Starting phenix.real_space_refine on Fri Aug 22 19:04:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b4y_44191/08_2025/9b4y_44191.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b4y_44191/08_2025/9b4y_44191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b4y_44191/08_2025/9b4y_44191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b4y_44191/08_2025/9b4y_44191.map" model { file = "/net/cci-nas-00/data/ceres_data/9b4y_44191/08_2025/9b4y_44191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b4y_44191/08_2025/9b4y_44191.cif" } resolution = 3.74 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= 0.002 sd= 0.018 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 49 5.16 5 C 4510 2.51 5 N 1228 2.21 5 O 1391 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7178 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 876, 6810 Classifications: {'peptide': 876} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 838} Chain: "B" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 368 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Time building chain proxies: 1.61, per 1000 atoms: 0.22 Number of scatterers: 7178 At special positions: 0 Unit cell: (100.28, 109, 84.584, 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 49 16.00 O 1391 8.00 N 1228 7.00 C 4510 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: 0.42 Conformation dependent library (CDL) restraints added in 261.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1760 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 0 sheets defined 84.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 removed outlier: 3.551A pdb=" N ILE A 6 " --> pdb=" O GLU A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 32 Processing helix chain 'A' and resid 32 through 46 removed outlier: 3.607A pdb=" N ASN A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 66 Processing helix chain 'A' and resid 69 through 82 Processing helix chain 'A' and resid 84 through 99 removed outlier: 3.877A pdb=" N LEU A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 124 removed outlier: 4.168A pdb=" N GLN A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N CYS A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) Proline residue: A 122 - end of helix Processing helix chain 'A' and resid 128 through 139 Processing helix chain 'A' and resid 143 through 161 Processing helix chain 'A' and resid 162 through 168 removed outlier: 5.216A pdb=" N ASP A 168 " --> pdb=" O GLN A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 180 removed outlier: 3.641A pdb=" N ILE A 173 " --> pdb=" O LYS A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 201 removed outlier: 3.868A pdb=" N LYS A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 201 " --> pdb=" O ALA A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 211 through 226 removed outlier: 3.519A pdb=" N VAL A 221 " --> pdb=" O PHE A 217 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 248 Processing helix chain 'A' and resid 249 through 256 removed outlier: 3.659A pdb=" N MET A 252 " --> pdb=" O TYR A 249 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N GLU A 253 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N THR A 254 " --> pdb=" O TYR A 251 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR A 255 " --> pdb=" O MET A 252 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 249 through 256' Processing helix chain 'A' and resid 259 through 269 removed outlier: 4.266A pdb=" N ILE A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 304 removed outlier: 3.639A pdb=" N ALA A 276 " --> pdb=" O ILE A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 330 Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 343 through 360 removed outlier: 3.610A pdb=" N GLY A 349 " --> pdb=" O CYS A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 375 Proline residue: A 369 - end of helix Processing helix chain 'A' and resid 379 through 393 removed outlier: 3.697A pdb=" N ARG A 383 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 417 removed outlier: 3.563A pdb=" N LEU A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Proline residue: A 404 - end of helix removed outlier: 3.666A pdb=" N GLN A 408 " --> pdb=" O PRO A 404 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 3.603A pdb=" N GLU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 439 removed outlier: 3.538A pdb=" N TRP A 430 " --> pdb=" O ASP A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.544A pdb=" N ILE A 444 " --> pdb=" O PRO A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 460 removed outlier: 4.259A pdb=" N ALA A 450 " --> pdb=" O ASP A 446 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 463 through 489 removed outlier: 4.030A pdb=" N ASN A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TRP A 472 " --> pdb=" O SER A 468 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA A 473 " --> pdb=" O ASN A 469 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 488 " --> pdb=" O ALA A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 514 removed outlier: 4.467A pdb=" N GLU A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LEU A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 522 No H-bonds generated for 'chain 'A' and resid 520 through 522' Processing helix chain 'A' and resid 523 through 538 Processing helix chain 'A' and resid 540 through 542 No H-bonds generated for 'chain 'A' and resid 540 through 542' Processing helix chain 'A' and resid 543 through 563 removed outlier: 3.704A pdb=" N GLN A 563 " --> pdb=" O GLN A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 593 Processing helix chain 'A' and resid 596 through 618 removed outlier: 3.652A pdb=" N LEU A 601 " --> pdb=" O HIS A 597 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLN A 602 " --> pdb=" O GLN A 598 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE A 603 " --> pdb=" O ASP A 599 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL A 606 " --> pdb=" O GLN A 602 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 618 " --> pdb=" O MET A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 640 removed outlier: 4.298A pdb=" N GLN A 625 " --> pdb=" O SER A 621 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 626 " --> pdb=" O GLY A 622 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP A 627 " --> pdb=" O GLY A 623 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N MET A 630 " --> pdb=" O GLU A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 646 removed outlier: 3.933A pdb=" N LYS A 645 " --> pdb=" O GLU A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 659 removed outlier: 3.510A pdb=" N LEU A 658 " --> pdb=" O LEU A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 682 removed outlier: 4.047A pdb=" N CYS A 667 " --> pdb=" O GLU A 663 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 672 " --> pdb=" O LEU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 702 removed outlier: 4.193A pdb=" N ASP A 690 " --> pdb=" O ILE A 686 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N GLU A 691 " --> pdb=" O PRO A 687 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 692 " --> pdb=" O PHE A 688 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 725 removed outlier: 4.307A pdb=" N GLN A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE A 717 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY A 718 " --> pdb=" O LEU A 714 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP A 719 " --> pdb=" O SER A 715 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 720 " --> pdb=" O VAL A 716 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA A 721 " --> pdb=" O PHE A 717 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 722 " --> pdb=" O GLY A 718 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 723 " --> pdb=" O ASP A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 745 removed outlier: 4.506A pdb=" N GLU A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N VAL A 734 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN A 737 " --> pdb=" O GLU A 733 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 745 " --> pdb=" O GLN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 778 removed outlier: 3.756A pdb=" N ASN A 759 " --> pdb=" O VAL A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 789 Processing helix chain 'A' and resid 793 through 807 Processing helix chain 'A' and resid 811 through 829 removed outlier: 3.542A pdb=" N CYS A 817 " --> pdb=" O GLY A 813 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 819 " --> pdb=" O VAL A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 839 removed outlier: 4.007A pdb=" N LYS A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU A 836 " --> pdb=" O ASP A 832 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 839 " --> pdb=" O LYS A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 853 removed outlier: 3.679A pdb=" N GLY A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG A 852 " --> pdb=" O THR A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 874 removed outlier: 3.530A pdb=" N GLU A 868 " --> pdb=" O TRP A 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 17 removed outlier: 3.593A pdb=" N PHE B 17 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 52 removed outlier: 3.553A pdb=" N ARG B 29 " --> pdb=" O THR B 25 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG B 30 " --> pdb=" O GLU B 26 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 34 " --> pdb=" O ARG B 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG B 50 " --> pdb=" O GLN B 46 " (cutoff:3.500A) 479 hydrogen bonds defined for protein. 1413 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: 0.93 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2443 1.35 - 1.46: 1392 1.46 - 1.58: 3381 1.58 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 7291 Sorted by residual: bond pdb=" N LYS B 18 " pdb=" CA LYS B 18 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.29e-02 6.01e+03 6.80e-01 bond pdb=" C LEU A 368 " pdb=" N PRO A 369 " ideal model delta sigma weight residual 1.335 1.343 -0.008 1.28e-02 6.10e+03 4.25e-01 bond pdb=" C LYS B 18 " pdb=" O LYS B 18 " ideal model delta sigma weight residual 1.235 1.243 -0.008 1.26e-02 6.30e+03 3.87e-01 bond pdb=" C ILE A 121 " pdb=" N PRO A 122 " ideal model delta sigma weight residual 1.335 1.342 -0.008 1.28e-02 6.10e+03 3.63e-01 bond pdb=" CA VAL A 323 " pdb=" C VAL A 323 " ideal model delta sigma weight residual 1.523 1.529 -0.006 9.20e-03 1.18e+04 3.59e-01 ... (remaining 7286 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 9760 1.78 - 3.55: 96 3.55 - 5.33: 24 5.33 - 7.11: 1 7.11 - 8.88: 1 Bond angle restraints: 9882 Sorted by residual: angle pdb=" N GLN A 569 " pdb=" CA GLN A 569 " pdb=" C GLN A 569 " ideal model delta sigma weight residual 114.56 109.85 4.71 1.27e+00 6.20e-01 1.38e+01 angle pdb=" C LEU A 129 " pdb=" N ILE A 130 " pdb=" CA ILE A 130 " ideal model delta sigma weight residual 120.33 123.19 -2.86 8.00e-01 1.56e+00 1.27e+01 angle pdb=" C LYS B 18 " pdb=" CA LYS B 18 " pdb=" CB LYS B 18 " ideal model delta sigma weight residual 110.42 115.69 -5.27 1.99e+00 2.53e-01 7.00e+00 angle pdb=" C LEU A 322 " pdb=" N VAL A 323 " pdb=" CA VAL A 323 " ideal model delta sigma weight residual 120.33 122.43 -2.10 8.00e-01 1.56e+00 6.86e+00 angle pdb=" CA LEU A 368 " pdb=" CB LEU A 368 " pdb=" CG LEU A 368 " ideal model delta sigma weight residual 116.30 125.18 -8.88 3.50e+00 8.16e-02 6.44e+00 ... (remaining 9877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.46: 4180 16.46 - 32.92: 247 32.92 - 49.39: 63 49.39 - 65.85: 17 65.85 - 82.31: 6 Dihedral angle restraints: 4513 sinusoidal: 1813 harmonic: 2700 Sorted by residual: dihedral pdb=" N CYS A 287 " pdb=" CA CYS A 287 " pdb=" CB CYS A 287 " pdb=" SG CYS A 287 " ideal model delta sinusoidal sigma weight residual 180.00 120.07 59.93 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N GLU A 398 " pdb=" CA GLU A 398 " pdb=" CB GLU A 398 " pdb=" CG GLU A 398 " ideal model delta sinusoidal sigma weight residual 180.00 120.48 59.52 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N MET A 181 " pdb=" CA MET A 181 " pdb=" CB MET A 181 " pdb=" CG MET A 181 " ideal model delta sinusoidal sigma weight residual -180.00 -121.51 -58.49 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 4510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 691 0.027 - 0.054: 315 0.054 - 0.080: 93 0.080 - 0.107: 47 0.107 - 0.134: 1 Chirality restraints: 1147 Sorted by residual: chirality pdb=" CA LEU A 368 " pdb=" N LEU A 368 " pdb=" C LEU A 368 " pdb=" CB LEU A 368 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA PRO A 258 " pdb=" N PRO A 258 " pdb=" C PRO A 258 " pdb=" CB PRO A 258 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.87e-01 chirality pdb=" CA PRO A 399 " pdb=" N PRO A 399 " pdb=" C PRO A 399 " pdb=" CB PRO A 399 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.82e-01 ... (remaining 1144 not shown) Planarity restraints: 1292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 396 " -0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO A 397 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 397 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 397 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 410 " 0.016 5.00e-02 4.00e+02 2.37e-02 9.02e-01 pdb=" N PRO A 411 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 411 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 411 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 185 " -0.013 5.00e-02 4.00e+02 2.02e-02 6.51e-01 pdb=" N PRO A 186 " 0.035 5.00e-02 4.00e+02 pdb=" CA PRO A 186 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO A 186 " -0.011 5.00e-02 4.00e+02 ... (remaining 1289 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 543 2.74 - 3.28: 8181 3.28 - 3.82: 12139 3.82 - 4.36: 14476 4.36 - 4.90: 22803 Nonbonded interactions: 58142 Sorted by model distance: nonbonded pdb=" OG1 THR A 618 " pdb=" O GLY A 620 " model vdw 2.199 3.040 nonbonded pdb=" OE2 GLU A 398 " pdb=" OG SER A 400 " model vdw 2.237 3.040 nonbonded pdb=" O ALA A 600 " pdb=" OG SER A 604 " model vdw 2.265 3.040 nonbonded pdb=" O ALA A 631 " pdb=" OG1 THR A 634 " model vdw 2.294 3.040 nonbonded pdb=" OG1 THR A 827 " pdb=" OE2 GLU A 868 " model vdw 2.300 3.040 ... (remaining 58137 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 7.200 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 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 : 0.002 0.016 7291 Z= 0.094 Angle : 0.523 8.884 9882 Z= 0.302 Chirality : 0.035 0.134 1147 Planarity : 0.003 0.053 1292 Dihedral : 12.309 82.309 2753 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.81 % Allowed : 7.72 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.29), residues: 915 helix: 0.70 (0.21), residues: 683 sheet: None (None), residues: 0 loop : -0.27 (0.45), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 593 TYR 0.005 0.001 TYR A 661 PHE 0.008 0.001 PHE A 204 TRP 0.005 0.001 TRP A 342 HIS 0.002 0.000 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00168 ( 7291) covalent geometry : angle 0.52340 ( 9882) hydrogen bonds : bond 0.26626 ( 479) hydrogen bonds : angle 6.71487 ( 1413) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 191 time to evaluate : 0.259 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.9391 (tmm) cc_final: 0.9120 (tmm) REVERT: A 80 TRP cc_start: 0.8024 (t-100) cc_final: 0.7613 (t-100) REVERT: A 146 MET cc_start: 0.9193 (tmm) cc_final: 0.8857 (tmm) REVERT: A 162 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7351 (p0) REVERT: A 206 LYS cc_start: 0.9416 (ptpp) cc_final: 0.9055 (tptp) REVERT: A 240 ASN cc_start: 0.8991 (t0) cc_final: 0.8568 (t0) REVERT: A 281 GLU cc_start: 0.8872 (tp30) cc_final: 0.8088 (tp30) REVERT: A 282 PHE cc_start: 0.8643 (t80) cc_final: 0.8381 (t80) REVERT: A 285 ASN cc_start: 0.9013 (m-40) cc_final: 0.8451 (m-40) REVERT: A 290 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8403 (tp30) REVERT: A 416 LEU cc_start: 0.9299 (mt) cc_final: 0.8812 (mt) REVERT: A 472 TRP cc_start: 0.7782 (m-90) cc_final: 0.7339 (m-90) REVERT: A 634 THR cc_start: 0.9459 (p) cc_final: 0.8723 (p) REVERT: A 643 PHE cc_start: 0.8499 (t80) cc_final: 0.8263 (t80) REVERT: A 714 LEU cc_start: 0.9588 (mt) cc_final: 0.9326 (mt) REVERT: A 717 PHE cc_start: 0.8450 (m-10) cc_final: 0.7392 (m-80) REVERT: A 728 PHE cc_start: 0.7831 (t80) cc_final: 0.7219 (t80) REVERT: B 24 SER cc_start: 0.9236 (m) cc_final: 0.8938 (p) REVERT: B 25 THR cc_start: 0.9156 (p) cc_final: 0.8627 (p) REVERT: B 27 MET cc_start: 0.8950 (mmm) cc_final: 0.8042 (mmm) REVERT: B 28 ARG cc_start: 0.8702 (mmm-85) cc_final: 0.8497 (ttt180) REVERT: B 30 ARG cc_start: 0.9072 (mtp85) cc_final: 0.8357 (mtp85) outliers start: 38 outliers final: 11 residues processed: 219 average time/residue: 0.0922 time to fit residues: 26.1780 Evaluate side-chains 149 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 614 MET Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 863 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 40.0000 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 77 GLN A 208 ASN A 220 GLN A 454 GLN ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS A 521 GLN A 522 ASN A 548 GLN A 576 GLN A 590 ASN A 596 GLN A 660 ASN A 682 GLN A 740 GLN A 744 GLN A 774 GLN B 35 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.053198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.039750 restraints weight = 57204.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.040669 restraints weight = 40572.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.041345 restraints weight = 31574.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.041826 restraints weight = 26174.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.042203 restraints weight = 22752.481| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7291 Z= 0.206 Angle : 0.816 12.790 9882 Z= 0.402 Chirality : 0.044 0.161 1147 Planarity : 0.005 0.062 1292 Dihedral : 6.224 55.453 1011 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.04 % Allowed : 16.46 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.28), residues: 915 helix: 0.56 (0.19), residues: 702 sheet: None (None), residues: 0 loop : -0.12 (0.48), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 613 TYR 0.018 0.002 TYR A 248 PHE 0.020 0.002 PHE A 503 TRP 0.009 0.002 TRP A 80 HIS 0.004 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 7291) covalent geometry : angle 0.81585 ( 9882) hydrogen bonds : bond 0.05844 ( 479) hydrogen bonds : angle 5.17235 ( 1413) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.232 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TRP cc_start: 0.8501 (t-100) cc_final: 0.7995 (t-100) REVERT: A 99 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7236 (pt) REVERT: A 146 MET cc_start: 0.9517 (tmm) cc_final: 0.9179 (tmm) REVERT: A 206 LYS cc_start: 0.9583 (ptpp) cc_final: 0.9383 (tptt) REVERT: A 239 GLN cc_start: 0.9738 (tt0) cc_final: 0.9338 (tm-30) REVERT: A 240 ASN cc_start: 0.9681 (t0) cc_final: 0.9225 (m-40) REVERT: A 281 GLU cc_start: 0.9299 (tp30) cc_final: 0.8792 (tp30) REVERT: A 282 PHE cc_start: 0.9568 (t80) cc_final: 0.9251 (t80) REVERT: A 285 ASN cc_start: 0.9454 (m-40) cc_final: 0.9047 (m110) REVERT: A 287 CYS cc_start: 0.9350 (OUTLIER) cc_final: 0.9093 (t) REVERT: A 291 MET cc_start: 0.8919 (mmm) cc_final: 0.8704 (mmm) REVERT: A 438 LEU cc_start: 0.9527 (mp) cc_final: 0.9292 (mp) REVERT: A 472 TRP cc_start: 0.8671 (m-90) cc_final: 0.7817 (m-90) REVERT: A 589 GLN cc_start: 0.9718 (mt0) cc_final: 0.9341 (mp10) REVERT: A 643 PHE cc_start: 0.9582 (t80) cc_final: 0.9070 (t80) REVERT: A 650 PHE cc_start: 0.9629 (t80) cc_final: 0.9299 (t80) REVERT: A 665 GLN cc_start: 0.9486 (mt0) cc_final: 0.9257 (mt0) REVERT: A 714 LEU cc_start: 0.9727 (mt) cc_final: 0.9329 (tp) REVERT: A 717 PHE cc_start: 0.8929 (m-10) cc_final: 0.7741 (m-80) REVERT: A 728 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.8343 (t80) REVERT: B 22 LYS cc_start: 0.7002 (mmmm) cc_final: 0.6575 (mppt) REVERT: B 45 ASP cc_start: 0.9468 (t0) cc_final: 0.9186 (t0) REVERT: B 49 LYS cc_start: 0.9151 (pttp) cc_final: 0.8732 (pttp) outliers start: 24 outliers final: 12 residues processed: 166 average time/residue: 0.0945 time to fit residues: 20.2565 Evaluate side-chains 139 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 863 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 13 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN A 196 ASN ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.051265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.038043 restraints weight = 59474.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.038920 restraints weight = 42213.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.039576 restraints weight = 32888.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.040051 restraints weight = 27332.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.040374 restraints weight = 23818.428| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7291 Z= 0.246 Angle : 0.831 15.756 9882 Z= 0.411 Chirality : 0.046 0.366 1147 Planarity : 0.005 0.064 1292 Dihedral : 5.910 54.248 998 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 23.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.30 % Allowed : 16.20 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.28), residues: 915 helix: 0.41 (0.19), residues: 687 sheet: None (None), residues: 0 loop : -0.23 (0.47), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 29 TYR 0.017 0.002 TYR A 248 PHE 0.024 0.002 PHE A 503 TRP 0.012 0.002 TRP A 80 HIS 0.006 0.002 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 7291) covalent geometry : angle 0.83084 ( 9882) hydrogen bonds : bond 0.04725 ( 479) hydrogen bonds : angle 5.15608 ( 1413) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.269 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: symmetry clash REVERT: A 80 TRP cc_start: 0.8659 (t-100) cc_final: 0.8142 (t-100) REVERT: A 146 MET cc_start: 0.9537 (tmm) cc_final: 0.9220 (tmm) REVERT: A 206 LYS cc_start: 0.9705 (ptpp) cc_final: 0.9354 (tptt) REVERT: A 239 GLN cc_start: 0.9751 (tt0) cc_final: 0.9395 (tm-30) REVERT: A 240 ASN cc_start: 0.9668 (t0) cc_final: 0.9180 (m-40) REVERT: A 282 PHE cc_start: 0.9562 (t80) cc_final: 0.9127 (t80) REVERT: A 285 ASN cc_start: 0.9428 (m-40) cc_final: 0.9217 (m110) REVERT: A 287 CYS cc_start: 0.9543 (OUTLIER) cc_final: 0.8762 (t) REVERT: A 291 MET cc_start: 0.9062 (mmm) cc_final: 0.8804 (mmm) REVERT: A 353 MET cc_start: 0.9218 (tpp) cc_final: 0.8731 (tpp) REVERT: A 388 MET cc_start: 0.9530 (tpp) cc_final: 0.9294 (tpp) REVERT: A 472 TRP cc_start: 0.8864 (m-90) cc_final: 0.7998 (m-90) REVERT: A 589 GLN cc_start: 0.9635 (mt0) cc_final: 0.9153 (mp10) REVERT: A 643 PHE cc_start: 0.9534 (t80) cc_final: 0.9112 (t80) REVERT: A 650 PHE cc_start: 0.9633 (t80) cc_final: 0.9251 (t80) REVERT: A 664 TYR cc_start: 0.9563 (p90) cc_final: 0.9090 (p90) REVERT: A 714 LEU cc_start: 0.9752 (mt) cc_final: 0.9528 (tp) REVERT: A 728 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8462 (t80) REVERT: B 22 LYS cc_start: 0.6824 (mmmm) cc_final: 0.6566 (mppt) REVERT: B 26 GLU cc_start: 0.9035 (tm-30) cc_final: 0.8321 (pp20) REVERT: B 27 MET cc_start: 0.9601 (mmm) cc_final: 0.9115 (mmm) REVERT: B 30 ARG cc_start: 0.9617 (mtp85) cc_final: 0.9397 (ttm-80) REVERT: B 42 LYS cc_start: 0.9781 (tppt) cc_final: 0.9574 (tptp) outliers start: 34 outliers final: 24 residues processed: 160 average time/residue: 0.0850 time to fit residues: 18.0132 Evaluate side-chains 148 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 676 ASP Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 863 ARG Chi-restraints excluded: chain B residue 18 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 0.0030 chunk 57 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 50.0000 overall best weight: 2.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 ASN A 740 GLN A 744 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.052185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.038340 restraints weight = 56373.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.039295 restraints weight = 40507.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.039995 restraints weight = 31648.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.040492 restraints weight = 26232.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.040910 restraints weight = 22768.599| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7291 Z= 0.156 Angle : 0.827 15.914 9882 Z= 0.388 Chirality : 0.045 0.238 1147 Planarity : 0.004 0.062 1292 Dihedral : 5.702 52.016 998 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.95 % Favored : 96.94 % Rotamer: Outliers : 3.42 % Allowed : 19.75 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.29), residues: 915 helix: 0.52 (0.20), residues: 687 sheet: None (None), residues: 0 loop : -0.12 (0.49), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 39 TYR 0.012 0.001 TYR A 248 PHE 0.026 0.001 PHE A 503 TRP 0.010 0.001 TRP A 430 HIS 0.004 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 7291) covalent geometry : angle 0.82703 ( 9882) hydrogen bonds : bond 0.04182 ( 479) hydrogen bonds : angle 4.83304 ( 1413) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.236 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TRP cc_start: 0.8635 (t-100) cc_final: 0.8099 (t-100) REVERT: A 146 MET cc_start: 0.9561 (tmm) cc_final: 0.9216 (tmm) REVERT: A 206 LYS cc_start: 0.9675 (ptpp) cc_final: 0.9292 (tptt) REVERT: A 239 GLN cc_start: 0.9718 (tt0) cc_final: 0.9382 (tm-30) REVERT: A 240 ASN cc_start: 0.9665 (t0) cc_final: 0.9237 (m-40) REVERT: A 252 MET cc_start: 0.9389 (mmm) cc_final: 0.9173 (mmm) REVERT: A 285 ASN cc_start: 0.9403 (m-40) cc_final: 0.9185 (m110) REVERT: A 287 CYS cc_start: 0.9532 (OUTLIER) cc_final: 0.8806 (t) REVERT: A 291 MET cc_start: 0.9039 (mmm) cc_final: 0.8801 (mmm) REVERT: A 353 MET cc_start: 0.9225 (tpp) cc_final: 0.8747 (tpt) REVERT: A 388 MET cc_start: 0.9496 (tpp) cc_final: 0.9209 (tpp) REVERT: A 436 CYS cc_start: 0.9719 (m) cc_final: 0.9218 (t) REVERT: A 472 TRP cc_start: 0.8786 (m-90) cc_final: 0.7947 (m-90) REVERT: A 503 PHE cc_start: 0.9658 (t80) cc_final: 0.9119 (t80) REVERT: A 533 MET cc_start: 0.9621 (mtt) cc_final: 0.9277 (mmm) REVERT: A 589 GLN cc_start: 0.9622 (mt0) cc_final: 0.9391 (mp10) REVERT: A 643 PHE cc_start: 0.9510 (t80) cc_final: 0.9033 (t80) REVERT: A 650 PHE cc_start: 0.9594 (t80) cc_final: 0.9126 (t80) REVERT: A 664 TYR cc_start: 0.9612 (p90) cc_final: 0.9075 (p90) REVERT: A 665 GLN cc_start: 0.9575 (mm110) cc_final: 0.9290 (mm-40) REVERT: A 714 LEU cc_start: 0.9729 (mt) cc_final: 0.9490 (tp) REVERT: A 728 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.8350 (t80) REVERT: B 18 LYS cc_start: 0.9076 (ttmm) cc_final: 0.8716 (ttmm) REVERT: B 22 LYS cc_start: 0.6726 (mmmm) cc_final: 0.6324 (mppt) REVERT: B 42 LYS cc_start: 0.9774 (tppt) cc_final: 0.9564 (tptp) outliers start: 27 outliers final: 16 residues processed: 157 average time/residue: 0.0770 time to fit residues: 16.0621 Evaluate side-chains 143 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 676 ASP Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 863 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 20 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 57 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 74 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 GLN ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.051730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.038237 restraints weight = 58782.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.039138 restraints weight = 42570.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.039810 restraints weight = 33507.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.040292 restraints weight = 27934.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.040640 restraints weight = 24369.116| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 7291 Z= 0.162 Angle : 0.805 17.074 9882 Z= 0.385 Chirality : 0.045 0.234 1147 Planarity : 0.004 0.062 1292 Dihedral : 5.876 61.625 998 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.50 % Favored : 96.39 % Rotamer: Outliers : 2.66 % Allowed : 21.65 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.29), residues: 915 helix: 0.56 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -0.08 (0.48), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 593 TYR 0.013 0.001 TYR A 248 PHE 0.022 0.002 PHE A 503 TRP 0.010 0.001 TRP A 80 HIS 0.004 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 7291) covalent geometry : angle 0.80503 ( 9882) hydrogen bonds : bond 0.04082 ( 479) hydrogen bonds : angle 4.84234 ( 1413) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.195 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TRP cc_start: 0.8620 (t-100) cc_final: 0.8076 (t-100) REVERT: A 146 MET cc_start: 0.9568 (tmm) cc_final: 0.9230 (tmm) REVERT: A 206 LYS cc_start: 0.9649 (ptpp) cc_final: 0.9280 (tptt) REVERT: A 282 PHE cc_start: 0.9521 (t80) cc_final: 0.9123 (t80) REVERT: A 285 ASN cc_start: 0.9385 (m-40) cc_final: 0.9101 (m110) REVERT: A 287 CYS cc_start: 0.9556 (OUTLIER) cc_final: 0.7713 (t) REVERT: A 291 MET cc_start: 0.9067 (mmm) cc_final: 0.8762 (mmm) REVERT: A 353 MET cc_start: 0.9278 (tpp) cc_final: 0.8794 (mmm) REVERT: A 354 LEU cc_start: 0.9763 (mm) cc_final: 0.9418 (tp) REVERT: A 388 MET cc_start: 0.9490 (tpp) cc_final: 0.9285 (tpp) REVERT: A 436 CYS cc_start: 0.9743 (m) cc_final: 0.9334 (t) REVERT: A 472 TRP cc_start: 0.8831 (m-90) cc_final: 0.7998 (m-90) REVERT: A 503 PHE cc_start: 0.9671 (t80) cc_final: 0.9185 (t80) REVERT: A 614 MET cc_start: 0.9614 (tpp) cc_final: 0.9403 (mmt) REVERT: A 643 PHE cc_start: 0.9450 (t80) cc_final: 0.9029 (t80) REVERT: A 650 PHE cc_start: 0.9587 (t80) cc_final: 0.9133 (t80) REVERT: A 664 TYR cc_start: 0.9620 (p90) cc_final: 0.9079 (p90) REVERT: A 665 GLN cc_start: 0.9632 (mm110) cc_final: 0.9313 (mm-40) REVERT: A 714 LEU cc_start: 0.9741 (mt) cc_final: 0.9496 (tp) REVERT: A 728 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8470 (t80) REVERT: B 26 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8067 (pp20) REVERT: B 27 MET cc_start: 0.9592 (mmm) cc_final: 0.9123 (mmm) REVERT: B 30 ARG cc_start: 0.9647 (mtp85) cc_final: 0.9404 (ttm-80) REVERT: B 42 LYS cc_start: 0.9786 (tppt) cc_final: 0.9573 (tptp) outliers start: 21 outliers final: 16 residues processed: 145 average time/residue: 0.0785 time to fit residues: 14.9343 Evaluate side-chains 142 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 863 ARG Chi-restraints excluded: chain B residue 18 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 48 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 56 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 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 = 0.4187 r_free = 0.4187 target = 0.080416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.073264 restraints weight = 54641.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.074612 restraints weight = 24323.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.075396 restraints weight = 13584.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.075902 restraints weight = 9094.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.076248 restraints weight = 6945.628| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7291 Z= 0.137 Angle : 0.828 18.716 9882 Z= 0.385 Chirality : 0.046 0.261 1147 Planarity : 0.004 0.062 1292 Dihedral : 5.717 57.147 996 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.17 % Favored : 96.72 % Rotamer: Outliers : 2.41 % Allowed : 22.78 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.29), residues: 915 helix: 0.57 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -0.01 (0.49), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 593 TYR 0.015 0.001 TYR A 248 PHE 0.021 0.002 PHE A 577 TRP 0.011 0.001 TRP A 430 HIS 0.003 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 7291) covalent geometry : angle 0.82790 ( 9882) hydrogen bonds : bond 0.03881 ( 479) hydrogen bonds : angle 4.68421 ( 1413) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.287 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TRP cc_start: 0.8402 (t-100) cc_final: 0.7870 (t-100) REVERT: A 146 MET cc_start: 0.9574 (tmm) cc_final: 0.9232 (tmm) REVERT: A 181 MET cc_start: 0.7673 (tpp) cc_final: 0.6911 (tpp) REVERT: A 206 LYS cc_start: 0.9579 (ptpp) cc_final: 0.9181 (tptt) REVERT: A 239 GLN cc_start: 0.9710 (tt0) cc_final: 0.9487 (pt0) REVERT: A 252 MET cc_start: 0.9408 (mmm) cc_final: 0.9178 (mmm) REVERT: A 281 GLU cc_start: 0.9180 (tp30) cc_final: 0.8604 (tp30) REVERT: A 282 PHE cc_start: 0.9538 (t80) cc_final: 0.9130 (t80) REVERT: A 287 CYS cc_start: 0.9533 (OUTLIER) cc_final: 0.8710 (t) REVERT: A 322 LEU cc_start: 0.9636 (mt) cc_final: 0.9317 (pp) REVERT: A 353 MET cc_start: 0.9378 (tpp) cc_final: 0.8976 (mmm) REVERT: A 388 MET cc_start: 0.9495 (tpp) cc_final: 0.9291 (tpp) REVERT: A 436 CYS cc_start: 0.9687 (m) cc_final: 0.9328 (t) REVERT: A 472 TRP cc_start: 0.8806 (OUTLIER) cc_final: 0.7982 (m-90) REVERT: A 503 PHE cc_start: 0.9526 (t80) cc_final: 0.9033 (t80) REVERT: A 529 TYR cc_start: 0.8469 (m-80) cc_final: 0.8003 (m-80) REVERT: A 533 MET cc_start: 0.9609 (mtt) cc_final: 0.9235 (mmm) REVERT: A 568 ILE cc_start: 0.6539 (OUTLIER) cc_final: 0.6166 (mm) REVERT: A 643 PHE cc_start: 0.9432 (t80) cc_final: 0.9013 (t80) REVERT: A 650 PHE cc_start: 0.9589 (t80) cc_final: 0.9131 (t80) REVERT: A 664 TYR cc_start: 0.9611 (p90) cc_final: 0.8912 (p90) REVERT: A 665 GLN cc_start: 0.9644 (mm110) cc_final: 0.9244 (mm110) REVERT: A 714 LEU cc_start: 0.9733 (mt) cc_final: 0.9503 (tp) REVERT: B 18 LYS cc_start: 0.8977 (ttmm) cc_final: 0.8729 (ttmm) REVERT: B 26 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8004 (pp20) REVERT: B 27 MET cc_start: 0.9509 (mmm) cc_final: 0.8905 (mmm) REVERT: B 29 ARG cc_start: 0.9592 (ttp80) cc_final: 0.9295 (tmm-80) REVERT: B 30 ARG cc_start: 0.9614 (mtp85) cc_final: 0.9380 (ttm-80) REVERT: B 42 LYS cc_start: 0.9741 (tppt) cc_final: 0.9523 (tptp) outliers start: 19 outliers final: 14 residues processed: 149 average time/residue: 0.0993 time to fit residues: 19.4194 Evaluate side-chains 144 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 472 TRP Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 863 ARG Chi-restraints excluded: chain B residue 23 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 20 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 508 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 = 0.3352 r_free = 0.3352 target = 0.050686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.037798 restraints weight = 59409.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.038706 restraints weight = 41970.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.039352 restraints weight = 32577.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.039814 restraints weight = 27034.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.040166 restraints weight = 23544.442| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7291 Z= 0.198 Angle : 0.825 18.317 9882 Z= 0.402 Chirality : 0.046 0.297 1147 Planarity : 0.004 0.058 1292 Dihedral : 5.757 55.280 996 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 23.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.93 % Favored : 95.96 % Rotamer: Outliers : 2.91 % Allowed : 24.30 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.29), residues: 915 helix: 0.56 (0.20), residues: 685 sheet: None (None), residues: 0 loop : -0.10 (0.49), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 593 TYR 0.013 0.001 TYR A 248 PHE 0.020 0.002 PHE A 577 TRP 0.010 0.002 TRP A 80 HIS 0.004 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 7291) covalent geometry : angle 0.82547 ( 9882) hydrogen bonds : bond 0.03823 ( 479) hydrogen bonds : angle 4.88018 ( 1413) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.296 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TRP cc_start: 0.8686 (t-100) cc_final: 0.8158 (t-100) REVERT: A 146 MET cc_start: 0.9573 (tmm) cc_final: 0.9206 (tmm) REVERT: A 181 MET cc_start: 0.7858 (tpp) cc_final: 0.7221 (tpp) REVERT: A 206 LYS cc_start: 0.9645 (ptpp) cc_final: 0.9198 (tptt) REVERT: A 252 MET cc_start: 0.9314 (mmm) cc_final: 0.9096 (mmm) REVERT: A 282 PHE cc_start: 0.9482 (t80) cc_final: 0.9050 (t80) REVERT: A 285 ASN cc_start: 0.9288 (m-40) cc_final: 0.9083 (m110) REVERT: A 287 CYS cc_start: 0.9306 (OUTLIER) cc_final: 0.8147 (t) REVERT: A 291 MET cc_start: 0.8751 (mmm) cc_final: 0.8492 (mmm) REVERT: A 353 MET cc_start: 0.9222 (tpp) cc_final: 0.8730 (mmm) REVERT: A 354 LEU cc_start: 0.9743 (mm) cc_final: 0.9401 (tp) REVERT: A 388 MET cc_start: 0.9496 (tpp) cc_final: 0.9241 (tpp) REVERT: A 436 CYS cc_start: 0.9733 (m) cc_final: 0.9326 (t) REVERT: A 503 PHE cc_start: 0.9657 (t80) cc_final: 0.9270 (t80) REVERT: A 533 MET cc_start: 0.9597 (mtt) cc_final: 0.9251 (mmm) REVERT: A 589 GLN cc_start: 0.9578 (mt0) cc_final: 0.9366 (mp10) REVERT: A 643 PHE cc_start: 0.9414 (t80) cc_final: 0.9048 (t80) REVERT: A 650 PHE cc_start: 0.9585 (t80) cc_final: 0.9173 (t80) REVERT: A 664 TYR cc_start: 0.9622 (p90) cc_final: 0.8910 (p90) REVERT: A 665 GLN cc_start: 0.9614 (mm110) cc_final: 0.9196 (mm110) REVERT: A 714 LEU cc_start: 0.9754 (mt) cc_final: 0.9534 (tp) REVERT: A 727 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8096 (mp0) REVERT: B 18 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8724 (ttmm) REVERT: B 42 LYS cc_start: 0.9787 (tppt) cc_final: 0.9580 (tptp) outliers start: 23 outliers final: 18 residues processed: 141 average time/residue: 0.1001 time to fit residues: 18.5979 Evaluate side-chains 139 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 727 GLU Chi-restraints excluded: chain A residue 863 ARG Chi-restraints excluded: chain B residue 18 LYS Chi-restraints excluded: chain B residue 23 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 5 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.051837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.038607 restraints weight = 57155.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.039537 restraints weight = 40534.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.040205 restraints weight = 31431.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.040713 restraints weight = 26050.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.041094 restraints weight = 22533.982| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7291 Z= 0.143 Angle : 0.859 19.058 9882 Z= 0.398 Chirality : 0.047 0.273 1147 Planarity : 0.004 0.061 1292 Dihedral : 5.668 51.945 996 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 20.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.50 % Favored : 96.39 % Rotamer: Outliers : 2.41 % Allowed : 25.32 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.29), residues: 915 helix: 0.57 (0.20), residues: 686 sheet: None (None), residues: 0 loop : 0.05 (0.49), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 593 TYR 0.016 0.001 TYR A 248 PHE 0.017 0.001 PHE A 503 TRP 0.050 0.003 TRP A 472 HIS 0.003 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 7291) covalent geometry : angle 0.85891 ( 9882) hydrogen bonds : bond 0.03685 ( 479) hydrogen bonds : angle 4.72145 ( 1413) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.219 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TRP cc_start: 0.8642 (t-100) cc_final: 0.8085 (t-100) REVERT: A 146 MET cc_start: 0.9571 (tmm) cc_final: 0.9364 (tpp) REVERT: A 181 MET cc_start: 0.7840 (tpp) cc_final: 0.7208 (tpp) REVERT: A 206 LYS cc_start: 0.9600 (ptpp) cc_final: 0.9193 (tptt) REVERT: A 239 GLN cc_start: 0.9727 (tt0) cc_final: 0.9338 (tm-30) REVERT: A 281 GLU cc_start: 0.9187 (tp30) cc_final: 0.8513 (tp30) REVERT: A 282 PHE cc_start: 0.9505 (t80) cc_final: 0.9047 (t80) REVERT: A 287 CYS cc_start: 0.9278 (OUTLIER) cc_final: 0.8072 (t) REVERT: A 291 MET cc_start: 0.8691 (mmm) cc_final: 0.8434 (mmm) REVERT: A 322 LEU cc_start: 0.9596 (mt) cc_final: 0.9295 (pp) REVERT: A 353 MET cc_start: 0.9319 (tpp) cc_final: 0.8794 (mmm) REVERT: A 354 LEU cc_start: 0.9725 (mm) cc_final: 0.9398 (tp) REVERT: A 388 MET cc_start: 0.9533 (tpp) cc_final: 0.9303 (tpp) REVERT: A 436 CYS cc_start: 0.9753 (m) cc_final: 0.9305 (t) REVERT: A 503 PHE cc_start: 0.9694 (t80) cc_final: 0.9341 (t80) REVERT: A 533 MET cc_start: 0.9626 (mtt) cc_final: 0.9258 (mmm) REVERT: A 593 ARG cc_start: 0.8947 (ptp90) cc_final: 0.8688 (ptp90) REVERT: A 643 PHE cc_start: 0.9414 (t80) cc_final: 0.9068 (t80) REVERT: A 650 PHE cc_start: 0.9618 (t80) cc_final: 0.9200 (t80) REVERT: A 664 TYR cc_start: 0.9647 (p90) cc_final: 0.9180 (p90) REVERT: A 714 LEU cc_start: 0.9761 (mt) cc_final: 0.9535 (tp) REVERT: A 727 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8076 (mp0) REVERT: B 18 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8756 (ttmm) REVERT: B 27 MET cc_start: 0.9626 (mmm) cc_final: 0.9411 (mmm) REVERT: B 42 LYS cc_start: 0.9791 (tppt) cc_final: 0.9587 (tptp) outliers start: 19 outliers final: 13 residues processed: 145 average time/residue: 0.0865 time to fit residues: 16.5350 Evaluate side-chains 139 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 727 GLU Chi-restraints excluded: chain A residue 863 ARG Chi-restraints excluded: chain B residue 18 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 50.0000 chunk 35 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 36 optimal weight: 0.3980 chunk 2 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.052754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.039369 restraints weight = 57041.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.040311 restraints weight = 40405.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.040995 restraints weight = 31491.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.041514 restraints weight = 26108.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.041902 restraints weight = 22654.339| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7291 Z= 0.147 Angle : 0.923 20.437 9882 Z= 0.426 Chirality : 0.048 0.283 1147 Planarity : 0.004 0.061 1292 Dihedral : 5.592 50.946 996 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.39 % Favored : 96.50 % Rotamer: Outliers : 2.03 % Allowed : 26.08 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.29), residues: 915 helix: 0.58 (0.20), residues: 686 sheet: None (None), residues: 0 loop : 0.02 (0.48), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 593 TYR 0.020 0.001 TYR A 248 PHE 0.016 0.001 PHE A 577 TRP 0.030 0.002 TRP A 472 HIS 0.002 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 7291) covalent geometry : angle 0.92259 ( 9882) hydrogen bonds : bond 0.03756 ( 479) hydrogen bonds : angle 4.65416 ( 1413) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.278 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TRP cc_start: 0.8607 (t-100) cc_final: 0.7961 (t-100) REVERT: A 181 MET cc_start: 0.7845 (tpp) cc_final: 0.7242 (tpp) REVERT: A 206 LYS cc_start: 0.9567 (ptpp) cc_final: 0.9176 (tptt) REVERT: A 239 GLN cc_start: 0.9705 (tt0) cc_final: 0.9494 (pt0) REVERT: A 281 GLU cc_start: 0.9157 (tp30) cc_final: 0.8451 (tp30) REVERT: A 282 PHE cc_start: 0.9485 (t80) cc_final: 0.9010 (t80) REVERT: A 322 LEU cc_start: 0.9568 (mt) cc_final: 0.9279 (pp) REVERT: A 353 MET cc_start: 0.9290 (tpp) cc_final: 0.8778 (mmm) REVERT: A 436 CYS cc_start: 0.9736 (m) cc_final: 0.9301 (t) REVERT: A 503 PHE cc_start: 0.9694 (t80) cc_final: 0.9330 (t80) REVERT: A 533 MET cc_start: 0.9617 (mtt) cc_final: 0.9250 (mmm) REVERT: A 568 ILE cc_start: 0.6589 (OUTLIER) cc_final: 0.5902 (mm) REVERT: A 589 GLN cc_start: 0.9607 (mt0) cc_final: 0.9005 (mp10) REVERT: A 643 PHE cc_start: 0.9387 (t80) cc_final: 0.9008 (t80) REVERT: A 650 PHE cc_start: 0.9588 (t80) cc_final: 0.9132 (t80) REVERT: A 664 TYR cc_start: 0.9660 (p90) cc_final: 0.9423 (p90) REVERT: A 665 GLN cc_start: 0.9669 (mm110) cc_final: 0.9464 (mm110) REVERT: A 714 LEU cc_start: 0.9727 (mt) cc_final: 0.9483 (tp) REVERT: A 727 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8110 (mp0) REVERT: B 18 LYS cc_start: 0.8906 (ttmm) cc_final: 0.8481 (ttmm) REVERT: B 30 ARG cc_start: 0.9696 (mtp85) cc_final: 0.9233 (ttm110) REVERT: B 42 LYS cc_start: 0.9788 (tppt) cc_final: 0.9587 (tptp) outliers start: 16 outliers final: 12 residues processed: 149 average time/residue: 0.0867 time to fit residues: 16.9669 Evaluate side-chains 140 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 727 GLU Chi-restraints excluded: chain A residue 863 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 65 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 84 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 39 optimal weight: 0.0010 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 GLN A 744 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.052980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.039583 restraints weight = 56866.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.040539 restraints weight = 40380.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.041224 restraints weight = 31448.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.041744 restraints weight = 26099.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.042044 restraints weight = 22663.200| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7291 Z= 0.153 Angle : 1.026 21.544 9882 Z= 0.461 Chirality : 0.050 0.333 1147 Planarity : 0.004 0.065 1292 Dihedral : 5.496 51.297 995 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.28 % Favored : 96.61 % Rotamer: Outliers : 1.65 % Allowed : 27.09 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.29), residues: 915 helix: 0.46 (0.20), residues: 691 sheet: None (None), residues: 0 loop : -0.01 (0.48), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 29 TYR 0.023 0.001 TYR A 248 PHE 0.018 0.001 PHE A 577 TRP 0.024 0.002 TRP A 472 HIS 0.002 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 7291) covalent geometry : angle 1.02591 ( 9882) hydrogen bonds : bond 0.03901 ( 479) hydrogen bonds : angle 4.66747 ( 1413) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.295 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TRP cc_start: 0.8600 (t-100) cc_final: 0.7946 (t-100) REVERT: A 181 MET cc_start: 0.7838 (tpp) cc_final: 0.7200 (tpp) REVERT: A 206 LYS cc_start: 0.9561 (ptpp) cc_final: 0.9163 (tptt) REVERT: A 281 GLU cc_start: 0.9108 (tp30) cc_final: 0.8414 (tp30) REVERT: A 282 PHE cc_start: 0.9473 (t80) cc_final: 0.8999 (t80) REVERT: A 322 LEU cc_start: 0.9541 (mt) cc_final: 0.9281 (pp) REVERT: A 353 MET cc_start: 0.9278 (tpp) cc_final: 0.8688 (mmm) REVERT: A 436 CYS cc_start: 0.9746 (m) cc_final: 0.9295 (t) REVERT: A 503 PHE cc_start: 0.9671 (t80) cc_final: 0.9306 (t80) REVERT: A 533 MET cc_start: 0.9609 (mtt) cc_final: 0.9251 (mmm) REVERT: A 568 ILE cc_start: 0.6603 (OUTLIER) cc_final: 0.5895 (mm) REVERT: A 589 GLN cc_start: 0.9556 (mt0) cc_final: 0.9267 (mp10) REVERT: A 643 PHE cc_start: 0.9342 (t80) cc_final: 0.8970 (t80) REVERT: A 650 PHE cc_start: 0.9550 (t80) cc_final: 0.9075 (t80) REVERT: A 664 TYR cc_start: 0.9641 (p90) cc_final: 0.9399 (p90) REVERT: A 665 GLN cc_start: 0.9659 (mm110) cc_final: 0.9452 (mm110) REVERT: A 714 LEU cc_start: 0.9729 (mt) cc_final: 0.9458 (tp) REVERT: A 727 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8121 (mp0) REVERT: B 26 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8300 (tm-30) REVERT: B 27 MET cc_start: 0.9614 (mmm) cc_final: 0.9404 (mmm) REVERT: B 42 LYS cc_start: 0.9793 (tppt) cc_final: 0.9586 (tptp) outliers start: 13 outliers final: 9 residues processed: 143 average time/residue: 0.1008 time to fit residues: 18.8768 Evaluate side-chains 140 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 727 GLU Chi-restraints excluded: chain A residue 863 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 13 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 87 optimal weight: 0.0370 chunk 42 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 overall best weight: 0.8062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 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 = 0.4007 r_free = 0.4007 target = 0.092575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.078493 restraints weight = 57128.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.080009 restraints weight = 26740.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.080914 restraints weight = 15648.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.081507 restraints weight = 10657.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.081889 restraints weight = 8177.326| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7291 Z= 0.148 Angle : 0.991 21.153 9882 Z= 0.454 Chirality : 0.049 0.325 1147 Planarity : 0.005 0.083 1292 Dihedral : 4.981 51.457 992 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.17 % Favored : 96.72 % Rotamer: Outliers : 1.27 % Allowed : 27.47 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.29), residues: 915 helix: 0.53 (0.20), residues: 692 sheet: None (None), residues: 0 loop : 0.03 (0.48), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG B 39 TYR 0.020 0.001 TYR A 248 PHE 0.017 0.001 PHE A 577 TRP 0.027 0.002 TRP A 430 HIS 0.008 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 7291) covalent geometry : angle 0.99146 ( 9882) hydrogen bonds : bond 0.03846 ( 479) hydrogen bonds : angle 4.60113 ( 1413) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1475.82 seconds wall clock time: 26 minutes 10.07 seconds (1570.07 seconds total)