Starting phenix.real_space_refine on Thu Mar 5 12:19:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gcc_29930/03_2026/8gcc_29930.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gcc_29930/03_2026/8gcc_29930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gcc_29930/03_2026/8gcc_29930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gcc_29930/03_2026/8gcc_29930.map" model { file = "/net/cci-nas-00/data/ceres_data/8gcc_29930/03_2026/8gcc_29930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gcc_29930/03_2026/8gcc_29930.cif" } resolution = 2.94 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= 0.065 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: 7 Type Number sf(0) Gaussians P 48 5.49 5 S 36 5.16 5 C 7393 2.51 5 N 2064 2.21 5 O 2158 1.98 5 F 6 1.80 5 H 10631 0.53 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-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22336 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 707, 10371 Classifications: {'peptide': 707} Link IDs: {'PTRANS': 25, 'TRANS': 681} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 423 Unresolved non-hydrogen angles: 525 Unresolved non-hydrogen dihedrals: 332 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 30, 'TYR:plan': 1, 'ASP:plan': 18, 'ARG:plan': 16, 'GLN:plan1': 4, 'ASN:plan1': 8, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 304 Chain: "B" Number of atoms: 10379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 707, 10379 Classifications: {'peptide': 707} Link IDs: {'PTRANS': 25, 'TRANS': 681} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 521 Unresolved non-hydrogen dihedrals: 330 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 30, 'TYR:plan': 1, 'ASP:plan': 18, 'ARG:plan': 15, 'GLN:plan1': 4, 'ASN:plan1': 8, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 301 Chain: "C" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 764 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "D" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 764 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'YWX': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'YWX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.93, per 1000 atoms: 0.18 Number of scatterers: 22336 At special positions: 0 Unit cell: (93.795, 109.005, 114.075, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 36 16.00 P 48 15.00 F 6 9.00 O 2158 8.00 N 2064 7.00 C 7393 6.00 H 10631 1.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 653.8 milliseconds 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2632 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 15 sheets defined 54.7% alpha, 9.0% beta 24 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 3.79 Creating SS restraints... Processing helix chain 'A' and resid 424 through 427 Processing helix chain 'A' and resid 436 through 446 removed outlier: 3.639A pdb=" N ALA A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 449 No H-bonds generated for 'chain 'A' and resid 447 through 449' Processing helix chain 'A' and resid 450 through 452 No H-bonds generated for 'chain 'A' and resid 450 through 452' Processing helix chain 'A' and resid 470 through 476 Processing helix chain 'A' and resid 477 through 488 Processing helix chain 'A' and resid 513 through 531 Processing helix chain 'A' and resid 531 through 536 removed outlier: 4.051A pdb=" N ILE A 535 " --> pdb=" O TRP A 531 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS A 536 " --> pdb=" O PRO A 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 531 through 536' Processing helix chain 'A' and resid 568 through 580 Processing helix chain 'A' and resid 581 through 586 Processing helix chain 'A' and resid 598 through 608 Processing helix chain 'A' and resid 609 through 613 removed outlier: 3.642A pdb=" N ARG A 613 " --> pdb=" O ASP A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 631 removed outlier: 3.664A pdb=" N ALA A 625 " --> pdb=" O ALA A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 648 Processing helix chain 'A' and resid 664 through 685 removed outlier: 4.913A pdb=" N ILE A 674 " --> pdb=" O ASP A 670 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LEU A 675 " --> pdb=" O LYS A 671 