Starting phenix.real_space_refine on Fri Jul 3 10:06:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j8q_61238/07_2026/9j8q_61238.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j8q_61238/07_2026/9j8q_61238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9j8q_61238/07_2026/9j8q_61238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j8q_61238/07_2026/9j8q_61238.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j8q_61238/07_2026/9j8q_61238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j8q_61238/07_2026/9j8q_61238.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.153 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 42 5.16 5 C 8734 2.51 5 N 2138 2.21 5 O 2136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13056 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 6145 Classifications: {'peptide': 799} Link IDs: {'PTRANS': 43, 'TRANS': 755} Chain breaks: 2 Chain: "B" Number of atoms: 6145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 6145 Classifications: {'peptide': 799} Link IDs: {'PTRANS': 43, 'TRANS': 755} Chain breaks: 2 Chain: "A" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 383 Unusual residues: {'J4U': 1, 'PGT': 11, 'PTY': 6} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 563 Unresolved non-hydrogen angles: 679 Unresolved non-hydrogen dihedrals: 465 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'PGT:plan-1': 7, 'PGT:plan-2': 8, 'PTY:plan-1': 6, 'PTY:plan-2': 6} Unresolved non-hydrogen planarities: 90 Chain: "B" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 383 Unusual residues: {'J4U': 1, 'PGT': 11, 'PTY': 6} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 563 Unresolved non-hydrogen angles: 679 Unresolved non-hydrogen dihedrals: 465 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'PGT:plan-1': 7, 'PGT:plan-2': 8, 'PTY:plan-1': 6, 'PTY:plan-2': 6} Unresolved non-hydrogen planarities: 90 Time building chain proxies: 3.02, per 1000 atoms: 0.23 Number of scatterers: 13056 At special positions: 0 Unit cell: (108.07, 123.05, 121.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 6 15.00 O 2136 8.00 N 2138 7.00 C 8734 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 601.6 milliseconds 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 6 sheets defined 69.5% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 33 through 56 Processing helix chain 'A' and resid 60 through 71 removed outlier: 3.610A pdb=" N VAL A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 102 removed outlier: 3.985A pdb=" N LEU A 90 " --> pdb=" O GLY A 86 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 125 removed outlier: 3.551A pdb=" N ALA A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 141 removed outlier: 4.025A pdb=" N ARG A 141 " --> pdb=" O ARG A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 174 removed outlier: 4.280A pdb=" N LEU A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) Proline residue: A 165 - end of helix Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 186 through 211 removed outlier: 3.633A pdb=" N HIS A 211 " --> pdb=" O PHE A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 261 removed outlier: 3.567A pdb=" N LEU A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 285 Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 307 through 323 removed outlier: 3.521A pdb=" N LEU A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 345 Processing helix chain 'A' and resid 355 through 377 Processing helix chain 'A' and resid 380 through 388 Processing helix chain 'A' and resid 392 through 419 removed outlier: 3.661A pdb=" N ASP A 397 " --> pdb=" O HIS A 393 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLN A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 444 removed outlier: 3.866A pdb=" N GLY A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 462 removed outlier: 3.506A pdb=" N PHE A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 475 removed outlier: 3.552A pdb=" N GLU A 474 " --> pdb=" O ARG A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 500 Processing helix chain 'A' and resid 506 through 512 removed outlier: 3.740A pdb=" N TRP A 510 " --> pdb=" O ASN A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 542 Processing helix chain 'A' and resid 553 through 566 Processing helix chain 'A' and resid 570 through 578 Processing helix chain 'A' and resid 610 through 628 Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 641 through 648 Processing helix chain 'A' and resid 672 through 689 Processing helix chain 'A' and resid 701 through 713 Processing helix chain 'A' and resid 729 through 734 Processing helix chain 'A' and resid 774 through 793 removed outlier: 4.320A pdb=" N MET A 778 " --> pdb=" O PRO A 774 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU A 779 " --> pdb=" O LYS A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 859 through 872 Processing helix chain 'B' and resid 34 through 56 Processing helix chain 'B' and resid 60 through 71 removed outlier: 3.610A pdb=" N VAL B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 102 removed outlier: 3.985A pdb=" N LEU B 90 " --> pdb=" O GLY B 86 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU B 91 " --> pdb=" O PHE B 87 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 125 removed outlier: 3.551A pdb=" N ALA B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 141 removed outlier: 4.025A pdb=" N ARG B 141 " --> pdb=" O ARG B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 174 removed outlier: 4.280A pdb=" N LEU B 160 " --> pdb=" O ALA B 156 " (cutoff:3.500A) Proline residue: B 165 - end of helix Processing helix chain 'B' and resid 175 through 184 Processing helix chain 'B' and resid 186 through 211 removed outlier: 3.633A pdb=" N HIS B 211 " --> pdb=" O PHE B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 261 removed outlier: 3.567A pdb=" N LEU B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 285 Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 307 through 323 removed outlier: 3.521A pdb=" N LEU