Starting phenix.real_space_refine on Fri Jul 3 10:11:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j8r_61239/07_2026/9j8r_61239.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j8r_61239/07_2026/9j8r_61239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9j8r_61239/07_2026/9j8r_61239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j8r_61239/07_2026/9j8r_61239.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j8r_61239/07_2026/9j8r_61239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j8r_61239/07_2026/9j8r_61239.map" } resolution = 3.4 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= 0.116 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): 0.01s 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: 2.45, per 1000 atoms: 0.19 Number of scatterers: 13056 At special positions: 0 Unit cell: (73.83, 121.98, 146.59, 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: 1.14 Conformation dependent library (CDL) restraints added in 422.7 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: 64 helices and 6 sheets defined 69.5% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 33 through 56 Processing helix chain 'A' and resid 60 through 71 removed outlier: 3.543A pdb=" N VAL A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 102 removed outlier: 3.942A pdb=" N LEU A 90 " --> pdb=" O GLY A 86 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 125 Processing helix chain 'A' and resid 130 through 141 removed outlier: 4.062A pdb=" N ARG A 141 " --> pdb=" O ARG A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 174 removed outlier: 4.258A 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: 3.627A pdb=" N HIS A 211 " --> pdb=" O PHE A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 261 removed outlier: 3.653A pdb=" N LEU A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 3.872A 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: 3.544A 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 391 removed outlier: 4.004A pdb=" N PHE A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 390 " --> pdb=" O HIS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 419 removed outlier: 3.687A pdb=" N ASP A 397 " --> pdb=" O HIS A 393 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 444 removed outlier: 3.603A pdb=" N LEU A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 462 Processing helix chain 'A' and resid 478 through 500 Processing helix chain 'A' and resid 506 through 512 removed outlier: 3.935A 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 569 through 578 removed outlier: 3.822A pdb=" N GLY A 572 " --> pdb=" O GLN A 569 " (cutoff:3.500A) 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 649 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: 4.353A 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: 3.542A pdb=" N VAL B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 102 removed outlier: 3.947A pdb=" N LEU B 90 " --> pdb=" O GLY B 86 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 91 " --> pdb=" O PHE B 87 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 125 Processing helix chain 'B' and resid 130 through 141 removed outlier: 4.060A pdb=" N ARG B 141 " --> pdb=" O ARG B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 174 removed outlier: 4.256A 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: 3.627A pdb=" N HIS B 211 " --> pdb=" O PHE B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 261 removed outlier: 3.647A pdb=" N LEU B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 3.874A 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: 3.549A 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 391 removed outlier: 3.999A pdb=" N PHE B 389 " --> pdb=" O GLU B 385 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 390 " --> pdb=" O HIS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 419 removed outlier: 3.692A pdb=" N ASP B 397 " --> pdb=" O HIS B 393 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLN B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 444 removed outlier: 3.601A pdb=" N LEU B 440 " --> pdb=" O ALA B 436 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY B 443 " --> pdb=" O SER B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 462 Processing helix chain 'B' and resid 478 through 500 Processing helix chain 'B' and resid 506 through 512 removed outlier: 3.933A 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 569 through 578 removed outlier: 3.824A pdb=" N GLY B 572 " --> pdb=" O GLN B 569 " (cutoff:3.500A) 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 649 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: 4.317A pdb=" N MET B 778 " --> pdb=" O PRO B 774 " (cutoff:3.500A) removed outlier: 4.351A 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 223 through 226 Processing sheet with id=AA2, first strand: chain 'A' and resid 581 through 584 removed outlier: 9.057A pdb=" N VAL A 633 " --> pdb=" O PRO A 855 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N TYR A 635 " --> pdb=" O ALA A 853 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA A 853 " --> pdb=" O TYR A 635 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU A 852 " --> pdb=" O LYS A 654 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LYS A 654 " --> pdb=" O LEU A 852 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N VAL A 854 " --> pdb=" O ALA A 652 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ALA A 652 " --> pdb=" O VAL A 854 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 800 " --> pdb=" O ALA A 659 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL A 661 " --> pdb=" O SER A 798 " (cutoff:3.500A) removed outlier: 5.212A 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: 6.831A