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 676 " --> pdb=" O GLU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 707 Processing helix chain 'A' and resid 714 through 725 Processing helix chain 'A' and resid 730 through 743 Processing helix chain 'A' and resid 783 through 788 Processing helix chain 'A' and resid 790 through 795 Processing helix chain 'A' and resid 816 through 822 Processing helix chain 'A' and resid 838 through 852 Processing helix chain 'A' and resid 901 through 915 Processing helix chain 'A' and resid 937 through 948 Processing helix chain 'A' and resid 949 through 954 Processing helix chain 'A' and resid 979 through 1025 removed outlier: 3.540A pdb=" N VAL A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1045 Processing helix chain 'A' and resid 1104 through 1111 Processing helix chain 'A' and resid 1118 through 1122 Processing helix chain 'A' and resid 1123 through 1146 removed outlier: 3.564A pdb=" N LYS A1146 " --> pdb=" O ALA A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1177 Proline residue: A1162 - end of helix Processing helix chain 'B' and resid 424 through 427 Processing helix chain 'B' and resid 436 through 446 removed outlier: 3.633A pdb=" N ALA B 444 " --> pdb=" O ALA B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 449 No H-bonds generated for 'chain 'B' and resid 447 through 449' Processing helix chain 'B' and resid 450 through 452 No H-bonds generated for 'chain 'B' and resid 450 through 452' Processing helix chain 'B' and resid 470 through 476 Processing helix chain 'B' and resid 477 through 488 Processing helix chain 'B' and resid 513 through 531 Processing helix chain 'B' and resid 531 through 536 removed outlier: 4.057A pdb=" N ILE B 535 " --> pdb=" O TRP B 531 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS B 536 " --> pdb=" O PRO B 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 531 through 536' Processing helix chain 'B' and resid 568 through 580 Processing helix chain 'B' and resid 581 through 586 Processing helix chain 'B' and resid 593 through 597 removed outlier: 4.106A pdb=" N SER B 597 " --> pdb=" O LEU B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 608 removed outlier: 3.504A pdb=" N GLY B 602 " --> pdb=" O GLY B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 removed outlier: 3.720A pdb=" N ARG B 613 " --> pdb=" O ASP B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 631 removed outlier: 3.608A pdb=" N ALA B 625 " --> pdb=" O ALA B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 648 Processing helix chain 'B' and resid 664 through 685 removed outlier: 4.918A pdb=" N ILE B 674 " --> pdb=" O ASP B 670 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LEU B 675 " --> pdb=" O LYS B 671 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE B 676 " --> pdb=" O GLU B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 707 Processing helix chain 'B' and resid 714 through 725 Processing helix chain 'B' and resid 730 through 743 Processing helix chain 'B' and resid 783 through 788 Processing helix chain 'B' and resid 790 through 795 Processing helix chain 'B' and resid 816 through 822 Processing helix chain 'B' and resid 838 through 852 Processing helix chain 'B' and resid 901 through 915 Processing helix chain 'B' and resid 937 through 948 Processing helix chain 'B' and resid 949 through 954 Processing helix chain 'B' and resid 979 through 1025 removed outlier: 3.543A pdb=" N VAL B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1045 Processing helix chain 'B' and resid 1104 through 1111 Processing helix chain 'B' and resid 1111 through 1116 Processing helix chain 'B' and resid 1118 through 1122 Processing helix chain 'B' and resid 1123 through 1146 removed outlier: 3.567A pdb=" N LYS B1146 " --> pdb=" O ALA B1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 1148 through 1177 Proline residue: B1162 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 454 through 458 removed outlier: 6.510A pdb=" N THR A 429 " --> pdb=" O GLY A 455 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N PHE A 457 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE A 431 " --> pdb=" O PHE A 457 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N LEU A 430 " --> pdb=" O MET A 507 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU A 506 " --> pdb=" O GLN A 542 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 565 through 566 removed outlier: 3.572A pdb=" N VAL A 549 " --> pdb=" O PHE A 566 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 712 through 713 Processing sheet with id=AA4, first strand: chain 'A' and resid 798 through 801 removed outlier: 3.753A pdb=" N LYS A 799 " --> pdb=" O VAL A 806 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A 804 " --> pdb=" O ASP A 801 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 868 through 873 removed outlier: 3.661A pdb=" N THR A 868 " --> pdb=" O THR A 880 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS A 876 " --> pdb=" O LYS A 872 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 883 through 885 Processing sheet with id=AA7, first strand: chain 'A' and resid 965 through 968 removed outlier: 4.328A pdb=" N ILE A 965 " --> pdb=" O TYR A 977 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 454 through 456 removed outlier: 6.589A pdb=" N THR B 429 " --> pdb=" O GLY B 455 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N LEU B 430 " --> pdb=" O MET B 507 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU B 506 " --> pdb=" O GLN B 542 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 565 through 566 removed outlier: 3.565A pdb=" N VAL B 549 " --> pdb=" O PHE B 566 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 712 through 713 Processing sheet with id=AB2, first strand: chain 'B' and resid 798 through 801 removed outlier: 3.739A pdb=" N LYS B 799 " --> pdb=" O VAL B 806 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU B 804 " --> pdb=" O ASP B 801 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 823 through 826 removed outlier: 3.600A pdb=" N GLY B 825 " --> pdb=" O THR B 832 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 868 through 873 removed outlier: 6.709A pdb=" N LYS B 876 " --> pdb=" O LYS B 872 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 883 through 885 Processing sheet with id=AB6, first strand: chain 'B' and resid 965 through 968 removed outlier: 4.327A pdb=" N ILE B 965 " --> pdb=" O TYR B 977 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1626 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 5.26 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10623 1.03 - 1.23: 50 1.23 - 1.42: 5178 1.42 - 1.62: 6781 1.62 - 1.81: 62 Bond restraints: 22694 Sorted by residual: bond pdb=" C5 YWX D 101 " pdb=" C6 YWX D 101 " ideal model delta sigma weight residual 1.372 1.521 -0.149 2.00e-02 2.50e+03 5.54e+01 bond pdb=" C5 YWX C 101 " pdb=" C6 YWX C 101 " ideal model delta sigma weight residual 1.372 1.519 -0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" C17 YWX D 101 " pdb=" C18 YWX D 101 " ideal model delta sigma weight residual 1.370 1.501 -0.131 2.00e-02 2.50e+03 4.27e+01 bond pdb=" C17 YWX C 101 " pdb=" C18 YWX C 101 " ideal model delta sigma weight residual 1.370 1.500 -0.130 2.00e-02 2.50e+03 4.23e+01 bond pdb=" C5 YWX C 101 " pdb=" N4 YWX C 101 " ideal model delta sigma weight residual 1.376 1.464 -0.088 2.00e-02 2.50e+03 1.92e+01 ... (remaining 22689 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 39943 1.48 - 2.95: 801 2.95 - 4.43: 65 4.43 - 5.91: 9 5.91 - 7.38: 4 Bond angle restraints: 40822 Sorted by residual: angle pdb=" N VAL B 652 " pdb=" CA VAL B 652 " pdb=" C VAL B 652 " ideal model delta sigma weight residual 111.91 109.33 2.58 8.90e-01 1.26e+00 8.38e+00 angle pdb=" N VAL A 652 " pdb=" CA VAL A 652 " pdb=" C VAL A 652 " ideal model delta sigma weight residual 111.91 109.36 2.55 8.90e-01 1.26e+00 8.19e+00 angle pdb=" CA ILE A1029 " pdb=" CB ILE A1029 " pdb=" CG1 ILE A1029 " ideal model delta sigma weight residual 110.40 114.94 -4.54 1.70e+00 3.46e-01 7.13e+00 angle pdb=" CA CYS B 477 " pdb=" CB CYS B 477 " pdb=" SG CYS B 477 " ideal model delta sigma weight residual 114.40 120.23 -5.83 2.30e+00 1.89e-01 6.43e+00 angle pdb=" SG CYS B 477 " pdb=" CB CYS B 477 " pdb=" HB3 CYS B 477 " ideal model delta sigma weight residual 108.00 100.62 7.38 3.00e+00 1.11e-01 6.06e+00 ... (remaining 40817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.81: 10035 34.81 - 69.62: 536 69.62 - 104.43: 21 104.43 - 139.24: 0 139.24 - 174.05: 2 Dihedral angle restraints: 10594 sinusoidal: 5712 harmonic: 4882 Sorted by residual: dihedral pdb=" C4' DA C 3 " pdb=" C3' DA C 3 " pdb=" O3' DA C 3 " pdb=" P DT C 4 " ideal model delta sinusoidal sigma weight residual 220.00 45.95 174.05 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG C 2 " pdb=" C3' DG C 2 " pdb=" O3' DG C 2 " pdb=" P DA C 3 " ideal model delta sinusoidal sigma weight residual 220.00 73.89 146.11 1 3.50e+01 8.16e-04 1.43e+01 dihedral pdb=" CA ASP A 615 " pdb=" CB ASP A 615 " pdb=" CG ASP A 615 " pdb=" OD1 ASP A 615 " ideal model delta sinusoidal sigma weight residual -30.00 -87.99 57.99 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 10591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1152 0.027 - 0.055: 434 0.055 - 0.082: 169 0.082 - 0.109: 78 0.109 - 0.137: 31 Chirality restraints: 1864 Sorted by residual: chirality pdb=" CA ILE A 960 " pdb=" N ILE A 960 " pdb=" C ILE A 960 " pdb=" CB ILE A 960 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CA ILE B 893 " pdb=" N ILE B 893 " pdb=" C ILE B 893 " pdb=" CB ILE B 893 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA ILE A 966 " pdb=" N ILE A 966 " pdb=" C ILE A 966 " pdb=" CB ILE A 966 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 1861 not shown) Planarity restraints: 3339 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C YWX D 101 " -0.049 2.00e-02 2.50e+03 8.07e-02 2.12e+02 pdb=" O YWX D 101 " -0.099 2.00e-02 2.50e+03 pdb=" C1 YWX D 101 " -0.099 2.00e-02 2.50e+03 pdb=" C16 YWX D 101 " 0.069 2.00e-02 2.50e+03 pdb=" C17 YWX D 101 " 0.092 2.00e-02 2.50e+03 pdb=" C18 YWX D 101 " 0.118 2.00e-02 2.50e+03 pdb=" C5 YWX D 101 " 0.096 2.00e-02 2.50e+03 pdb=" C6 YWX D 101 " 0.050 2.00e-02 2.50e+03 pdb=" C7 YWX D 101 " -0.054 2.00e-02 2.50e+03 pdb=" C8 YWX D 101 " -0.018 2.00e-02 2.50e+03 pdb=" C9 YWX D 101 " -0.134 2.00e-02 2.50e+03 pdb=" N4 YWX D 101 " 0.048 2.00e-02 2.50e+03 pdb=" N5 YWX D 101 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C YWX C 101 " 0.010 2.00e-02 2.50e+03 2.31e-02 1.74e+01 pdb=" O YWX C 101 " 0.015 2.00e-02 2.50e+03 pdb=" C1 YWX C 101 " 0.030 2.00e-02 2.50e+03 pdb=" C16 YWX C 101 " -0.036 2.00e-02 2.50e+03 pdb=" C17 YWX C 101 " -0.032 2.00e-02 2.50e+03 pdb=" C18 YWX C 101 " -0.018 2.00e-02 2.50e+03 pdb=" C5 YWX C 101 " -0.016 2.00e-02 2.50e+03 pdb=" C6 YWX C 101 " -0.012 2.00e-02 2.50e+03 pdb=" C7 YWX C 101 " 0.013 2.00e-02 2.50e+03 pdb=" C8 YWX C 101 " -0.006 2.00e-02 2.50e+03 pdb=" C9 YWX C 101 " 0.049 2.00e-02 2.50e+03 pdb=" N4 YWX C 101 " -0.007 2.00e-02 2.50e+03 pdb=" N5 YWX C 101 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N YWX C 101 " 0.033 2.00e-02 2.50e+03 2.98e-02 1.55e+01 pdb=" C1 YWX C 101 " -0.048 2.00e-02 2.50e+03 pdb=" C2 YWX C 101 " 0.002 2.00e-02 2.50e+03 pdb=" C3 YWX C 101 " 0.013 2.00e-02 2.50e+03 pdb=" C4 YWX C 101 " -0.027 2.00e-02 2.50e+03 pdb=" N1 YWX C 101 " 0.042 2.00e-02 2.50e+03 pdb=" N2 YWX C 101 " -0.014 2.00e-02 2.50e+03 ... (remaining 3336 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 984 2.17 - 2.78: 41730 2.78 - 3.38: 62579 3.38 - 3.99: 84369 3.99 - 4.60: 130792 Nonbonded interactions: 320454 Sorted by model distance: nonbonded pdb=" O ARG A 451 " pdb="HH11 ARG A 451 " model vdw 1.560 2.450 nonbonded pdb=" O ARG B 451 " pdb="HH11 ARG B 451 " model vdw 1.560 2.450 nonbonded pdb=" HH TYR A 995 " pdb=" OD2 ASP A1156 " model vdw 1.586 2.450 nonbonded pdb=" HH TYR B 995 " pdb=" OD2 ASP B1156 " model vdw 1.587 2.450 nonbonded pdb=" O ALA B 632 " pdb="HH22 ARG B 639 " model vdw 1.599 2.450 ... (remaining 320449 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 409 through 1117 or (resid 1118 and (name N or name CA or \ name C or name O or name CB or name CG or name CD or name NE or name H or name H \ A or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3)) or r \ esid 1119 through 1177)) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.590 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: 0.120 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 24.140 Find NCS groups from input model: 0.210 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:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 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 : 0.005 0.149 12065 Z= 0.232 Angle : 0.529 5.931 16582 Z= 0.291 Chirality : 0.039 0.137 1864 Planarity : 0.004 0.081 1949 Dihedral : 19.921 174.051 4368 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.54 % Allowed : 18.17 % Favored : 79.29 % 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: 1.52 (0.24), residues: 1402 helix: 2.65 (0.21), residues: 672 sheet: -1.56 (0.44), residues: 158 loop : -0.19 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 451 TYR 0.011 0.001 TYR B1111 PHE 0.011 0.001 PHE B 676 TRP 0.010 0.001 TRP A 642 HIS 0.003 0.001 HIS B 612 Details of bonding type rmsd covalent geometry : bond 0.00498 (12063) covalent geometry : angle 0.52854 (16582) hydrogen bonds : bond 0.12672 ( 630) hydrogen bonds : angle 5.14221 ( 1726) Misc. bond : bond 0.00040 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 427 ARG cc_start: 0.8216 (mtm110) cc_final: 0.7996 (mtp180) outliers start: 25 outliers final: 25 residues processed: 131 average time/residue: 1.0746 time to fit residues: 153.5831 Evaluate side-chains 126 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 1123 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN B1166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.146393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.121994 restraints weight = 36970.127| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.41 r_work: 0.3296 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.0489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12065 Z= 0.159 Angle : 0.507 4.033 16582 Z= 0.285 Chirality : 0.039 0.145 1864 Planarity : 0.004 0.037 1949 Dihedral : 17.770 175.168 2156 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.65 % Allowed : 16.24 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.24), residues: 1402 helix: 2.68 (0.20), residues: 678 sheet: -1.39 (0.45), residues: 154 loop : -0.12 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1033 TYR 0.008 0.001 TYR B 994 PHE 0.011 0.001 PHE B 676 TRP 0.009 0.001 TRP A 642 HIS 0.002 0.000 HIS B 724 Details of bonding type rmsd covalent geometry : bond 0.00364 (12063) covalent geometry : angle 0.50671 (16582) hydrogen bonds : bond 0.05149 ( 630) hydrogen bonds : angle 4.33942 ( 1726) Misc. bond : bond 0.00043 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 451 ARG cc_start: 0.6434 (tpt90) cc_final: 0.6218 (tpt90) REVERT: B 1140 GLU cc_start: 0.7621 (tp30) cc_final: 0.7246 (tp30) outliers start: 36 outliers final: 14 residues processed: 155 average time/residue: 1.1676 time to fit residues: 196.3806 Evaluate side-chains 128 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 1123 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 116 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 138 optimal weight: 0.1980 chunk 50 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN B1166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.146041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.121603 restraints weight = 37022.466| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.41 r_work: 0.3290 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.0656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12065 Z= 0.172 Angle : 0.507 4.292 16582 Z= 0.285 Chirality : 0.039 0.144 1864 Planarity : 0.004 0.032 1949 Dihedral : 17.597 174.733 2140 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.35 % Allowed : 16.85 % Favored : 79.80 % 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: 1.60 (0.24), residues: 1402 helix: 2.65 (0.20), residues: 680 sheet: -1.43 (0.45), residues: 154 loop : -0.14 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1033 TYR 0.009 0.001 TYR A 994 PHE 0.011 0.001 PHE A 676 TRP 0.008 0.001 TRP A 642 HIS 0.002 0.001 HIS B 724 Details of bonding type rmsd covalent geometry : bond 0.00399 (12063) covalent geometry : angle 0.50748 (16582) hydrogen bonds : bond 0.05094 ( 630) hydrogen bonds : angle 4.18694 ( 1726) Misc. bond : bond 0.00056 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 723 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7661 (tm-30) REVERT: A 1044 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.6864 (mp-120) REVERT: B 723 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7685 (tm-30) REVERT: B 1044 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.6878 (mp-120) REVERT: B 1045 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7437 (mtt-85) REVERT: B 1140 GLU cc_start: 0.7635 (tp30) cc_final: 0.7253 (tp30) outliers start: 33 outliers final: 13 residues processed: 155 average time/residue: 1.2371 time to fit residues: 207.6477 Evaluate side-chains 132 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 793 ASP Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 1044 GLN Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 1044 GLN Chi-restraints excluded: chain B residue 1045 ARG Chi-restraints excluded: chain B residue 1123 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN B 920 GLN B1166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.144646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.120125 restraints weight = 37137.917| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.42 r_work: 0.3252 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.0752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12065 Z= 0.208 Angle : 0.528 5.071 16582 Z= 0.296 Chirality : 0.041 0.144 1864 Planarity : 0.004 0.033 1949 Dihedral : 17.607 174.119 2135 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.37 % Allowed : 15.43 % Favored : 80.20 % 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: 1.41 (0.24), residues: 1402 helix: 2.51 (0.20), residues: 680 sheet: -1.58 (0.45), residues: 154 loop : -0.24 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 451 TYR 0.010 0.001 TYR B 994 PHE 0.012 0.001 PHE B 676 TRP 0.010 0.002 TRP B 861 HIS 0.003 0.001 HIS A 612 Details of bonding type rmsd covalent geometry : bond 0.00488 (12063) covalent geometry : angle 0.52818 (16582) hydrogen bonds : bond 0.05222 ( 630) hydrogen bonds : angle 4.17036 ( 1726) Misc. bond : bond 0.00059 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Evaluate side-chains 166 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 123 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 723 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7643 (tm-30) REVERT: A 1044 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.6846 (mp-120) REVERT: A 1139 ASP cc_start: 0.7831 (m-30) cc_final: 0.7410 (m-30) REVERT: B 723 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7669 (tm-30) REVERT: B 1044 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.6957 (mp-120) REVERT: B 1139 ASP cc_start: 0.7747 (m-30) cc_final: 0.7524 (m-30) REVERT: B 1140 GLU cc_start: 0.7634 (tp30) cc_final: 0.7258 (tp30) outliers start: 43 outliers final: 17 residues processed: 164 average time/residue: 1.1446 time to fit residues: 204.3658 Evaluate side-chains 136 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 1044 GLN Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 1044 GLN Chi-restraints excluded: chain B residue 1123 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 29 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 32 optimal weight: 0.1980 chunk 105 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 89 optimal weight: 0.0980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN B1166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.147075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122744 restraints weight = 36701.623| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.40 r_work: 0.3300 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12065 Z= 0.133 Angle : 0.492 4.823 16582 Z= 0.277 Chirality : 0.039 0.142 1864 Planarity : 0.003 0.033 1949 Dihedral : 17.547 175.004 2134 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.64 % Allowed : 17.46 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.24), residues: 1402 helix: 2.76 (0.20), residues: 680 sheet: -1.45 (0.45), residues: 154 loop : -0.17 (0.28), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 451 TYR 0.007 0.001 TYR A 994 PHE 0.010 0.001 PHE B 676 TRP 0.008 0.001 TRP A 642 HIS 0.002 0.000 HIS B 724 Details of bonding type rmsd covalent geometry : bond 0.00303 (12063) covalent geometry : angle 0.49174 (16582) hydrogen bonds : bond 0.04858 ( 630) hydrogen bonds : angle 4.03188 ( 1726) Misc. bond : bond 0.00032 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 723 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7566 (tm-30) REVERT: A 958 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7463 (mt-10) REVERT: A 1044 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.6834 (mp-120) REVERT: B 723 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7590 (tm-30) REVERT: B 1044 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.6907 (mp-120) REVERT: B 1139 ASP cc_start: 0.7743 (m-30) cc_final: 0.7463 (m-30) REVERT: B 1140 GLU cc_start: 0.7611 (tp30) cc_final: 0.7253 (tp30) outliers start: 26 outliers final: 11 residues processed: 149 average time/residue: 1.1738 time to fit residues: 189.3772 Evaluate side-chains 133 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 1044 GLN Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 1044 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 119 optimal weight: 0.0570 chunk 127 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 68 optimal weight: 0.0050 chunk 78 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 overall best weight: 0.6114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN B1166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.147668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.123384 restraints weight = 36936.654| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.41 r_work: 0.3309 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12065 Z= 0.127 Angle : 0.489 4.801 16582 Z= 0.275 Chirality : 0.038 0.140 1864 Planarity : 0.003 0.032 1949 Dihedral : 17.470 174.856 2128 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.13 % Allowed : 17.16 % Favored : 80.71 % 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: 1.78 (0.24), residues: 1402 helix: 2.87 (0.20), residues: 680 sheet: -1.66 (0.50), residues: 124 loop : -0.16 (0.27), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 978 TYR 0.007 0.001 TYR A 530 PHE 0.010 0.001 PHE A 676 TRP 0.008 0.001 TRP A 642 HIS 0.002 0.000 HIS B 724 Details of bonding type rmsd covalent geometry : bond 0.00291 (12063) covalent geometry : angle 0.48853 (16582) hydrogen bonds : bond 0.04756 ( 630) hydrogen bonds : angle 3.96171 ( 1726) Misc. bond : bond 0.00025 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 723 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7608 (tm-30) REVERT: A 958 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7454 (mt-10) REVERT: A 1044 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.6909 (mp-120) REVERT: B 723 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7613 (tm-30) REVERT: B 1117 MET cc_start: 0.8395 (mtm) cc_final: 0.8193 (mtp) REVERT: B 1139 ASP cc_start: 0.7734 (m-30) cc_final: 0.7402 (m-30) REVERT: B 1140 GLU cc_start: 0.7609 (tp30) cc_final: 0.7263 (tp30) outliers start: 21 outliers final: 11 residues processed: 145 average time/residue: 1.2047 time to fit residues: 189.0861 Evaluate side-chains 133 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1044 GLN Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1123 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 125 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN B1166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.146970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.122537 restraints weight = 36974.110| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.41 r_work: 0.3288 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12065 Z= 0.148 Angle : 0.498 4.781 16582 Z= 0.280 Chirality : 0.039 0.141 1864 Planarity : 0.003 0.032 1949 Dihedral : 17.413 174.212 2123 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.94 % Allowed : 16.95 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.24), residues: 1402 helix: 2.85 (0.20), residues: 680 sheet: -1.42 (0.47), residues: 144 loop : -0.16 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 978 TYR 0.008 0.001 TYR A 994 PHE 0.010 0.001 PHE A 676 TRP 0.008 0.001 TRP A 642 HIS 0.002 0.000 HIS B 724 Details of bonding type rmsd covalent geometry : bond 0.00344 (12063) covalent geometry : angle 0.49781 (16582) hydrogen bonds : bond 0.04800 ( 630) hydrogen bonds : angle 3.95590 ( 1726) