REVERT: D 576 MET cc_start: -0.0283 (mtp) cc_final: -0.0616 (mtp) REVERT: D 701 MET cc_start: 0.6620 (OUTLIER) cc_final: 0.6182 (pmm) REVERT: D 711 MET cc_start: 0.6261 (mmp) cc_final: 0.5639 (mmm) outliers start: 77 outliers final: 50 residues processed: 236 average time/residue: 0.0933 time to fit residues: 32.7573 Evaluate side-chains 226 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 169 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 376 TYR Chi-restraints excluded: chain A residue 498 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 647 GLN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 676 CYS Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 481 GLU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 662 SER Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 498 PHE Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 733 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 498 PHE Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain D residue 701 MET Chi-restraints excluded: chain D residue 733 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 55 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 109 optimal weight: 0.4980 chunk 43 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 647 GLN C 695 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.149235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.126562 restraints weight = 27515.556| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.61 r_work: 0.3848 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3721 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12992 Z= 0.114 Angle : 0.541 7.595 17676 Z= 0.276 Chirality : 0.045 0.139 2060 Planarity : 0.004 0.040 2336 Dihedral : 6.831 66.741 1863 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 5.63 % Allowed : 22.54 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.20), residues: 1664 helix: 0.78 (0.28), residues: 326 sheet: -0.23 (0.29), residues: 295 loop : -0.12 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 452 TYR 0.014 0.001 TYR D 581 PHE 0.014 0.001 PHE C 596 TRP 0.006 0.001 TRP D 688 HIS 0.003 0.001 HIS A 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (12992) covalent geometry : angle 0.54058 / 0.28 (17676) hydrogen bonds : bond 0.04362 / 2.91 ( 357) hydrogen bonds : angle 5.61339 / 3.92 ( 978) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 174 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 TYR cc_start: 0.7079 (OUTLIER) cc_final: 0.6456 (p90) REVERT: A 582 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7876 (tp) REVERT: A 682 HIS cc_start: 0.7997 (t-90) cc_final: 0.7771 (t-90) REVERT: A 711 MET cc_start: 0.6344 (ppp) cc_final: 0.5897 (ppp) REVERT: A 735 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.6636 (mtt90) REVERT: B 336 MET cc_start: 0.7925 (mmm) cc_final: 0.7298 (mmm) REVERT: B 444 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8222 (mp0) REVERT: B 481 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: B 696 MET cc_start: 0.3460 (mmm) cc_final: 0.2382 (mmt) REVERT: C 436 SER cc_start: 0.3393 (OUTLIER) cc_final: 0.3079 (p) REVERT: C 491 THR cc_start: 0.7754 (OUTLIER) cc_final: 0.7493 (p) REVERT: C 566 ASP cc_start: 0.6415 (t0) cc_final: 0.5690 (m-30) REVERT: D 498 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.8138 (m-10) REVERT: D 576 MET cc_start: -0.0238 (mtp) cc_final: -0.0464 (mtp) REVERT: D 711 MET cc_start: 0.6480 (mmp) cc_final: 0.5925 (mmm) outliers start: 80 outliers final: 53 residues processed: 236 average time/residue: 0.0890 time to fit residues: 31.1362 Evaluate side-chains 228 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 168 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 376 TYR Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 498 PHE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 647 GLN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 481 GLU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 662 SER Chi-restraints excluded: chain B residue 676 CYS Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 498 PHE Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 721 GLU Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 498 PHE Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain D residue 662 SER Chi-restraints excluded: chain D residue 731 MET Chi-restraints excluded: chain D residue 733 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 25 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 137 optimal weight: 0.3980 chunk 134 optimal weight: 7.9990 chunk 53 optimal weight: 0.2980 chunk 156 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 157 optimal weight: 7.9990 chunk 43 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.149982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.127448 restraints weight = 27406.739| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 2.60 r_work: 0.3863 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12992 Z= 0.106 Angle : 0.527 6.836 17676 Z= 0.267 Chirality : 0.044 0.139 2060 Planarity : 0.004 0.036 2336 Dihedral : 6.344 66.385 1842 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 5.63 % Allowed : 23.52 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.14 (0.20), residues: 1664 helix: 1.03 (0.28), residues: 328 sheet: -0.09 (0.30), residues: 275 loop : -0.09 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 458 TYR 0.015 0.001 TYR C 673 PHE 0.012 0.001 PHE C 596 TRP 0.005 0.001 TRP D 688 HIS 0.005 0.001 HIS D 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (12992) covalent geometry : angle 0.52737 / 0.27 (17676) hydrogen bonds : bond 0.03900 / 2.61 ( 357) hydrogen bonds : angle 5.35540 / 3.72 ( 978) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 175 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 TYR cc_start: 0.7229 (OUTLIER) cc_final: 0.6579 (p90) REVERT: A 582 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7802 (tp) REVERT: A 682 HIS cc_start: 0.8056 (t-90) cc_final: 0.7837 (t-90) REVERT: A 711 MET cc_start: 0.6571 (ppp) cc_final: 0.6155 (ppp) REVERT: A 735 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.6599 (mtt90) REVERT: B 336 MET cc_start: 0.7863 (mmm) cc_final: 0.7297 (mmm) REVERT: B 481 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: B 696 MET cc_start: 0.3466 (mmm) cc_final: 0.2374 (mmt) REVERT: B 711 MET cc_start: 0.7122 (mpp) cc_final: 0.6910 (mpp) REVERT: C 436 SER cc_start: 0.3443 (OUTLIER) cc_final: 0.3122 (p) REVERT: C 566 ASP cc_start: 0.6527 (t0) cc_final: 0.5923 (m-30) REVERT: D 498 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.8126 (m-10) REVERT: D 576 MET cc_start: -0.0230 (mtp) cc_final: -0.0431 (mtp) REVERT: D 711 MET cc_start: 0.6540 (mmp) cc_final: 0.6026 (mmm) outliers start: 80 outliers final: 57 residues processed: 239 average time/residue: 0.0851 time to fit residues: 30.3941 Evaluate side-chains 227 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 164 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 376 TYR Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 498 PHE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 647 GLN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 481 GLU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 662 SER Chi-restraints excluded: chain B residue 676 CYS Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 498 PHE Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 721 GLU Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 498 PHE Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 701 MET Chi-restraints excluded: chain D residue 731 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 87 optimal weight: 2.9990 chunk 34 optimal weight: 0.0770 chunk 107 optimal weight: 0.4980 chunk 70 optimal weight: 0.0040 chunk 43 optimal weight: 0.9990 chunk 160 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 146 optimal weight: 0.7980 overall best weight: 0.4752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.150803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.128142 restraints weight = 27398.231| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.64 r_work: 0.3872 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3743 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12992 Z= 0.098 Angle : 0.525 7.781 17676 Z= 0.265 Chirality : 0.044 0.142 2060 Planarity : 0.004 0.037 2336 Dihedral : 6.135 66.460 1833 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 6.13 % Allowed : 23.03 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.20 (0.20), residues: 1664 helix: 1.25 (0.28), residues: 325 sheet: -0.10 (0.29), residues: 281 loop : -0.09 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 699 TYR 0.012 0.001 TYR D 581 PHE 0.011 0.001 PHE C 596 TRP 0.008 0.001 TRP B 680 HIS 0.003 0.001 HIS A 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (12992) covalent geometry : angle 0.52466 / 0.26 (17676) hydrogen bonds : bond 0.03636 / 2.44 ( 357) hydrogen bonds : angle 5.17385 / 3.60 ( 978) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 173 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 TYR cc_start: 0.7149 (OUTLIER) cc_final: 0.6510 (p90) REVERT: A 582 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7776 (tp) REVERT: A 682 HIS cc_start: 0.8101 (t-90) cc_final: 0.7865 (t-90) REVERT: A 711 MET cc_start: 0.6584 (ppp) cc_final: 0.6277 (ppp) REVERT: A 735 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.6547 (mtt90) REVERT: B 336 MET cc_start: 0.7763 (mmm) cc_final: 0.7185 (mmm) REVERT: B 481 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: B 696 MET cc_start: 0.3343 (mmm) cc_final: 0.2289 (mmt) REVERT: C 336 MET cc_start: 0.4161 (mmm) cc_final: 0.3893 (mmm) REVERT: C 436 SER cc_start: 0.3472 (OUTLIER) cc_final: 0.3129 (p) REVERT: C 566 ASP cc_start: 0.6641 (t0) cc_final: 0.6311 (m-30) REVERT: D 498 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.8132 (m-10) REVERT: D 711 MET cc_start: 0.6571 (mmp) cc_final: 0.6024 (mmm) outliers start: 87 outliers final: 61 residues processed: 240 average time/residue: 0.1008 time to fit residues: 35.7869 Evaluate side-chains 234 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 167 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 376 TYR Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 498 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 647 GLN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 481 GLU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 662 SER Chi-restraints excluded: chain B residue 676 CYS Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 498 PHE Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 721 GLU Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 498 PHE Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 701 MET Chi-restraints excluded: chain D residue 731 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 154 optimal weight: 0.9990 chunk 81 optimal weight: 0.0670 chunk 123 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 496 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.144851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.122102 restraints weight = 27524.663| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.59 r_work: 0.3779 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 12992 Z= 0.248 Angle : 0.668 7.600 17676 Z= 0.344 Chirality : 0.049 0.167 2060 Planarity : 0.005 0.042 2336 Dihedral : 6.766 59.186 1831 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 5.77 % Allowed : 24.15 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.57 (0.19), residues: 1664 helix: 0.18 (0.27), residues: 322 sheet: -0.65 (0.28), residues: 297 loop : -0.42 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 523 TYR 0.018 0.002 TYR D 581 PHE 0.013 0.002 PHE D 330 TRP 0.012 0.002 TRP C 680 HIS 0.009 0.001 HIS D 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.25 (12992) covalent geometry : angle 0.66805 / 0.34 (17676) hydrogen bonds : bond 0.04707 / 3.16 ( 357) hydrogen bonds : angle 5.77092 / 3.98 ( 978) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 173 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 MET cc_start: 0.7734 (mmm) cc_final: 0.7367 (mmp) REVERT: A 376 TYR cc_start: 0.7241 (OUTLIER) cc_final: 0.6565 (p90) REVERT: A 682 HIS cc_start: 0.8108 (t-90) cc_final: 0.7843 (t-90) REVERT: A 711 MET cc_start: 0.6656 (ppp) cc_final: 0.6234 (ppp) REVERT: A 735 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.6967 (mtt90) REVERT: B 336 MET cc_start: 0.8151 (mmm) cc_final: 0.7526 (mmm) REVERT: B 696 MET cc_start: 0.3486 (mmm) cc_final: 0.2639 (mmt) REVERT: C 436 SER cc_start: 0.4298 (OUTLIER) cc_final: 0.3964 (p) REVERT: C 566 ASP cc_start: 0.6961 (t0) cc_final: 0.5909 (m-30) REVERT: D 498 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.8267 (m-10) REVERT: D 586 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7582 (mp) REVERT: D 711 MET cc_start: 0.6530 (mmp) cc_final: 0.5897 (mmm) outliers start: 82 outliers final: 63 residues processed: 238 average time/residue: 0.0888 time to fit residues: 31.5919 Evaluate side-chains 235 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 167 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 376 TYR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 498 PHE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 647 GLN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 662 SER Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 676 CYS Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 711 MET Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 498 PHE Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 733 ILE Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 498 PHE Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 662 SER Chi-restraints excluded: chain D residue 731 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 114 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 chunk 154 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.148156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.125360 restraints weight = 27412.255| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.67 r_work: 0.3828 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12992 Z= 0.117 Angle : 0.563 8.802 17676 Z= 0.286 Chirality : 0.045 0.161 2060 Planarity : 0.004 0.039 2336 Dihedral : 6.400 61.982 1827 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 5.35 % Allowed : 25.14 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.19 (0.20), residues: 1664 helix: 0.75 (0.28), residues: 325 sheet: -0.40 (0.29), residues: 278 loop : -0.27 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 699 TYR 0.013 0.001 TYR D 581 PHE 0.014 0.001 PHE D 330 TRP 0.010 0.001 TRP B 680 HIS 0.010 0.001 HIS D 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (12992) covalent geometry : angle 0.56330 / 0.29 (17676) hydrogen bonds : bond 0.03751 / 2.51 ( 357) hydrogen bonds : angle 5.35830 / 3.69 ( 978) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 167 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 MET cc_start: 0.7429 (mmm) cc_final: 0.6999 (mmp) REVERT: A 376 TYR cc_start: 0.6989 (OUTLIER) cc_final: 0.6343 (p90) REVERT: A 582 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7864 (tp) REVERT: A 711 MET cc_start: 0.6389 (ppp) cc_final: 0.6062 (ppp) REVERT: A 735 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.6729 (mtt90) REVERT: B 336 MET cc_start: 0.7600 (mmm) cc_final: 0.7161 (mmm) REVERT: B 696 MET cc_start: 0.3460 (mmm) cc_final: 0.2515 (mmt) REVERT: C 436 SER cc_start: 0.3600 (OUTLIER) cc_final: 0.3319 (p) REVERT: C 566 ASP cc_start: 0.6823 (t0) cc_final: 0.6243 (m-30) REVERT: D 326 MET cc_start: 0.5525 (ppp) cc_final: 0.5017 (ppp) REVERT: D 498 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.8147 (m-10) REVERT: D 711 MET cc_start: 0.6522 (mmp) cc_final: 0.6019 (mmm) outliers start: 76 outliers final: 58 residues processed: 226 average time/residue: 0.0865 time to fit residues: 29.2920 Evaluate side-chains 226 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 163 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 376 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 498 PHE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 647 GLN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 676 CYS Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 662 SER Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 676 CYS Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 498 PHE Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 498 PHE Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain D residue 731 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 102 optimal weight: 0.9980 chunk 157 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 125 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 chunk 37 optimal weight: 10.0000 chunk 109 optimal weight: 0.0770 chunk 72 optimal weight: 0.9990 chunk 163 optimal weight: 5.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.149167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.126568 restraints weight = 27177.911| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.64 r_work: 0.3846 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3717 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12992 Z= 0.110 Angle : 0.546 7.034 17676 Z= 0.277 Chirality : 0.045 0.179 2060 Planarity : 0.004 0.064 2336 Dihedral : 6.194 62.457 1825 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 5.00 % Allowed : 25.85 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.06 (0.20), residues: 1664 helix: 1.01 (0.28), residues: 325 sheet: -0.30 (0.29), residues: 278 loop : -0.24 (0.19), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 699 TYR 0.012 0.001 TYR C 673 PHE 0.014 0.001 PHE D 330 TRP 0.011 0.001 TRP B 680 HIS 0.010 0.001 HIS D 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (12992) covalent geometry : angle 0.54564 / 0.28 (17676) hydrogen bonds : bond 0.03536 / 2.38 ( 357) hydrogen bonds : angle 5.16549 / 3.56 ( 978) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 168 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 MET cc_start: 0.7602 (mmm) cc_final: 0.7181 (mmp) REVERT: A 376 TYR cc_start: 0.7200 (OUTLIER) cc_final: 0.6560 (p90) REVERT: A 582 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7978 (tp) REVERT: A 711 MET cc_start: 0.6553 (ppp) cc_final: 0.6193 (ppp) REVERT: A 735 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.6749 (mtt90) REVERT: B 336 MET cc_start: 0.7745 (mmm) cc_final: 0.7358 (mmm) REVERT: B 696 MET cc_start: 0.3374 (mmm) cc_final: 0.2421 (mmt) REVERT: C 436 SER cc_start: 0.3947 (OUTLIER) cc_final: 0.3625 (p) REVERT: C 566 ASP cc_start: 0.6718 (t0) cc_final: 0.6309 (m-30) REVERT: C 576 MET cc_start: -0.1071 (tpt) cc_final: -0.2384 (ttm) REVERT: D 326 MET cc_start: 0.6276 (ppp) cc_final: 0.5860 (ppp) REVERT: D 498 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8153 (m-10) REVERT: D 711 MET cc_start: 0.6478 (mmp) cc_final: 0.6227 (mmm) outliers start: 71 outliers final: 58 residues processed: 226 average time/residue: 0.0852 time to fit residues: 28.9764 Evaluate side-chains 227 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 164 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 376 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 498 PHE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 647 GLN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 676 CYS Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 662 SER Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 676 CYS Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 398 GLN Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 498 PHE Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 498 PHE Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 731 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 45 optimal weight: 0.0770 chunk 147 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.0770 chunk 155 optimal weight: 0.0770 chunk 141 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 110 optimal weight: 0.0060 overall best weight: 0.1470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 357 GLN A 681 HIS ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.162003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.139855 restraints weight = 27282.150| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 2.62 r_work: 0.3896 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3769 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12992 Z= 0.094 Angle : 0.538 7.471 17676 Z= 0.268 Chirality : 0.044 0.172 2060 Planarity : 0.004 0.052 2336 Dihedral : 5.779 63.052 1823 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.87 % Allowed : 26.41 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.18 (0.20), residues: 1664 helix: 1.36 (0.28), residues: 324 sheet: -0.10 (0.29), residues: 286 loop : -0.16 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 699 TYR 0.013 0.001 TYR C 673 PHE 0.014 0.001 PHE D 330 TRP 0.013 0.001 TRP B 680 HIS 0.004 0.001 HIS C 674 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.09 (12992) covalent geometry : angle 0.53829 / 0.27 (17676) hydrogen bonds : bond 0.03191 / 2.14 ( 357) hydrogen bonds : angle 4.93227 / 3.41 ( 978) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 179 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 MET cc_start: 0.7641 (mmm) cc_final: 0.7272 (mmp) REVERT: A 582 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7852 (tp) REVERT: A 711 MET cc_start: 0.6646 (ppp) cc_final: 0.6362 (ppp) REVERT: A 735 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.6632 (mtt90) REVERT: B 336 MET cc_start: 0.7642 (mmm) cc_final: 0.7335 (mmm) REVERT: B 511 LEU cc_start: 0.6090 (OUTLIER) cc_final: 0.5727 (tt) REVERT: B 696 MET cc_start: 0.3671 (mmm) cc_final: 0.2347 (mmt) REVERT: C 436 SER cc_start: 0.3565 (OUTLIER) cc_final: 0.3185 (p) REVERT: C 566 ASP cc_start: 0.7082 (t0) cc_final: 0.6828 (m-30) REVERT: C 576 MET cc_start: -0.1090 (tpt) cc_final: -0.2373 (ttm) REVERT: C 682 HIS cc_start: 0.7002 (t-90) cc_final: 0.6483 (m-70) REVERT: D 326 MET cc_start: 0.6718 (ppp) cc_final: 0.6282 (ppp) REVERT: D 498 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.8123 (m-10) outliers start: 55 outliers final: 40 residues processed: 226 average time/residue: 0.1002 time to fit residues: 33.7359 Evaluate side-chains 216 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 171 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 498 PHE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 676 CYS Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 676 CYS Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain C residue 398 GLN Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 498 PHE Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 498 PHE Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 731 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 135 optimal weight: 0.1980 chunk 85 optimal weight: 2.9990 chunk 84 optimal weight: 0.0010 chunk 120 optimal weight: 0.1980 chunk 76 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.161825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.139437 restraints weight = 27289.546| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 2.70 r_work: 0.3885 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12992 Z= 0.098 Angle : 0.541 8.235 17676 Z= 0.271 Chirality : 0.044 0.166 2060 Planarity : 0.004 0.049 2336 Dihedral : 5.445 54.968 1818 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.80 % Allowed : 26.62 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.19 (0.20), residues: 1664 helix: 1.31 (0.28), residues: 321 sheet: -0.03 (0.29), residues: 285 loop : -0.14 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 458 TYR 0.020 0.001 TYR C 673 PHE 0.014 0.001 PHE D 330 TRP 0.013 0.001 TRP B 680 HIS 0.006 0.001 HIS D 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (12992) covalent geometry : angle 0.54145 / 0.27 (17676) hydrogen bonds : bond 0.03216 / 2.16 ( 357) hydrogen bonds : angle 4.91468 / 3.40 ( 978) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 171 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 MET cc_start: 0.7481 (mmm) cc_final: 0.7097 (mmp) REVERT: A 582 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7838 (tp) REVERT: A 711 MET cc_start: 0.6497 (ppp) cc_final: 0.6116 (ppp) REVERT: A 735 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.6353 (mtt90) REVERT: B 336 MET cc_start: 0.7372 (mmm) cc_final: 0.7068 (mmm) REVERT: B 481 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: B 511 LEU cc_start: 0.6153 (OUTLIER) cc_final: 0.5762 (tt) REVERT: B 579 LYS cc_start: 0.7295 (tptp) cc_final: 0.6900 (tptp) REVERT: B 696 MET cc_start: 0.3787 (mmm) cc_final: 0.2462 (mmt) REVERT: B 711 MET cc_start: 0.6971 (mpp) cc_final: 0.6703 (mpp) REVERT: C 436 SER cc_start: 0.3129 (OUTLIER) cc_final: 0.2780 (p) REVERT: C 566 ASP cc_start: 0.6526 (t0) cc_final: 0.6180 (m-30) REVERT: C 576 MET cc_start: -0.1209 (tpt) cc_final: -0.2404 (ttm) REVERT: C 682 HIS cc_start: 0.6812 (t-90) cc_final: 0.6357 (m-70) REVERT: D 326 MET cc_start: 0.6529 (ppp) cc_final: 0.6102 (ppp) REVERT: D 498 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.8159 (m-10) REVERT: D 696 MET cc_start: 0.2388 (mmm) cc_final: 0.1441 (mmm) outliers start: 54 outliers final: 45 residues processed: 218 average time/residue: 0.0926 time to fit residues: 30.3993 Evaluate side-chains 221 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 170 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 498 PHE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 676 CYS Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 481 GLU Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 676 CYS Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain C residue 398 GLN Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 498 PHE Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 498 PHE Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 731 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 104 optimal weight: 2.9990 chunk 133 optimal weight: 0.0670 chunk 88 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 chunk 113 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.161153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.138290 restraints weight = 27079.054| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 2.76 r_work: 0.3872 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3746 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12992 Z= 0.106 Angle : 0.547 7.226 17676 Z= 0.274 Chirality : 0.045 0.155 2060 Planarity : 0.004 0.049 2336 Dihedral : 5.400 55.678 1818 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.73 % Allowed : 26.97 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.16 (0.20), residues: 1664 helix: 1.24 (0.28), residues: 321 sheet: -0.03 (0.29), residues: 285 loop : -0.16 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 410 TYR 0.023 0.001 TYR C 673 PHE 0.013 0.001 PHE D 330 TRP 0.012 0.001 TRP B 680 HIS 0.006 0.001 HIS D 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (12992) covalent geometry : angle 0.54672 / 0.27 (17676) hydrogen bonds : bond 0.03305 / 2.21 ( 357) hydrogen bonds : angle 4.91899 / 3.40 ( 978) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2684.81 seconds wall clock time: 46 minutes 45.76 seconds (2805.76 seconds total)