pdb=" N ARG A 737 " --> pdb=" O ASN A 752 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ASN A 752 " --> pdb=" O ARG A 737 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA A 739 " --> pdb=" O PHE A 750 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N PHE A 750 " --> pdb=" O ALA A 739 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL A 741 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 9.197A pdb=" N VAL A 748 " --> pdb=" O VAL A 769 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N VAL A 769 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N PHE A 750 " --> pdb=" O MET A 767 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N MET A 767 " --> pdb=" O PHE A 750 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ASN A 752 " --> pdb=" O ASP A 765 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP A 765 " --> pdb=" O ASN A 752 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 223 through 226 Processing sheet with id=AA5, first strand: chain 'B' and resid 581 through 584 removed outlier: 9.050A pdb=" N VAL B 633 " --> pdb=" O PRO B 855 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N TYR B 635 " --> pdb=" O ALA B 853 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALA B 853 " --> pdb=" O TYR B 635 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU B 852 " --> pdb=" O LYS B 654 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LYS B 654 " --> pdb=" O LEU B 852 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL B 854 " --> pdb=" O ALA B 652 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ALA B 652 " --> pdb=" O VAL B 854 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY B 800 " --> pdb=" O ALA B 659 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL B 661 " --> pdb=" O SER B 798 " (cutoff:3.500A) removed outlier: 5.211A 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: 6.833A pdb=" N ARG B 737 " --> pdb=" O ASN B 752 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ASN B 752 " --> pdb=" O ARG B 737 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA B 739 " --> pdb=" O PHE B 750 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N PHE B 750 " --> pdb=" O ALA B 739 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL B 741 " --> pdb=" O VAL B 748 " (cutoff:3.500A) removed outlier: 9.195A pdb=" N VAL B 748 " --> pdb=" O VAL B 769 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N VAL B 769 " --> pdb=" O VAL B 748 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N PHE B 750 " --> pdb=" O MET B 767 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N MET B 767 " --> pdb=" O PHE B 750 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASN B 752 " --> pdb=" O ASP B 765 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP B 765 " --> pdb=" O ASN B 752 " (cutoff:3.500A) 889 hydrogen bonds defined for protein. 2583 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.87 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2238 1.32 - 1.45: 3022 1.45 - 1.57: 7974 1.57 - 1.70: 12 1.70 - 1.82: 68 Bond restraints: 13314 Sorted by residual: bond pdb=" C1 PGT A 912 " pdb=" O3P PGT A 912 " ideal model delta sigma weight residual 1.408 1.459 -0.051 2.00e-02 2.50e+03 6.41e+00 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 6.18e+00 bond pdb=" C1 PGT A 902 " pdb=" O3P PGT A 902 " ideal model delta sigma weight residual 1.408 1.457 -0.049 2.00e-02 2.50e+03 6.02e+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 5.81e+00 bond pdb=" C4 PGT A 912 " pdb=" O4P PGT A 912 " ideal model delta sigma weight residual 1.410 1.458 -0.048 2.00e-02 2.50e+03 5.75e+00 ... (remaining 13309 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 17321 2.27 - 4.54: 584 4.54 - 6.81: 7 6.81 - 9.07: 0 9.07 - 11.34: 6 Bond angle restraints: 17918 Sorted by residual: angle pdb=" N PRO A 469 " pdb=" CA PRO A 469 " pdb=" CB PRO A 469 " ideal model delta sigma weight residual 103.25 98.65 4.60 1.05e+00 9.07e-01 1.92e+01 angle pdb=" N PRO B 469 " pdb=" CA PRO B 469 " pdb=" CB PRO B 469 " ideal model delta sigma weight residual 103.25 99.00 4.25 1.05e+00 9.07e-01 1.64e+01 angle pdb=" O3P PGT A 912 " pdb=" P PGT A 912 " pdb=" O4P PGT A 912 " ideal model delta sigma weight residual 92.82 104.16 -11.34 3.00e+00 1.11e-01 1.43e+01 angle pdb=" O3P PGT B 914 " pdb=" P PGT B 914 " pdb=" O4P PGT B 914 " ideal model delta sigma weight residual 92.82 104.11 -11.29 3.00e+00 1.11e-01 1.42e+01 angle pdb=" O3P PGT B 902 " pdb=" P PGT B 902 " pdb=" O4P PGT B 902 " ideal model delta sigma weight residual 92.82 103.74 -10.92 3.00e+00 1.11e-01 1.32e+01 ... (remaining 17913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.66: 7111 15.66 - 31.31: 725 31.31 - 46.97: 214 46.97 - 62.62: 112 62.62 - 78.28: 10 Dihedral angle restraints: 8172 sinusoidal: 3566 harmonic: 4606 Sorted by residual: 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 -163.87 -16.13 0 5.00e+00 4.00e-02 1.04e+01 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 -163.89 -16.11 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA ILE B 391 " pdb=" C ILE B 391 " pdb=" N PRO B 392 " pdb=" CA PRO B 392 " ideal model delta harmonic sigma weight residual 180.00 164.28 15.72 0 5.00e+00 4.00e-02 9.88e+00 ... (remaining 8169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1747 0.080 - 0.159: 300 0.159 - 0.239: 3 0.239 - 0.318: 0 0.318 - 0.398: 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 2.33 0.40 2.00e-01 2.50e+01 3.96e+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 2.34 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CA ILE B 391 " pdb=" N ILE B 391 " pdb=" C ILE B 391 " pdb=" CB ILE B 391 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.55e-01 ... (remaining 2049 not shown) Planarity restraints: 2176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 425 " -0.022 2.00e-02 2.50e+03 1.13e-02 3.21e+00 pdb=" CG TRP B 425 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TRP B 425 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP B 425 " 0.013 2.00e-02 2.50e+03 pdb=" NE1 TRP B 425 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP B 425 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 425 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 425 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 425 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 425 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 PGT A 918 " 0.030 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C12 PGT A 918 " -0.009 2.00e-02 2.50e+03 pdb=" O11 PGT A 918 " -0.012 2.00e-02 2.50e+03 pdb=" O3 PGT A 918 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 463 " -0.137 9.50e-02 1.11e+02 6.17e-02 2.48e+00 pdb=" NE ARG B 463 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 463 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 463 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 463 " -0.003 2.00e-02 2.50e+03 ... (remaining 2173 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3399 2.82 - 3.34: 12037 3.34 - 3.86: 20732 3.86 - 4.38: 24533 4.38 - 4.90: 42637 Nonbonded interactions: 103338 Sorted by model distance: nonbonded pdb=" O LEU A 515 " pdb=" NH2 ARG A 521 " model vdw 2.297 3.120 nonbonded pdb=" O LEU B 515 " pdb=" NH2 ARG B 521 " model vdw 2.302 3.120 nonbonded pdb=" O ALA A 252 " pdb=" OG1 THR A 256 " model vdw 2.450 3.040 nonbonded pdb=" O ALA B 252 " pdb=" OG1 THR B 256 " model vdw 2.451 3.040 nonbonded pdb=" O ARG B 341 " pdb=" OG1 THR B 345 " model vdw 2.452 3.040 ... (remaining 103333 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: 0.04 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: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.590 Find NCS groups from input model: 0.300 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 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 0.051 13314 Z= 0.474 Angle : 1.051 11.342 17918 Z= 0.734 Chirality : 0.053 0.398 2052 Planarity : 0.005 0.062 2176 Dihedral : 15.316 78.280 5196 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.66 % Favored : 96.22 % Rotamer: Outliers : 1.28 % Allowed : 4.33 % Favored : 94.39 % 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: -1.35 (0.18), residues: 1586 helix: -0.48 (0.14), residues: 1048 sheet: -0.05 (0.39), residues: 152 loop : -2.02 (0.26), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 137 TYR 0.016 0.002 TYR A 318 PHE 0.024 0.003 PHE A 444 TRP 0.022 0.003 TRP B 425 HIS 0.004 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00736 / 0.47 (13314) covalent geometry : angle 1.05116 / 0.73 (17918) hydrogen bonds : bond 0.19149 / 13.03 ( 889) hydrogen bonds : angle 7.14763 / 5.18 ( 2583) *********************** 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 326 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 310 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.8053 (tp) cc_final: 0.7795 (tt) REVERT: A 108 ARG cc_start: 0.5879 (ptp-110) cc_final: 0.5452 (ptt-90) REVERT: A 173 LEU cc_start: 0.7711 (tp) cc_final: 0.7364 (mt) REVERT: A 264 GLU cc_start: 0.8159 (tt0) cc_final: 0.7455 (mm-30) REVERT: A 445 ASP cc_start: 0.8406 (m-30) cc_final: 0.8135 (m-30) REVERT: A 447 GLU cc_start: 0.6725 (mp0) cc_final: 0.5939 (mp0) REVERT: A 504 HIS cc_start: 0.7868 (m-70) cc_final: 0.7566 (m90) REVERT: A 511 TRP cc_start: 0.6994 (m-90) cc_final: 0.6158 (m100) REVERT: A 593 MET cc_start: 0.8260 (ptp) cc_final: 0.7964 (ptt) REVERT: A 597 ARG cc_start: 0.6394 (mmt90) cc_final: 0.6079 (mtp180) REVERT: A 638 ARG cc_start: 0.8035 (mtp85) cc_final: 0.7800 (mtp85) REVERT: A 657 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7384 (mm-30) REVERT: A 733 LEU cc_start: 0.8200 (mm) cc_final: 0.7831 (mm) REVERT: A 760 GLU cc_start: 0.8336 (mp0) cc_final: 0.7726 (tp30) REVERT: A 770 HIS cc_start: 0.4740 (OUTLIER) cc_final: 0.4464 (t-90) REVERT: A 846 ASP cc_start: 0.6866 (t0) cc_final: 0.6602 (m-30) REVERT: B 107 MET cc_start: 0.5551 (tpp) cc_final: 0.5072 (tmm) REVERT: B 173 LEU cc_start: 0.7861 (tp) cc_final: 0.7583 (mt) REVERT: B 207 PHE cc_start: 0.6883 (t80) cc_final: 0.6670 (t80) REVERT: B 210 ARG cc_start: 0.7429 (tpp80) cc_final: 0.7133 (ttp-110) REVERT: B 212 ARG cc_start: 0.7131 (tmm-80) cc_final: 0.6925 (ptm-80) REVERT: B 238 ARG cc_start: 0.7030 (mtm-85) cc_final: 0.6567 (ptm160) REVERT: B 338 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7148 (mm-30) REVERT: B 385 GLU cc_start: 0.8019 (tt0) cc_final: 0.7394 (mm-30) REVERT: B 473 MET cc_start: 0.8445 (mmt) cc_final: 0.8238 (mmt) REVERT: B 502 ASP cc_start: 0.8544 (m-30) cc_final: 0.8157 (t0) REVERT: B 507 ASN cc_start: 0.8407 (m-40) cc_final: 0.8189 (m-40) REVERT: B 513 PHE cc_start: 0.8372 (m-80) cc_final: 0.8140 (m-80) REVERT: B 589 ASP cc_start: 0.8440 (t0) cc_final: 0.8118 (t0) REVERT: B 599 ARG cc_start: 0.7923 (tpt90) cc_final: 0.7225 (ttt180) REVERT: B 604 LEU cc_start: 0.7504 (mm) cc_final: 0.6891 (tp) REVERT: B 657 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7421 (mp0) REVERT: B 658 GLU cc_start: 0.7473 (tm-30) cc_final: 0.6926 (tm-30) REVERT: B 671 LYS cc_start: 0.8505 (mttt) cc_final: 0.8279 (ptmt) REVERT: B 675 MET cc_start: 0.5925 (tpt) cc_final: 0.5703 (tpt) REVERT: B 737 ARG cc_start: 0.7042 (mtp85) cc_final: 0.6550 (mtp-110) REVERT: B 755 GLU cc_start: 0.8877 (tt0) cc_final: 0.8149 (pt0) REVERT: B 756 THR cc_start: 0.7697 (p) cc_final: 0.7147 (t) REVERT: B 760 GLU cc_start: 0.7695 (mp0) cc_final: 0.7145 (tp30) REVERT: B 775 LYS cc_start: 0.7402 (mmtt) cc_final: 0.7121 (mmtm) REVERT: B 842 LYS cc_start: 0.8107 (mtpp) cc_final: 0.7666 (tptp) REVERT: B 848 GLU cc_start: 0.6959 (tt0) cc_final: 0.6570 (mt-10) outliers start: 16 outliers final: 0 residues processed: 318 average time/residue: 0.1134 time to fit residues: 50.0431 Evaluate side-chains 215 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 770 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.0270 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 4.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN A 500 ASN ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 GLN B 122 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.184927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.134667 restraints weight = 14373.717| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 3.93 r_work: 0.2810 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13314 Z= 0.136 Angle : 0.543 7.579 17918 Z= 0.267 Chirality : 0.036 0.182 2052 Planarity : 0.004 0.036 2176 Dihedral : 11.325 59.795 2442 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.40 % Allowed : 9.62 % Favored : 87.98 % 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: 2.04 (0.21), residues: 1586 helix: 2.33 (0.15), residues: 1060 sheet: 0.49 (0.42), residues: 152 loop : -1.23 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 341 TYR 0.013 0.001 TYR A 605 PHE 0.021 0.001 PHE A 839 TRP 0.010 0.001 TRP A 446 HIS 0.004 0.001 HIS B 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (13314) covalent geometry : angle 0.54302 / 0.27 (17918) hydrogen bonds : bond 0.04620 / 3.21 ( 889) hydrogen bonds : angle 4.34737 / 3.23 ( 2583) *********************** 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 262 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 232 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 VAL cc_start: 0.8638 (t) cc_final: 0.8221 (m) REVERT: A 164 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7671 (mp) REVERT: A 511 TRP cc_start: 0.7393 (m-90) cc_final: 0.6608 (m100) REVERT: A 593 MET cc_start: 0.9068 (ptp) cc_final: 0.8836 (ptt) REVERT: A 658 GLU cc_start: 0.8275 (tm-30) cc_final: 0.8028 (tm-30) REVERT: A 706 LYS cc_start: 0.8531 (mttm) cc_final: 0.7904 (tptt) REVERT: A 733 LEU cc_start: 0.8696 (mm) cc_final: 0.8301 (mm) REVERT: A 746 LYS cc_start: 0.7271 (pttm) cc_final: 0.6933 (ptmt) REVERT: B 107 MET cc_start: 0.6925 (tpp) cc_final: 0.6533 (tmm) REVERT: B 173 LEU cc_start: 0.8445 (tp) cc_final: 0.8210 (mt) REVERT: B 212 ARG cc_start: 0.7474 (tmm-80) cc_final: 0.6783 (ttp80) REVERT: B 338 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8321 (mm-30) REVERT: B 385 GLU cc_start: 0.8295 (tt0) cc_final: 0.7962 (mm-30) REVERT: B 500 ASN cc_start: 0.9309 (m-40) cc_final: 0.9108 (m-40) REVERT: B 504 HIS cc_start: 0.7892 (OUTLIER) cc_final: 0.7663 (t-90) REVERT: B 507 ASN cc_start: 0.8818 (m-40) cc_final: 0.8605 (m-40) REVERT: B 558 GLN cc_start: 0.8467 (tp40) cc_final: 0.8261 (tp40) REVERT: B 565 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8314 (ttp-110) REVERT: B 589 ASP cc_start: 0.8530 (t0) cc_final: 0.8280 (t0) REVERT: B 616 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8482 (mp0) REVERT: B 673 LYS cc_start: 0.8150 (mmtt) cc_final: 0.7842 (ptpp) REVERT: B 838 ARG cc_start: 0.8028 (ptp90) cc_final: 0.7777 (ptt-90) REVERT: B 842 LYS cc_start: 0.8086 (mtpp) cc_final: 0.7810 (tptp) outliers start: 30 outliers final: 13 residues processed: 248 average time/residue: 0.1032 time to fit residues: 36.2761 Evaluate side-chains 209 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 192 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 504 HIS Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 565 ARG Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 783 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 136 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 109 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.183929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.132310 restraints weight = 14364.236| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 3.43 r_work: 0.2808 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13314 Z= 0.132 Angle : 0.513 8.624 17918 Z= 0.247 Chirality : 0.036 0.169 2052 Planarity : 0.004 0.038 2176 Dihedral : 10.768 59.492 2440 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.64 % Allowed : 12.10 % Favored : 85.26 % 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: 2.60 (0.21), residues: 1586 helix: 2.77 (0.15), residues: 1058 sheet: 0.76 (0.42), residues: 142 loop : -1.02 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 838 TYR 0.018 0.001 TYR A 605 PHE 0.020 0.001 PHE B 839 TRP 0.014 0.001 TRP A 847 HIS 0.004 0.001 HIS B 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (13314) covalent geometry : angle 0.51349 / 0.25 (17918) hydrogen bonds : bond 0.04209 / 2.94 ( 889) hydrogen bonds : angle 4.07506 / 3.03 ( 2583) *********************** 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 240 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 VAL cc_start: 0.8650 (t) cc_final: 0.8269 (m) REVERT: A 212 ARG cc_start: 0.7555 (tmm-80) cc_final: 0.7269 (ttp80) REVERT: A 511 TRP cc_start: 0.7288 (m-90) cc_final: 0.6415 (m100) REVERT: A 562 ARG cc_start: 0.8190 (tmm-80) cc_final: 0.7963 (tmm-80) REVERT: A 593 MET cc_start: 0.9011 (ptp) cc_final: 0.8809 (ptt) REVERT: A 636 GLN cc_start: 0.8760 (mt0) cc_final: 0.8446 (tt0) REVERT: A 733 LEU cc_start: 0.8685 (mm) cc_final: 0.8301 (mm) REVERT: A 746 LYS cc_start: 0.7199 (pttm) cc_final: 0.6789 (ptmt) REVERT: B 93 TYR cc_start: 0.6639 (t80) cc_final: 0.6274 (t80) REVERT: B 107 MET cc_start: 0.6991 (tpp) cc_final: 0.6607 (tmm) REVERT: B 173 LEU cc_start: 0.8433 (tp) cc_final: 0.8097 (mt) REVERT: B 385 GLU cc_start: 0.8259 (tt0) cc_final: 0.7875 (mm-30) REVERT: B 558 GLN cc_start: 0.8522 (tp40) cc_final: 0.8317 (tp40) REVERT: B 565 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8223 (ttp-110) REVERT: B 589 ASP cc_start: 0.8523 (t0) cc_final: 0.8265 (t0) REVERT: B 673 LYS cc_start: 0.8177 (mmtt) cc_final: 0.7961 (ptpp) REVERT: B 675 MET cc_start: 0.6085 (mmm) cc_final: 0.5770 (ttt) REVERT: B 838 ARG cc_start: 0.8103 (ptp90) cc_final: 0.7826 (ptt-90) REVERT: B 842 LYS cc_start: 0.8146 (mtpp) cc_final: 0.7785 (tptp) outliers start: 33 outliers final: 13 residues processed: 224 average time/residue: 0.1039 time to fit residues: 32.6370 Evaluate side-chains 201 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 736 PHE Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 565 ARG Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain B residue 783 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 24 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 134 optimal weight: 0.1980 chunk 91 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.183026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.131694 restraints weight = 14346.716| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 3.29 r_work: 0.2854 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13314 Z= 0.128 Angle : 0.517 9.671 17918 Z= 0.243 Chirality : 0.036 0.174 2052 Planarity : 0.004 0.038 2176 Dihedral : 10.520 58.409 2440 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.56 % Allowed : 13.46 % Favored : 83.97 % 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: 2.85 (0.21), residues: 1586 helix: 2.94 (0.15), residues: 1048 sheet: 0.85 (0.42), residues: 152 loop : -0.81 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 212 TYR 0.016 0.001 TYR A 605 PHE 0.015 0.001 PHE A 839 TRP 0.011 0.001 TRP A 446 HIS 0.002 0.001 HIS B 629 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (13314) covalent geometry : angle 0.51712 / 0.24 (17918) hydrogen bonds : bond 0.03973 / 2.77 ( 889) hydrogen bonds : angle 3.95009 / 2.93 ( 2583) *********************** 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 227 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 195 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8604 (mp) REVERT: A 103 VAL cc_start: 0.8696 (t) cc_final: 0.8335 (m) REVERT: A 175 ASP cc_start: 0.6642 (m-30) cc_final: 0.6279 (t0) REVERT: A 177 ASP cc_start: 0.7252 (p0) cc_final: 0.6874 (m-30) REVERT: A 212 ARG cc_start: 0.7605 (tmm-80) cc_final: 0.7290 (ttp80) REVERT: A 511 TRP cc_start: 0.7293 (m-90) cc_final: 0.6449 (m100) REVERT: A 562 ARG cc_start: 0.8189 (tmm-80) cc_final: 0.7963 (tmm-80) REVERT: A 636 GLN cc_start: 0.8747 (mt0) cc_final: 0.8500 (tt0) REVERT: A 653 LEU cc_start: 0.8638 (mt) cc_final: 0.8428 (mt) REVERT: A 733 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8343 (mm) REVERT: A 746 LYS cc_start: 0.7266 (pttm) cc_final: 0.6874 (ptmt) REVERT: A 759 ARG cc_start: 0.6987 (mmt90) cc_final: 0.6575 (mmt90) REVERT: A 764 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.8006 (pp) REVERT: A 838 ARG cc_start: 0.8911 (tpp80) cc_final: 0.8560 (ptp-170) REVERT: B 93 TYR cc_start: 0.6696 (t80) cc_final: 0.6225 (t80) REVERT: B 107 MET cc_start: 0.7112 (tpp) cc_final: 0.6714 (tmm) REVERT: B 385 GLU cc_start: 0.8146 (tt0) cc_final: 0.7849 (mm-30) REVERT: B 558 GLN cc_start: 0.8550 (tp40) cc_final: 0.8321 (tp40) REVERT: B 589 ASP cc_start: 0.8562 (t0) cc_final: 0.8325 (t0) REVERT: B 601 MET cc_start: 0.9266 (mtp) cc_final: 0.9011 (mtp) REVERT: B 838 ARG cc_start: 0.8036 (ptp90) cc_final: 0.7766 (ptt-90) REVERT: B 842 LYS cc_start: 0.8170 (mtpp) cc_final: 0.7593 (tptp) outliers start: 32 outliers final: 16 residues processed: 212 average time/residue: 0.1290 time to fit residues: 38.8019 Evaluate side-chains 205 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 736 PHE Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 693 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 132 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 123 optimal weight: 0.8980 chunk 141 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.182064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.130611 restraints weight = 14444.291| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 3.48 r_work: 0.2838 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13314 Z= 0.130 Angle : 0.509 8.791 17918 Z= 0.239 Chirality : 0.036 0.174 2052 Planarity : 0.004 0.039 2176 Dihedral : 10.435 59.912 2440 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.21 % Allowed : 13.62 % Favored : 83.17 % 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: 2.95 (0.21), residues: 1586 helix: 2.93 (0.15), residues: 1060 sheet: 1.03 (0.41), residues: 154 loop : -0.67 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 665 TYR 0.008 0.001 TYR B 93 PHE 0.018 0.001 PHE B 839 TRP 0.014 0.001 TRP A 847 HIS 0.002 0.001 HIS A 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (13314) covalent geometry : angle 0.50906 / 0.24 (17918) hydrogen bonds : bond 0.03956 / 2.76 ( 889) hydrogen bonds : angle 3.88778 / 2.88 ( 2583) *********************** 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 236 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 196 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8635 (mp) REVERT: A 103 VAL cc_start: 0.8710 (t) cc_final: 0.8335 (m) REVERT: A 350 ARG cc_start: 0.6448 (mmp80) cc_final: 0.5743 (mmm160) REVERT: A 511 TRP cc_start: 0.7336 (m-90) cc_final: 0.6530 (m100) REVERT: A 562 ARG cc_start: 0.8194 (tmm-80) cc_final: 0.7987 (tmm-80) REVERT: A 636 GLN cc_start: 0.8771 (mt0) cc_final: 0.8522 (tt0) REVERT: A 706 LYS cc_start: 0.8588 (mttm) cc_final: 0.7987 (tptt) REVERT: A 733 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8345 (mm) REVERT: A 746 LYS cc_start: 0.7265 (pttm) cc_final: 0.6896 (ptmt) REVERT: A 759 ARG cc_start: 0.6799 (mmt90) cc_final: 0.6283 (mmt90) REVERT: A 838 ARG cc_start: 0.8905 (tpp80) cc_final: 0.8558 (ptp-170) REVERT: B 93 TYR cc_start: 0.6737 (t80) cc_final: 0.6280 (t80) REVERT: B 107 MET cc_start: 0.7139 (tpp) cc_final: 0.6735 (tmm) REVERT: B 126 LEU cc_start: 0.6518 (OUTLIER) cc_final: 0.6076 (tp) REVERT: B 385 GLU cc_start: 0.8197 (tt0) cc_final: 0.7830 (mm-30) REVERT: B 558 GLN cc_start: 0.8569 (tp40) cc_final: 0.8333 (tp40) REVERT: B 589 ASP cc_start: 0.8603 (t0) cc_final: 0.8400 (t0) REVERT: B 601 MET cc_start: 0.9258 (mtp) cc_final: 0.8992 (mtp) REVERT: B 838 ARG cc_start: 0.7998 (ptp90) cc_final: 0.7716 (ptt-90) REVERT: B 842 LYS cc_start: 0.8145 (mtpp) cc_final: 0.7754 (tptp) outliers start: 40 outliers final: 24 residues processed: 217 average time/residue: 0.1309 time to fit residues: 40.6891 Evaluate side-chains 212 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 736 PHE Chi-restraints excluded: chain A residue 775 LYS Chi-restraints excluded: chain A residue 782 MET Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 693 GLU Chi-restraints excluded: chain B residue 733 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 121 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 141 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.180599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.130526 restraints weight = 14301.750| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.48 r_work: 0.2843 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3321 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= 0.145 Angle : 0.528 8.730 17918 Z= 0.247 Chirality : 0.036 0.179 2052 Planarity : 0.004 0.041 2176 Dihedral : 10.484 59.031 2440 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.88 % Allowed : 14.02 % Favored : 83.09 % 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: 3.02 (0.21), residues: 1586 helix: 2.96 (0.15), residues: 1060 sheet: 0.97 (0.39), residues: 162 loop : -0.54 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 212 TYR 0.008 0.001 TYR B 93 PHE 0.011 0.001 PHE B 444 TRP 0.012 0.001 TRP A 682 HIS 0.003 0.001 HIS B 629 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.14 (13314) covalent geometry : angle 0.52784 / 0.25 (17918) hydrogen bonds : bond 0.04091 / 2.86 ( 889) hydrogen bonds : angle 3.89990 / 2.89 ( 2583) *********************** 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 231 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8653 (mp) REVERT: A 103 VAL cc_start: 0.8762 (t) cc_final: 0.8365 (m) REVERT: A 175 ASP cc_start: 0.6702 (m-30) cc_final: 0.6434 (t0) REVERT: A 177 ASP cc_start: 0.7326 (p0) cc_final: 0.6972 (m-30) REVERT: A 511 TRP cc_start: 0.7366 (m-90) cc_final: 0.6562 (m100) REVERT: A 636 GLN cc_start: 0.8785 (mt0) cc_final: 0.8508 (tt0) REVERT: A 733 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8329 (mm) REVERT: A 746 LYS cc_start: 0.7263 (pttm) cc_final: 0.6872 (ptmt) REVERT: A 842 LYS cc_start: 0.8928 (mtpt) cc_final: 0.8650 (mttt) REVERT: B 93 TYR cc_start: 0.6750 (t80) cc_final: 0.6279 (t80) REVERT: B 107 MET cc_start: 0.7148 (tpp) cc_final: 0.6728 (tmm) REVERT: B 126 LEU cc_start: 0.6378 (OUTLIER) cc_final: 0.5970 (tp) REVERT: B 385 GLU cc_start: 0.8204 (tt0) cc_final: 0.7823 (mm-30) REVERT: B 558 GLN cc_start: 0.8511 (tp40) cc_final: 0.8304 (tp40) REVERT: B 579 ASP cc_start: 0.8252 (p0) cc_final: 0.7513 (t0) REVERT: B 589 ASP cc_start: 0.8649 (t0) cc_final: 0.8439 (t0) REVERT: B 601 MET cc_start: 0.9257 (mtp) cc_final: 0.9009 (mtp) REVERT: B 753 LEU cc_start: 0.8806 (mt) cc_final: 0.7838 (pp) REVERT: B 838 ARG cc_start: 0.8017 (ptp90) cc_final: 0.7737 (ptt-90) REVERT: B 842 LYS cc_start: 0.8186 (mtpp) cc_final: 0.7770 (tptp) outliers start: 36 outliers final: 25 residues processed: 212 average time/residue: 0.1260 time to fit residues: 38.1808 Evaluate side-chains 215 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 736 PHE Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 693 GLU Chi-restraints excluded: chain B residue 733 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 152 optimal weight: 0.7980 chunk 128 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.181038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.130245 restraints weight = 14450.157| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.48 r_work: 0.2853 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3437 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= 0.137 Angle : 0.524 9.094 17918 Z= 0.245 Chirality : 0.036 0.177 2052 Planarity : 0.004 0.041 2176 Dihedral : 10.418 59.754 2440 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.80 % Allowed : 14.82 % Favored : 82.37 % 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: 3.00 (0.15), residues: 1060 sheet: 1.07 (0.39), residues: 162 loop : -0.46 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 665 TYR 0.008 0.001 TYR B 93 PHE 0.011 0.001 PHE B 839 TRP 0.010 0.001 TRP A 446 HIS 0.004 0.001 HIS A 794 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (13314) covalent geometry : angle 0.52378 / 0.24 (17918) hydrogen bonds : bond 0.03961 / 2.76 ( 889) hydrogen bonds : angle 3.85108 / 2.85 ( 2583) *********************** 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 230 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 195 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8611 (mp) REVERT: A 141 ARG cc_start: 0.8389 (mtt180) cc_final: 0.8148 (mtt180) REVERT: A 175 ASP cc_start: 0.6726 (m-30) cc_final: 0.6452 (t0) REVERT: A 350 ARG cc_start: 0.6552 (mmp80) cc_final: 0.5875 (mmm160) REVERT: A 511 TRP cc_start: 0.7329 (m-90) cc_final: 0.6576 (m100) REVERT: A 636 GLN cc_start: 0.8800 (mt0) cc_final: 0.8567 (tt0) REVERT: A 733 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8326 (mm) REVERT: A 746 LYS cc_start: 0.7226 (pttm) cc_final: 0.6855 (ptmt) REVERT: A 841 ASP cc_start: 0.8002 (m-30) cc_final: 0.7737 (m-30) REVERT: A 842 LYS cc_start: 0.8928 (mtpt) cc_final: 0.8648 (mttt) REVERT: B 93 TYR cc_start: 0.6768 (t80) cc_final: 0.6278 (t80) REVERT: B 107 MET cc_start: 0.7171 (tpp) cc_final: 0.6748 (tmm) REVERT: B 118 PHE cc_start: 0.8901 (m-80) cc_final: 0.8688 (m-80) REVERT: B 126 LEU cc_start: 0.6505 (OUTLIER) cc_final: 0.6081 (tp) REVERT: B 385 GLU cc_start: 0.8209 (tt0) cc_final: 0.7810 (mm-30) REVERT: B 558 GLN cc_start: 0.8528 (tp40) cc_final: 0.8319 (tp40) REVERT: B 601 MET cc_start: 0.9255 (mtp) cc_final: 0.9046 (mtt) REVERT: B 673 LYS cc_start: 0.7344 (ptpp) cc_final: 0.7009 (ptmm) REVERT: B 753 LEU cc_start: 0.8819 (mt) cc_final: 0.7814 (pp) REVERT: B 838 ARG cc_start: 0.7991 (ptp90) cc_final: 0.7709 (ptt-90) REVERT: B 842 LYS cc_start: 0.8211 (mtpp) cc_final: 0.7856 (tptp) outliers start: 35 outliers final: 21 residues processed: 212 average time/residue: 0.1307 time to fit residues: 39.4906 Evaluate side-chains 212 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 736 PHE Chi-restraints excluded: chain A residue 775 LYS Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 693 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 43 optimal weight: 0.5980 chunk 142 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 53 optimal weight: 0.0570 chunk 4 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 34 optimal weight: 0.0020 chunk 106 optimal weight: 4.9990 chunk 113 optimal weight: 0.0040 chunk 47 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.184110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.133199 restraints weight = 14319.417| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.26 r_work: 0.2917 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13314 Z= 0.100 Angle : 0.501 9.438 17918 Z= 0.236 Chirality : 0.035 0.163 2052 Planarity : 0.004 0.038 2176 Dihedral : 9.844 58.373 2440 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.08 % Allowed : 15.79 % Favored : 82.13 % 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: 3.30 (0.21), residues: 1586 helix: 3.16 (0.15), residues: 1052 sheet: 1.17 (0.39), residues: 162 loop : -0.35 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 562 TYR 0.008 0.001 TYR B 93 PHE 0.012 0.001 PHE A 843 TRP 0.016 0.001 TRP A 847 HIS 0.002 0.000 HIS B 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (13314) covalent geometry : angle 0.50100 / 0.24 (17918) hydrogen bonds : bond 0.03402 / 2.37 ( 889) hydrogen bonds : angle 3.71828 / 2.75 ( 2583) *********************** 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 223 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 VAL cc_start: 0.8778 (t) cc_final: 0.8374 (m) REVERT: A 175 ASP cc_start: 0.6565 (m-30) cc_final: 0.6293 (t0) REVERT: A 350 ARG cc_start: 0.6557 (mmp80) cc_final: 0.5938 (mmm160) REVERT: A 511 TRP cc_start: 0.7274 (m-90) cc_final: 0.6538 (m100) REVERT: A 636 GLN cc_start: 0.8730 (mt0) cc_final: 0.8443 (tt0) REVERT: A 733 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8298 (mm) REVERT: A 746 LYS cc_start: 0.7213 (pttm) cc_final: 0.6892 (ptmt) REVERT: A 838 ARG cc_start: 0.8896 (tpp80) cc_final: 0.8571 (ptp-170) REVERT: A 841 ASP cc_start: 0.7968 (m-30) cc_final: 0.7691 (m-30) REVERT: B 93 TYR cc_start: 0.6707 (t80) cc_final: 0.6236 (t80) REVERT: B 107 MET cc_start: 0.7123 (tpp) cc_final: 0.6713 (tmm) REVERT: B 126 LEU cc_start: 0.6603 (OUTLIER) cc_final: 0.6126 (tp) REVERT: B 338 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8232 (mm-30) REVERT: B 385 GLU cc_start: 0.8135 (tt0) cc_final: 0.7731 (mm-30) REVERT: B 558 GLN cc_start: 0.8507 (tp40) cc_final: 0.8290 (tp40) REVERT: B 601 MET cc_start: 0.9254 (mtp) cc_final: 0.9045 (mtt) REVERT: B 673 LYS cc_start: 0.7305 (ptpp) cc_final: 0.6977 (ptmm) REVERT: B 838 ARG cc_start: 0.8010 (ptp90) cc_final: 0.7690 (ptt-90) REVERT: B 842 LYS cc_start: 0.8074 (mtpp) cc_final: 0.7773 (tptp) outliers start: 26 outliers final: 19 residues processed: 212 average time/residue: 0.1268 time to fit residues: 38.4711 Evaluate side-chains 206 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 736 PHE Chi-restraints excluded: chain A residue 775 LYS Chi-restraints excluded: chain A residue 782 MET Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 693 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 113 optimal weight: 0.3980 chunk 105 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 636 GLN ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.180481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.132291 restraints weight = 14650.314| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.78 r_work: 0.2831 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13314 Z= 0.130 Angle : 0.537 9.548 17918 Z= 0.250 Chirality : 0.036 0.164 2052 Planarity : 0.004 0.039 2176 Dihedral : 9.926 59.209 2440 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.24 % Allowed : 16.27 % 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: 3.20 (0.21), residues: 1586 helix: 3.07 (0.15), residues: 1056 sheet: 1.23 (0.38), residues: 162 loop : -0.44 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 665 TYR 0.018 0.001 TYR A 605 PHE 0.011 0.001 PHE A 843 TRP 0.011 0.001 TRP A 847 HIS 0.003 0.001 HIS A 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (13314) covalent geometry : angle 0.53703 / 0.25 (17918) hydrogen bonds : bond 0.03781 / 2.63 ( 889) hydrogen bonds : angle 3.79717 / 2.81 ( 2583) *********************** 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 220 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8670 (mp) REVERT: A 103 VAL cc_start: 0.8738 (t) cc_final: 0.8345 (m) REVERT: A 175 ASP cc_start: 0.6528 (m-30) cc_final: 0.6232 (t0) REVERT: A 350 ARG cc_start: 0.6430 (mmp80) cc_final: 0.5901 (mmm160) REVERT: A 511 TRP cc_start: 0.7348 (m-90) cc_final: 0.6615 (m100) REVERT: A 580 LYS cc_start: 0.8974 (ptpp) cc_final: 0.8522 (mtpp) REVERT: A 733 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8269 (mm) REVERT: A 746 LYS cc_start: 0.7168 (pttm) cc_final: 0.6841 (ptmt) REVERT: A 841 ASP cc_start: 0.8048 (m-30) cc_final: 0.7788 (m-30) REVERT: A 842 LYS cc_start: 0.8932 (mtpt) cc_final: 0.8630 (mttt) REVERT: B 93 TYR cc_start: 0.6824 (t80) cc_final: 0.6333 (t80) REVERT: B 107 MET cc_start: 0.7224 (tpp) cc_final: 0.6801 (tmm) REVERT: B 118 PHE cc_start: 0.8920 (m-80) cc_final: 0.8700 (m-80) REVERT: B 385 GLU cc_start: 0.8117 (tt0) cc_final: 0.7603 (mm-30) REVERT: B 558 GLN cc_start: 0.8572 (tp40) cc_final: 0.8344 (tp40) REVERT: B 601 MET cc_start: 0.9240 (mtp) cc_final: 0.9029 (mtt) REVERT: B 673 LYS cc_start: 0.7318 (ptpp) cc_final: 0.6976 (ptmm) REVERT: B 838 ARG cc_start: 0.8006 (ptp90) cc_final: 0.7684 (ptt-90) REVERT: B 842 LYS cc_start: 0.8127 (mtpp) cc_final: 0.7736 (tptp) outliers start: 28 outliers final: 21 residues processed: 209 average time/residue: 0.1335 time to fit residues: 39.5418 Evaluate side-chains 210 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 736 PHE Chi-restraints excluded: chain A residue 775 LYS Chi-restraints excluded: chain A residue 782 MET Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 693 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 78 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.181099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.131570 restraints weight = 14680.067| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 3.71 r_work: 0.2854 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13314 Z= 0.119 Angle : 0.530 9.989 17918 Z= 0.247 Chirality : 0.035 0.164 2052 Planarity : 0.004 0.039 2176 Dihedral : 9.843 59.432 2440 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.00 % Allowed : 16.19 % 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: 3.21 (0.21), residues: 1586 helix: 3.08 (0.15), residues: 1056 sheet: 1.50 (0.39), residues: 152 loop : -0.53 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 665 TYR 0.018 0.001 TYR A 605 PHE 0.023 0.001 PHE A 839 TRP 0.010 0.001 TRP A 847 HIS 0.002 0.001 HIS B 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (13314) covalent geometry : angle 0.52974 / 0.25 (17918) hydrogen bonds : bond 0.03688 / 2.56 ( 889) hydrogen bonds : angle 3.77014 / 2.79 ( 2583) ********************** 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 216 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8668 (mp) REVERT: A 103 VAL cc_start: 0.8802 (t) cc_final: 0.8409 (m) REVERT: A 175 ASP cc_start: 0.6454 (m-30) cc_final: 0.6156 (t0) REVERT: A 350 ARG cc_start: 0.6430 (mmp80) cc_final: 0.5891 (mmm160) REVERT: A 511 TRP cc_start: 0.7324 (m-90) cc_final: 0.6599 (m100) REVERT: A 580 LYS cc_start: 0.8983 (ptpp) cc_final: 0.8556 (mtpp) REVERT: A 646 MET cc_start: 0.8773 (ttm) cc_final: 0.8499 (ttp) REVERT: A 733 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8186 (mm) REVERT: A 746 LYS cc_start: 0.7137 (pttm) cc_final: 0.6840 (ptmt) REVERT: A 841 ASP cc_start: 0.8016 (m-30) cc_final: 0.7808 (m-30) REVERT: A 842 LYS cc_start: 0.8912 (mtpt) cc_final: 0.8618 (mttt) REVERT: B 93 TYR cc_start: 0.6821 (t80) cc_final: 0.6332 (t80) REVERT: B 107 MET cc_start: 0.7225 (tpp) cc_final: 0.6811 (tmm) REVERT: B 118 PHE cc_start: 0.8899 (m-80) cc_final: 0.8686 (m-80) REVERT: B 385 GLU cc_start: 0.8052 (tt0) cc_final: 0.7585 (mm-30) REVERT: B 558 GLN cc_start: 0.8532 (tp40) cc_final: 0.8303 (tp40) REVERT: B 601 MET cc_start: 0.9224 (mtp) cc_final: 0.9018 (mtt) REVERT: B 673 LYS cc_start: 0.7289 (ptpp) cc_final: 0.6972 (ptmm) REVERT: B 838 ARG cc_start: 0.7982 (ptp90) cc_final: 0.7683 (ptt-90) REVERT: B 842 LYS cc_start: 0.8101 (mtpp) cc_final: 0.7720 (tptp) outliers start: 25 outliers final: 21 residues processed: 205 average time/residue: 0.1316 time to fit residues: 38.3691 Evaluate side-chains 208 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 736 PHE Chi-restraints excluded: chain A residue 775 LYS Chi-restraints excluded: chain A residue 782 MET Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 693 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 76 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 60 optimal weight: 0.2980 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 129 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 81 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.181079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.132042 restraints weight = 14614.740| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 3.53 r_work: 0.2858 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13314 Z= 0.120 Angle : 0.529 9.060 17918 Z= 0.246 Chirality : 0.035 0.163 2052 Planarity : 0.004 0.041 2176 Dihedral : 9.753 59.519 2440 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.16 % Allowed : 16.51 % Favored : 81.33 % 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: 3.22 (0.21), residues: 1586 helix: 3.08 (0.15), residues: 1056 sheet: 1.53 (0.39), residues: 152 loop : -0.52 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 665 TYR 0.018 0.001 TYR A 605 PHE 0.011 0.001 PHE A 843 TRP 0.010 0.001 TRP A 446 HIS 0.002 0.001 HIS A 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (13314) covalent geometry : angle 0.52908 / 0.25 (17918) hydrogen bonds : bond 0.03680 / 2.56 ( 889) hydrogen bonds : angle 3.76494 / 2.78 ( 2583) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2910.21 seconds wall clock time: 50 minutes 45.08 seconds (3045.08 seconds total)