B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 345 Processing helix chain 'B' and resid 355 through 377 Processing helix chain 'B' and resid 380 through 388 Processing helix chain 'B' and resid 392 through 419 removed outlier: 3.661A pdb=" N ASP B 397 " --> pdb=" O HIS B 393 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 398 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLN B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 444 removed outlier: 3.866A pdb=" N GLY B 443 " --> pdb=" O SER B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 462 removed outlier: 3.506A pdb=" N PHE B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 475 removed outlier: 3.552A pdb=" N GLU B 474 " --> pdb=" O ARG B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 500 Processing helix chain 'B' and resid 506 through 512 removed outlier: 3.740A pdb=" N TRP B 510 " --> pdb=" O ASN B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 542 Processing helix chain 'B' and resid 553 through 566 Processing helix chain 'B' and resid 570 through 578 Processing helix chain 'B' and resid 610 through 628 Processing helix chain 'B' and resid 638 through 640 No H-bonds generated for 'chain 'B' and resid 638 through 640' Processing helix chain 'B' and resid 641 through 648 Processing helix chain 'B' and resid 672 through 689 Processing helix chain 'B' and resid 701 through 713 Processing helix chain 'B' and resid 729 through 734 Processing helix chain 'B' and resid 774 through 793 removed outlier: 4.320A pdb=" N MET B 778 " --> pdb=" O PRO B 774 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU B 779 " --> pdb=" O LYS B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 842 Processing helix chain 'B' and resid 859 through 872 Processing sheet with id=AA1, first strand: chain 'A' and resid 212 through 213 removed outlier: 4.941A pdb=" N LEU A 224 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 581 through 584 removed outlier: 9.025A pdb=" N VAL A 633 " --> pdb=" O PRO A 855 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N TYR A 635 " --> pdb=" O ALA A 853 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA A 853 " --> pdb=" O TYR A 635 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU A 852 " --> pdb=" O LYS A 654 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LYS A 654 " --> pdb=" O LEU A 852 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL A 854 " --> pdb=" O ALA A 652 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ALA A 652 " --> pdb=" O VAL A 854 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY A 800 " --> pdb=" O ALA A 659 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL A 661 " --> pdb=" O SER A 798 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N SER A 798 " --> pdb=" O VAL A 661 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 690 through 695 removed outlier: 6.851A pdb=" N ARG A 737 " --> pdb=" O ASN A 752 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ASN A 752 " --> pdb=" O ARG A 737 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA A 739 " --> pdb=" O PHE A 750 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N PHE A 750 " --> pdb=" O ALA A 739 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL A 741 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 9.219A pdb=" N VAL A 748 " --> pdb=" O VAL A 769 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N VAL A 769 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N PHE A 750 " --> pdb=" O MET A 767 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N MET A 767 " --> pdb=" O PHE A 750 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ASN A 752 " --> pdb=" O ASP A 765 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP A 765 " --> pdb=" O ASN A 752 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 212 through 213 removed outlier: 4.941A pdb=" N LEU B 224 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 581 through 584 removed outlier: 9.025A pdb=" N VAL B 633 " --> pdb=" O PRO B 855 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N TYR B 635 " --> pdb=" O ALA B 853 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA B 853 " --> pdb=" O TYR B 635 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU B 852 " --> pdb=" O LYS B 654 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LYS B 654 " --> pdb=" O LEU B 852 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL B 854 " --> pdb=" O ALA B 652 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ALA B 652 " --> pdb=" O VAL B 854 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 800 " --> pdb=" O ALA B 659 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL B 661 " --> pdb=" O SER B 798 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N SER B 798 " --> pdb=" O VAL B 661 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 690 through 695 removed outlier: 6.851A pdb=" N ARG B 737 " --> pdb=" O ASN B 752 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ASN B 752 " --> pdb=" O ARG B 737 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA B 739 " --> pdb=" O PHE B 750 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N PHE B 750 " --> pdb=" O ALA B 739 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL B 741 " --> pdb=" O VAL B 748 " (cutoff:3.500A) removed outlier: 9.219A pdb=" N VAL B 748 " --> pdb=" O VAL B 769 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N VAL B 769 " --> pdb=" O VAL B 748 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N PHE B 750 " --> pdb=" O MET B 767 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N MET B 767 " --> pdb=" O PHE B 750 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ASN B 752 " --> pdb=" O ASP B 765 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP B 765 " --> pdb=" O ASN B 752 " (cutoff:3.500A) 885 hydrogen bonds defined for protein. 2565 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2290 1.33 - 1.45: 3128 1.45 - 1.58: 7816 1.58 - 1.70: 12 1.70 - 1.83: 68 Bond restraints: 13314 Sorted by residual: bond pdb=" C1 PGT B 914 " pdb=" O3P PGT B 914 " ideal model delta sigma weight residual 1.408 1.458 -0.050 2.00e-02 2.50e+03 6.34e+00 bond pdb=" C1 PGT A 912 " pdb=" O3P PGT A 912 " ideal model delta sigma weight residual 1.408 1.458 -0.050 2.00e-02 2.50e+03 6.34e+00 bond pdb=" C1 PGT B 904 " pdb=" O3P PGT B 904 " ideal model delta sigma weight residual 1.408 1.456 -0.048 2.00e-02 2.50e+03 5.69e+00 bond pdb=" C1 PGT A 902 " pdb=" O3P PGT A 902 " ideal model delta sigma weight residual 1.408 1.456 -0.048 2.00e-02 2.50e+03 5.69e+00 bond pdb=" C4 PGT B 914 " pdb=" O4P PGT B 914 " ideal model delta sigma weight residual 1.410 1.457 -0.047 2.00e-02 2.50e+03 5.51e+00 ... (remaining 13309 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 17186 2.25 - 4.50: 714 4.50 - 6.75: 12 6.75 - 9.00: 0 9.00 - 11.25: 6 Bond angle restraints: 17918 Sorted by residual: angle pdb=" N PRO B 469 " pdb=" CA PRO B 469 " pdb=" CB PRO B 469 " ideal model delta sigma weight residual 103.25 99.03 4.22 1.05e+00 9.07e-01 1.61e+01 angle pdb=" N PRO A 469 " pdb=" CA PRO A 469 " pdb=" CB PRO A 469 " ideal model delta sigma weight residual 103.25 99.03 4.22 1.05e+00 9.07e-01 1.61e+01 angle pdb=" N ILE A 391 " pdb=" CA ILE A 391 " pdb=" CB ILE A 391 " ideal model delta sigma weight residual 111.67 108.34 3.33 8.50e-01 1.38e+00 1.53e+01 angle pdb=" N ILE B 391 " pdb=" CA ILE B 391 " pdb=" CB ILE B 391 " ideal model delta sigma weight residual 111.67 108.34 3.33 8.50e-01 1.38e+00 1.53e+01 angle pdb=" O3P PGT A 912 " pdb=" P PGT A 912 " pdb=" O4P PGT A 912 " ideal model delta sigma weight residual 92.82 104.07 -11.25 3.00e+00 1.11e-01 1.41e+01 ... (remaining 17913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.79: 7056 15.79 - 31.57: 766 31.57 - 47.36: 220 47.36 - 63.15: 122 63.15 - 78.93: 8 Dihedral angle restraints: 8172 sinusoidal: 3566 harmonic: 4606 Sorted by residual: dihedral pdb=" CA GLY B 289 " pdb=" C GLY B 289 " pdb=" N GLY B 290 " pdb=" CA GLY B 290 " ideal model delta harmonic sigma weight residual 180.00 -162.87 -17.13 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA GLY A 289 " pdb=" C GLY A 289 " pdb=" N GLY A 290 " pdb=" CA GLY A 290 " ideal model delta harmonic sigma weight residual -180.00 -162.87 -17.13 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ILE A 602 " pdb=" C ILE A 602 " pdb=" N ALA A 603 " pdb=" CA ALA A 603 " ideal model delta harmonic sigma weight residual 180.00 163.87 16.13 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 8169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1698 0.075 - 0.150: 346 0.150 - 0.225: 6 0.225 - 0.299: 0 0.299 - 0.374: 2 Chirality restraints: 2052 Sorted by residual: chirality pdb=" C06 J4U A 901 " pdb=" C02 J4U A 901 " pdb=" C05 J4U A 901 " pdb=" C07 J4U A 901 " both_signs ideal model delta sigma weight residual False 2.73 2.35 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" C06 J4U B 903 " pdb=" C02 J4U B 903 " pdb=" C05 J4U B 903 " pdb=" C07 J4U B 903 " both_signs ideal model delta sigma weight residual False 2.73 2.35 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" C2 PGT A 902 " pdb=" C1 PGT A 902 " pdb=" C3 PGT A 902 " pdb=" O2 PGT A 902 " both_signs ideal model delta sigma weight residual False 2.35 2.55 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 2049 not shown) Planarity restraints: 2176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 466 " 0.023 2.00e-02 2.50e+03 1.49e-02 3.91e+00 pdb=" CG PHE A 466 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 466 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 466 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 466 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 466 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 466 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 466 " 0.023 2.00e-02 2.50e+03 1.49e-02 3.91e+00 pdb=" CG PHE B 466 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE B 466 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 466 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE B 466 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 466 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 466 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 PGT B 902 " -0.033 2.00e-02 2.50e+03 1.91e-02 3.63e+00 pdb=" C12 PGT B 902 " 0.010 2.00e-02 2.50e+03 pdb=" O11 PGT B 902 " 0.013 2.00e-02 2.50e+03 pdb=" O3 PGT B 902 " 0.011 2.00e-02 2.50e+03 ... (remaining 2173 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 323 2.71 - 3.26: 12735 3.26 - 3.80: 19722 3.80 - 4.35: 26284 4.35 - 4.90: 44214 Nonbonded interactions: 103278 Sorted by model distance: nonbonded pdb=" O LEU B 515 " pdb=" NH2 ARG B 521 " model vdw 2.161 3.120 nonbonded pdb=" O LEU A 515 " pdb=" NH2 ARG A 521 " model vdw 2.161 3.120 nonbonded pdb=" O ILE B 564 " pdb=" OG SER B 567 " model vdw 2.396 3.040 nonbonded pdb=" O ILE A 564 " pdb=" OG SER A 567 " model vdw 2.396 3.040 nonbonded pdb=" NH1 ARG B 419 " pdb=" OD1 ASP B 623 " model vdw 2.397 3.120 ... (remaining 103273 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 872 or resid 902 or (resid 904 and (name C32 or \ name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C3 \ 9 or name C40)) or (resid 909 and (name C32 or name C33 or name C34 or name C35 \ or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name \ C42 or name C43 or name C44 or name C45)) or (resid 910 and (name C34 or name C3 \ 5 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or nam \ e C42 or name C43 or name C44 or name C45)) or (resid 911 and (name C32 or name \ C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or n \ ame C40 or name C41 or name C42 or name C43 or name C44 or name C45 or name C46 \ or name C47 or name C48)) or (resid 912 and (name C34 or name C35 or name C36 or \ name C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C4 \ 3 or name C44 or name C45 or name C46 or name C47 or name C48)) or (resid 915 th \ rough 916 and (name C11 or name C12 or name C13 or name C14 or name C15 or name \ C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or n \ ame C23 or name C24 or name C8 )))) selection = (chain 'B' and (resid 33 through 872 or (resid 902 and (name C1 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C2 or name C20 or name C3 or name C31 or name C32 or name C3 \ 3 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or nam \ e C4 or name C40 or name O11 or name O1P or name O2 or name O2P or name O3 or na \ me O31 or name O3P or name O4P or name P )) or (resid 904 and (name C32 or name \ C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or n \ ame C40)) or resid 909 or (resid 910 and (name C34 or name C35 or name C36 or na \ me C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 o \ r name C44 or name C45)) or resid 911 through 912 or resid 915 through 916)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.640 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 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 : 0.007 0.050 13314 Z= 0.485 Angle : 1.073 11.247 17918 Z= 0.743 Chirality : 0.054 0.374 2052 Planarity : 0.006 0.061 2176 Dihedral : 15.727 78.933 5196 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.66 % Favored : 96.22 % Rotamer: Outliers : 1.60 % Allowed : 6.25 % Favored : 92.15 % 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 are not related in a simple way. whole: -1.90 (0.18), residues: 1586 helix: -1.01 (0.13), residues: 1062 sheet: -0.02 (0.42), residues: 152 loop : -2.02 (0.27), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 137 TYR 0.022 0.003 TYR A 505 PHE 0.030 0.003 PHE B 444 TRP 0.020 0.003 TRP A 510 HIS 0.006 0.002 HIS B 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00749 / 0.48 (13314) covalent geometry : angle 1.07284 / 0.74 (17918) hydrogen bonds : bond 0.18746 / 12.75 ( 885) hydrogen bonds : angle 7.49380 / 5.49 ( 2565) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 228 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.6475 (tpp) cc_final: 0.5967 (tmm) REVERT: A 148 GLU cc_start: 0.7242 (mt-10) cc_final: 0.7030 (mt-10) REVERT: A 173 LEU cc_start: 0.8060 (tp) cc_final: 0.7836 (mt) REVERT: A 340 ARG cc_start: 0.6132 (ttp80) cc_final: 0.5902 (ttp80) REVERT: A 464 ARG cc_start: 0.7457 (mtt90) cc_final: 0.6586 (mtm110) REVERT: A 508 GLN cc_start: 0.7699 (pt0) cc_final: 0.6771 (mm-40) REVERT: A 511 TRP cc_start: 0.7906 (m-90) cc_final: 0.7410 (m-90) REVERT: A 612 MET cc_start: 0.5014 (tpp) cc_final: 0.4806 (tpp) REVERT: A 738 ILE cc_start: 0.8379 (mp) cc_final: 0.7880 (tp) REVERT: A 756 THR cc_start: 0.7835 (p) cc_final: 0.7513 (t) REVERT: A 760 GLU cc_start: 0.7753 (mp0) cc_final: 0.7346 (tp30) REVERT: A 767 MET cc_start: 0.7912 (tmm) cc_final: 0.7318 (tmm) REVERT: A 840 LYS cc_start: 0.7212 (mmtp) cc_final: 0.6916 (mmtp) REVERT: A 848 GLU cc_start: 0.6703 (tt0) cc_final: 0.6343 (tt0) REVERT: A 860 PRO cc_start: 0.6787 (Cg_exo) cc_final: 0.6573 (Cg_endo) REVERT: B 107 MET cc_start: 0.6472 (tpp) cc_final: 0.5964 (tmm) REVERT: B 148 GLU cc_start: 0.7242 (mt-10) cc_final: 0.7030 (mt-10) REVERT: B 173 LEU cc_start: 0.8060 (tp) cc_final: 0.7836 (mt) REVERT: B 340 ARG cc_start: 0.6131 (ttp80) cc_final: 0.5901 (ttp80) REVERT: B 464 ARG cc_start: 0.7458 (mtt90) cc_final: 0.6588 (mtm110) REVERT: B 508 GLN cc_start: 0.7700 (pt0) cc_final: 0.6771 (mm-40) REVERT: B 511 TRP cc_start: 0.7907 (m-90) cc_final: 0.7410 (m-90) REVERT: B 612 MET cc_start: 0.5013 (tpp) cc_final: 0.4805 (tpp) REVERT: B 738 ILE cc_start: 0.8379 (mp) cc_final: 0.7881 (tp) REVERT: B 756 THR cc_start: 0.7832 (p) cc_final: 0.7510 (t) REVERT: B 760 GLU cc_start: 0.7755 (mp0) cc_final: 0.7346 (tp30) REVERT: B 767 MET cc_start: 0.7914 (tmm) cc_final: 0.7318 (tmm) REVERT: B 840 LYS cc_start: 0.7215 (mmtp) cc_final: 0.6918 (mmtp) REVERT: B 848 GLU cc_start: 0.6702 (tt0) cc_final: 0.6345 (tt0) REVERT: B 860 PRO cc_start: 0.6785 (Cg_exo) cc_final: 0.6572 (Cg_endo) outliers start: 20 outliers final: 4 residues processed: 242 average time/residue: 0.1393 time to fit residues: 46.6462 Evaluate side-chains 182 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 178 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 469 PRO Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 469 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.0370 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.0170 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.3980 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN A 305 GLN B 122 ASN B 305 GLN B 504 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.191860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.150962 restraints weight = 12988.498| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.26 r_work: 0.3227 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13314 Z= 0.115 Angle : 0.508 8.016 17918 Z= 0.248 Chirality : 0.035 0.166 2052 Planarity : 0.005 0.047 2176 Dihedral : 11.097 59.711 2448 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.68 % Allowed : 10.58 % Favored : 87.74 % 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 are not related in a simple way. whole: 2.06 (0.21), residues: 1586 helix: 2.37 (0.16), residues: 1046 sheet: 0.20 (0.40), residues: 152 loop : -1.01 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 341 TYR 0.006 0.001 TYR A 139 PHE 0.011 0.001 PHE B 87 TRP 0.010 0.001 TRP A 446 HIS 0.002 0.001 HIS A 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (13314) covalent geometry : angle 0.50789 / 0.25 (17918) hydrogen bonds : bond 0.04157 / 2.84 ( 885) hydrogen bonds : angle 4.27384 / 3.16 ( 2565) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8570 (mp) REVERT: A 107 MET cc_start: 0.7995 (tpp) cc_final: 0.7686 (tpt) REVERT: A 340 ARG cc_start: 0.8302 (ttp80) cc_final: 0.7971 (ttp80) REVERT: A 464 ARG cc_start: 0.8561 (mtt90) cc_final: 0.8117 (mtm110) REVERT: A 511 TRP cc_start: 0.8108 (m-90) cc_final: 0.7797 (m-90) REVERT: A 567 SER cc_start: 0.7966 (p) cc_final: 0.7405 (m) REVERT: A 580 LYS cc_start: 0.8776 (ptpp) cc_final: 0.8340 (mtmm) REVERT: A 597 ARG cc_start: 0.7456 (mtt-85) cc_final: 0.7245 (mtt-85) REVERT: A 860 PRO cc_start: 0.7683 (Cg_exo) cc_final: 0.7386 (Cg_endo) REVERT: B 47 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8595 (mp) REVERT: B 107 MET cc_start: 0.8011 (tpp) cc_final: 0.7702 (tpt) REVERT: B 340 ARG cc_start: 0.8303 (ttp80) cc_final: 0.7973 (ttp80) REVERT: B 464 ARG cc_start: 0.8549 (mtt90) cc_final: 0.8113 (mtm110) REVERT: B 511 TRP cc_start: 0.8110 (m-90) cc_final: 0.7797 (m-90) REVERT: B 567 SER cc_start: 0.7978 (p) cc_final: 0.7427 (m) REVERT: B 580 LYS cc_start: 0.8776 (ptpp) cc_final: 0.8338 (mtmm) REVERT: B 597 ARG cc_start: 0.7452 (mtt-85) cc_final: 0.7238 (mtt-85) REVERT: B 860 PRO cc_start: 0.7681 (Cg_exo) cc_final: 0.7384 (Cg_endo) outliers start: 21 outliers final: 9 residues processed: 176 average time/residue: 0.1109 time to fit residues: 29.0745 Evaluate side-chains 155 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 504 HIS Chi-restraints excluded: chain B residue 574 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 136 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 120 optimal weight: 0.3980 chunk 37 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 71 optimal weight: 10.0000 chunk 119 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN B 122 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.190404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.149175 restraints weight = 13194.020| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.38 r_work: 0.3285 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13314 Z= 0.116 Angle : 0.485 7.213 17918 Z= 0.232 Chirality : 0.035 0.171 2052 Planarity : 0.004 0.042 2176 Dihedral : 10.400 58.833 2440 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.32 % Allowed : 12.58 % Favored : 85.10 % 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 are not related in a simple way. whole: 2.71 (0.21), residues: 1586 helix: 2.89 (0.15), residues: 1048 sheet: 0.41 (0.39), residues: 152 loop : -0.83 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 597 TYR 0.008 0.001 TYR B 505 PHE 0.012 0.001 PHE B 839 TRP 0.009 0.001 TRP A 446 HIS 0.010 0.001 HIS B 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (13314) covalent geometry : angle 0.48550 / 0.23 (17918) hydrogen bonds : bond 0.03909 / 2.66 ( 885) hydrogen bonds : angle 3.94929 / 2.93 ( 2565) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8560 (mp) REVERT: A 107 MET cc_start: 0.8013 (tpp) cc_final: 0.7661 (tpt) REVERT: A 173 LEU cc_start: 0.8244 (tp) cc_final: 0.8010 (mt) REVERT: A 340 ARG cc_start: 0.8354 (ttp80) cc_final: 0.7901 (ttp80) REVERT: A 464 ARG cc_start: 0.8608 (mtt90) cc_final: 0.8166 (mtm110) REVERT: A 511 TRP cc_start: 0.8200 (m-90) cc_final: 0.7451 (m100) REVERT: A 567 SER cc_start: 0.7710 (p) cc_final: 0.7386 (m) REVERT: A 580 LYS cc_start: 0.8815 (ptpp) cc_final: 0.8443 (mtmm) REVERT: A 738 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.7983 (tp) REVERT: A 860 PRO cc_start: 0.7676 (Cg_exo) cc_final: 0.7420 (Cg_endo) REVERT: B 47 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8539 (mp) REVERT: B 107 MET cc_start: 0.8029 (tpp) cc_final: 0.7678 (tpt) REVERT: B 173 LEU cc_start: 0.8243 (tp) cc_final: 0.8006 (mt) REVERT: B 340 ARG cc_start: 0.8356 (ttp80) cc_final: 0.7906 (ttp80) REVERT: B 464 ARG cc_start: 0.8605 (mtt90) cc_final: 0.8163 (mtm110) REVERT: B 511 TRP cc_start: 0.8202 (m-90) cc_final: 0.7448 (m100) REVERT: B 567 SER cc_start: 0.7721 (p) cc_final: 0.7395 (m) REVERT: B 580 LYS cc_start: 0.8816 (ptpp) cc_final: 0.8443 (mtmm) REVERT: B 738 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.7983 (tp) REVERT: B 860 PRO cc_start: 0.7678 (Cg_exo) cc_final: 0.7423 (Cg_endo) outliers start: 29 outliers final: 12 residues processed: 181 average time/residue: 0.1161 time to fit residues: 31.0229 Evaluate side-chains 157 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 852 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 24 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 119 optimal weight: 0.7980 chunk 137 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.190163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.151390 restraints weight = 13199.612| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.26 r_work: 0.3301 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13314 Z= 0.133 Angle : 0.497 6.773 17918 Z= 0.235 Chirality : 0.036 0.185 2052 Planarity : 0.004 0.043 2176 Dihedral : 10.311 58.150 2440 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.88 % Allowed : 12.58 % Favored : 84.54 % 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 are not related in a simple way. whole: 2.83 (0.21), residues: 1586 helix: 2.93 (0.15), residues: 1050 sheet: 0.72 (0.39), residues: 152 loop : -0.77 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 597 TYR 0.006 0.001 TYR B 259 PHE 0.013 0.001 PHE B 444 TRP 0.010 0.001 TRP B 446 HIS 0.003 0.001 HIS A 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 (13314) covalent geometry : angle 0.49712 / 0.23 (17918) hydrogen bonds : bond 0.04037 / 2.76 ( 885) hydrogen bonds : angle 3.86971 / 2.87 ( 2565) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8553 (mp) REVERT: A 107 MET cc_start: 0.7973 (tpp) cc_final: 0.7623 (tpt) REVERT: A 173 LEU cc_start: 0.8225 (tp) cc_final: 0.7976 (mt) REVERT: A 340 ARG cc_start: 0.8308 (ttp80) cc_final: 0.7951 (ttp80) REVERT: A 464 ARG cc_start: 0.8585 (mtt90) cc_final: 0.8189 (mtm110) REVERT: A 511 TRP cc_start: 0.8201 (m-90) cc_final: 0.7509 (m100) REVERT: A 567 SER cc_start: 0.7636 (p) cc_final: 0.7321 (m) REVERT: A 580 LYS cc_start: 0.8895 (ptpp) cc_final: 0.8532 (mtmm) REVERT: A 604 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8136 (tp) REVERT: A 738 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7960 (tp) REVERT: B 47 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8547 (mp) REVERT: B 107 MET cc_start: 0.7982 (tpp) cc_final: 0.7635 (tpt) REVERT: B 173 LEU cc_start: 0.8213 (tp) cc_final: 0.7967 (mt) REVERT: B 340 ARG cc_start: 0.8304 (ttp80) cc_final: 0.7949 (ttp80) REVERT: B 464 ARG cc_start: 0.8584 (mtt90) cc_final: 0.8192 (mtm110) REVERT: B 511 TRP cc_start: 0.8188 (m-90) cc_final: 0.7503 (m100) REVERT: B 567 SER cc_start: 0.7646 (p) cc_final: 0.7326 (m) REVERT: B 580 LYS cc_start: 0.8896 (ptpp) cc_final: 0.8529 (mtmm) REVERT: B 604 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8141 (tp) REVERT: B 738 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7962 (tp) outliers start: 36 outliers final: 18 residues processed: 174 average time/residue: 0.1127 time to fit residues: 29.3287 Evaluate side-chains 168 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 854 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 132 optimal weight: 0.0000 chunk 118 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 chunk 141 optimal weight: 6.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.190579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.151213 restraints weight = 13261.089| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.28 r_work: 0.3289 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13314 Z= 0.123 Angle : 0.480 6.920 17918 Z= 0.228 Chirality : 0.035 0.180 2052 Planarity : 0.004 0.044 2176 Dihedral : 10.047 59.985 2440 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.24 % Allowed : 13.06 % Favored : 84.70 % 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 are not related in a simple way. whole: 3.00 (0.21), residues: 1586 helix: 3.03 (0.15), residues: 1046 sheet: 0.91 (0.37), residues: 154 loop : -0.64 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 597 TYR 0.009 0.001 TYR B 259 PHE 0.011 0.001 PHE A 444 TRP 0.009 0.001 TRP A 446 HIS 0.003 0.001 HIS B 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (13314) covalent geometry : angle 0.48003 / 0.23 (17918) hydrogen bonds : bond 0.03825 / 2.62 ( 885) hydrogen bonds : angle 3.76210 / 2.80 ( 2565) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8545 (mp) REVERT: A 107 MET cc_start: 0.7943 (tpp) cc_final: 0.7593 (tpt) REVERT: A 173 LEU cc_start: 0.8188 (tp) cc_final: 0.7932 (mt) REVERT: A 340 ARG cc_start: 0.8262 (ttp80) cc_final: 0.7819 (ttp80) REVERT: A 464 ARG cc_start: 0.8593 (mtt90) cc_final: 0.8182 (mtm110) REVERT: A 511 TRP cc_start: 0.8196 (m-90) cc_final: 0.7523 (m100) REVERT: A 567 SER cc_start: 0.7644 (p) cc_final: 0.7285 (m) REVERT: A 580 LYS cc_start: 0.8917 (ptpp) cc_final: 0.8643 (mtmm) REVERT: A 738 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.7936 (tp) REVERT: B 47 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8546 (mp) REVERT: B 107 MET cc_start: 0.7959 (tpp) cc_final: 0.7610 (tpt) REVERT: B 173 LEU cc_start: 0.8186 (tp) cc_final: 0.7927 (mt) REVERT: B 340 ARG cc_start: 0.8255 (ttp80) cc_final: 0.7814 (ttp80) REVERT: B 464 ARG cc_start: 0.8590 (mtt90) cc_final: 0.8181 (mtm110) REVERT: B 511 TRP cc_start: 0.8185 (m-90) cc_final: 0.7517 (m100) REVERT: B 567 SER cc_start: 0.7633 (p) cc_final: 0.7276 (m) REVERT: B 580 LYS cc_start: 0.8924 (ptpp) cc_final: 0.8646 (mtmm) REVERT: B 738 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7942 (tp) outliers start: 28 outliers final: 22 residues processed: 164 average time/residue: 0.1104 time to fit residues: 27.1791 Evaluate side-chains 159 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 854 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 121 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 155 optimal weight: 9.9990 chunk 85 optimal weight: 0.6980 chunk 141 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.188875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.150716 restraints weight = 13168.067| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.23 r_work: 0.3300 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13314 Z= 0.146 Angle : 0.507 7.365 17918 Z= 0.239 Chirality : 0.036 0.192 2052 Planarity : 0.004 0.046 2176 Dihedral : 10.224 58.058 2440 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.21 % Allowed : 13.86 % Favored : 82.93 % 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 are not related in a simple way. whole: 2.99 (0.21), residues: 1586 helix: 3.00 (0.15), residues: 1050 sheet: 1.02 (0.38), residues: 154 loop : -0.67 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 597 TYR 0.006 0.001 TYR B 789 PHE 0.013 0.001 PHE B 444 TRP 0.009 0.001 TRP A 446 HIS 0.003 0.001 HIS B 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (13314) covalent geometry : angle 0.50680 / 0.24 (17918) hydrogen bonds : bond 0.04142 / 2.83 ( 885) hydrogen bonds : angle 3.81111 / 2.83 ( 2565) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 0.507 Fit side-chains REVERT: A 47 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8541 (mp) REVERT: A 107 MET cc_start: 0.7970 (tpp) cc_final: 0.7605 (tpt) REVERT: A 173 LEU cc_start: 0.8198 (tp) cc_final: 0.7829 (mt) REVERT: A 340 ARG cc_start: 0.8289 (ttp80) cc_final: 0.7913 (ttp80) REVERT: A 464 ARG cc_start: 0.8620 (mtt90) cc_final: 0.8199 (mtm110) REVERT: A 511 TRP cc_start: 0.8235 (m-90) cc_final: 0.7571 (m100) REVERT: A 567 SER cc_start: 0.7697 (p) cc_final: 0.7382 (m) REVERT: A 580 LYS cc_start: 0.8939 (ptpp) cc_final: 0.8698 (mtmm) REVERT: A 738 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7979 (tp) REVERT: B 47 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8540 (mp) REVERT: B 107 MET cc_start: 0.7972 (tpp) cc_final: 0.7611 (tpt) REVERT: B 173 LEU cc_start: 0.8195 (tp) cc_final: 0.7896 (mt) REVERT: B 340 ARG cc_start: 0.8281 (ttp80) cc_final: 0.7909 (ttp80) REVERT: B 464 ARG cc_start: 0.8613 (mtt90) cc_final: 0.8186 (mtm110) REVERT: B 511 TRP cc_start: 0.8231 (m-90) cc_final: 0.7553 (m100) REVERT: B 567 SER cc_start: 0.7679 (p) cc_final: 0.7369 (m) REVERT: B 580 LYS cc_start: 0.8947 (ptpp) cc_final: 0.8703 (mtmm) REVERT: B 738 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.7984 (tp) outliers start: 40 outliers final: 28 residues processed: 172 average time/residue: 0.1090 time to fit residues: 28.2936 Evaluate side-chains 171 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 854 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 152 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.186261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.147261 restraints weight = 13247.035| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.32 r_work: 0.3264 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13314 Z= 0.146 Angle : 0.515 7.691 17918 Z= 0.244 Chirality : 0.036 0.192 2052 Planarity : 0.004 0.046 2176 Dihedral : 10.232 58.242 2440 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.04 % Allowed : 15.14 % Favored : 81.81 % 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 are not related in a simple way. whole: 2.93 (0.21), residues: 1586 helix: 2.92 (0.15), residues: 1056 sheet: 1.06 (0.38), residues: 154 loop : -0.66 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 597 TYR 0.009 0.001 TYR A 259 PHE 0.015 0.001 PHE A 839 TRP 0.009 0.001 TRP A 446 HIS 0.003 0.001 HIS B 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (13314) covalent geometry : angle 0.51461 / 0.24 (17918) hydrogen bonds : bond 0.04124 / 2.81 ( 885) hydrogen bonds : angle 3.82362 / 2.84 ( 2565) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 134 time to evaluate : 0.532 Fit side-chains REVERT: A 47 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8552 (mp) REVERT: A 107 MET cc_start: 0.7979 (tpp) cc_final: 0.7616 (tpt) REVERT: A 173 LEU cc_start: 0.8198 (tp) cc_final: 0.7815 (mt) REVERT: A 340 ARG cc_start: 0.8291 (ttp80) cc_final: 0.7914 (ttp80) REVERT: A 464 ARG cc_start: 0.8658 (mtt90) cc_final: 0.8222 (mtm110) REVERT: A 511 TRP cc_start: 0.8225 (m-90) cc_final: 0.7563 (m100) REVERT: A 567 SER cc_start: 0.7789 (p) cc_final: 0.7387 (m) REVERT: A 580 LYS cc_start: 0.8939 (ptpp) cc_final: 0.8692 (mtmm) REVERT: A 738 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7981 (tp) REVERT: B 47 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8544 (mp) REVERT: B 107 MET cc_start: 0.7976 (tpp) cc_final: 0.7613 (tpt) REVERT: B 173 LEU cc_start: 0.8196 (tp) cc_final: 0.7803 (mt) REVERT: B 340 ARG cc_start: 0.8286 (ttp80) cc_final: 0.7911 (ttp80) REVERT: B 464 ARG cc_start: 0.8654 (mtt90) cc_final: 0.8218 (mtm110) REVERT: B 511 TRP cc_start: 0.8211 (m-90) cc_final: 0.7553 (m100) REVERT: B 567 SER cc_start: 0.7776 (p) cc_final: 0.7374 (m) REVERT: B 580 LYS cc_start: 0.8945 (ptpp) cc_final: 0.8699 (mtmm) REVERT: B 738 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.7974 (tp) outliers start: 38 outliers final: 32 residues processed: 159 average time/residue: 0.1111 time to fit residues: 26.6017 Evaluate side-chains 165 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 854 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 43 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 106 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.187548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.147073 restraints weight = 13158.290| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.40 r_work: 0.3199 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13314 Z= 0.123 Angle : 0.491 7.887 17918 Z= 0.234 Chirality : 0.035 0.182 2052 Planarity : 0.004 0.045 2176 Dihedral : 9.921 59.175 2440 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.29 % Allowed : 14.90 % Favored : 81.81 % 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 are not related in a simple way. whole: 3.10 (0.21), residues: 1586 helix: 3.04 (0.15), residues: 1044 sheet: 1.11 (0.38), residues: 154 loop : -0.43 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 597 TYR 0.005 0.001 TYR B 259 PHE 0.021 0.001 PHE B 839 TRP 0.007 0.001 TRP A 446 HIS 0.003 0.001 HIS B 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (13314) covalent geometry : angle 0.49110 / 0.23 (17918) hydrogen bonds : bond 0.03803 / 2.59 ( 885) hydrogen bonds : angle 3.72662 / 2.77 ( 2565) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 0.440 Fit side-chains REVERT: A 47 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8552 (mp) REVERT: A 107 MET cc_start: 0.8058 (tpp) cc_final: 0.7675 (tpt) REVERT: A 173 LEU cc_start: 0.8255 (tp) cc_final: 0.7877 (mt) REVERT: A 340 ARG cc_start: 0.8415 (ttp80) cc_final: 0.8004 (ttp80) REVERT: A 464 ARG cc_start: 0.8731 (mtt90) cc_final: 0.8263 (mtm110) REVERT: A 511 TRP cc_start: 0.8270 (m-90) cc_final: 0.7608 (m100) REVERT: A 567 SER cc_start: 0.7876 (p) cc_final: 0.7476 (m) REVERT: A 580 LYS cc_start: 0.8966 (ptpp) cc_final: 0.8723 (mtmm) REVERT: A 738 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.7995 (tp) REVERT: B 47 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8543 (mp) REVERT: B 107 MET cc_start: 0.8039 (tpp) cc_final: 0.7658 (tpt) REVERT: B 173 LEU cc_start: 0.8258 (tp) cc_final: 0.7883 (mt) REVERT: B 340 ARG cc_start: 0.8402 (ttp80) cc_final: 0.7991 (ttp80) REVERT: B 464 ARG cc_start: 0.8723 (mtt90) cc_final: 0.8245 (mtm110) REVERT: B 511 TRP cc_start: 0.8267 (m-90) cc_final: 0.7610 (m100) REVERT: B 567 SER cc_start: 0.7862 (p) cc_final: 0.7462 (m) REVERT: B 580 LYS cc_start: 0.8967 (ptpp) cc_final: 0.8730 (mtmm) REVERT: B 738 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.7988 (tp) outliers start: 41 outliers final: 33 residues processed: 161 average time/residue: 0.1114 time to fit residues: 26.9276 Evaluate side-chains 170 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 854 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 113 optimal weight: 0.0770 chunk 105 optimal weight: 0.0980 chunk 7 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 68 optimal weight: 0.2980 chunk 121 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.189134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.148542 restraints weight = 13270.995| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.28 r_work: 0.3263 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13314 Z= 0.106 Angle : 0.476 8.431 17918 Z= 0.226 Chirality : 0.035 0.171 2052 Planarity : 0.004 0.044 2176 Dihedral : 9.495 58.384 2440 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.12 % Allowed : 15.30 % Favored : 81.57 % 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 are not related in a simple way. whole: 3.31 (0.21), residues: 1586 helix: 3.18 (0.15), residues: 1044 sheet: 1.16 (0.37), residues: 154 loop : -0.28 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 597 TYR 0.009 0.001 TYR B 259 PHE 0.007 0.001 PHE B 444 TRP 0.007 0.001 TRP A 446 HIS 0.004 0.000 HIS B 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (13314) covalent geometry : angle 0.47625 / 0.23 (17918) hydrogen bonds : bond 0.03502 / 2.39 ( 885) hydrogen bonds : angle 3.61332 / 2.69 ( 2565) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 136 time to evaluate : 0.462 Fit side-chains REVERT: A 47 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8576 (mp) REVERT: A 107 MET cc_start: 0.8014 (tpp) cc_final: 0.7651 (tpt) REVERT: A 173 LEU cc_start: 0.8141 (tp) cc_final: 0.7825 (mt) REVERT: A 340 ARG cc_start: 0.8357 (ttp80) cc_final: 0.7971 (ttp80) REVERT: A 464 ARG cc_start: 0.8677 (mtt90) cc_final: 0.8252 (mtm110) REVERT: A 511 TRP cc_start: 0.8175 (m-90) cc_final: 0.7534 (m100) REVERT: A 567 SER cc_start: 0.7808 (p) cc_final: 0.7458 (m) REVERT: A 580 LYS cc_start: 0.8907 (ptpp) cc_final: 0.8658 (mtmm) REVERT: A 738 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7934 (tp) REVERT: B 47 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8571 (mp) REVERT: B 107 MET cc_start: 0.8009 (tpp) cc_final: 0.7646 (tpt) REVERT: B 173 LEU cc_start: 0.8126 (tp) cc_final: 0.7785 (mt) REVERT: B 340 ARG cc_start: 0.8355 (ttp80) cc_final: 0.7970 (ttp80) REVERT: B 464 ARG cc_start: 0.8675 (mtt90) cc_final: 0.8253 (mtm110) REVERT: B 511 TRP cc_start: 0.8175 (m-90) cc_final: 0.7540 (m100) REVERT: B 567 SER cc_start: 0.7805 (p) cc_final: 0.7446 (m) REVERT: B 580 LYS cc_start: 0.8909 (ptpp) cc_final: 0.8662 (mtmm) REVERT: B 738 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7935 (tp) outliers start: 39 outliers final: 29 residues processed: 165 average time/residue: 0.1118 time to fit residues: 27.7294 Evaluate side-chains 167 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 854 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 78 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 57 optimal weight: 0.4980 chunk 101 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 106 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 504 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.190936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.151471 restraints weight = 13271.246| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.24 r_work: 0.3319 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13314 Z= 0.113 Angle : 0.492 8.647 17918 Z= 0.235 Chirality : 0.035 0.172 2052 Planarity : 0.004 0.044 2176 Dihedral : 9.463 59.322 2440 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.88 % Allowed : 15.62 % Favored : 81.49 % 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 are not related in a simple way. whole: 3.29 (0.21), residues: 1586 helix: 3.16 (0.16), residues: 1042 sheet: 1.08 (0.37), residues: 156 loop : -0.21 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 597 TYR 0.005 0.001 TYR B 259 PHE 0.012 0.001 PHE B 839 TRP 0.007 0.001 TRP A 446 HIS 0.004 0.001 HIS B 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (13314) covalent geometry : angle 0.49202 / 0.24 (17918) hydrogen bonds : bond 0.03596 / 2.46 ( 885) hydrogen bonds : angle 3.63966 / 2.71 ( 2565) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 0.458 Fit side-chains REVERT: A 47 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8584 (mp) REVERT: A 107 MET cc_start: 0.7961 (tpp) cc_final: 0.7609 (tpt) REVERT: A 173 LEU cc_start: 0.8093 (tp) cc_final: 0.7753 (mt) REVERT: A 224 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7822 (tt) REVERT: A 340 ARG cc_start: 0.8297 (ttp80) cc_final: 0.7932 (ttp80) REVERT: A 511 TRP cc_start: 0.8130 (m-90) cc_final: 0.7513 (m100) REVERT: A 567 SER cc_start: 0.7753 (p) cc_final: 0.7389 (m) REVERT: A 580 LYS cc_start: 0.8872 (ptpp) cc_final: 0.8572 (mtmm) REVERT: A 738 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7849 (tp) REVERT: B 47 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8578 (mp) REVERT: B 107 MET cc_start: 0.7954 (tpp) cc_final: 0.7602 (tpt) REVERT: B 173 LEU cc_start: 0.8068 (tp) cc_final: 0.7717 (mt) REVERT: B 340 ARG cc_start: 0.8300 (ttp80) cc_final: 0.7935 (ttp80) REVERT: B 511 TRP cc_start: 0.8130 (m-90) cc_final: 0.7518 (m100) REVERT: B 567 SER cc_start: 0.7754 (p) cc_final: 0.7394 (m) REVERT: B 580 LYS cc_start: 0.8875 (ptpp) cc_final: 0.8571 (mtmm) REVERT: B 738 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7852 (tp) outliers start: 36 outliers final: 28 residues processed: 158 average time/residue: 0.1125 time to fit residues: 26.5538 Evaluate side-chains 162 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 504 HIS Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 854 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 76 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 60 optimal weight: 0.2980 chunk 87 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 504 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.189434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.151377 restraints weight = 13208.835| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.10 r_work: 0.3309 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13314 Z= 0.136 Angle : 0.520 8.293 17918 Z= 0.247 Chirality : 0.036 0.181 2052 Planarity : 0.004 0.045 2176 Dihedral : 9.691 57.634 2440 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.80 % Allowed : 15.95 % Favored : 81.25 % 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 are not related in a simple way. whole: 3.18 (0.21), residues: 1586 helix: 3.08 (0.16), residues: 1044 sheet: 1.11 (0.36), residues: 154 loop : -0.32 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 597 TYR 0.010 0.001 TYR B 259 PHE 0.020 0.001 PHE B 839 TRP 0.008 0.001 TRP A 446 HIS 0.003 0.001 HIS B 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (13314) covalent geometry : angle 0.51999 / 0.25 (17918) hydrogen bonds : bond 0.03897 / 2.66 ( 885) hydrogen bonds : angle 3.71648 / 2.76 ( 2565) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2664.19 seconds wall clock time: 46 minutes 41.76 seconds (2801.76 seconds total)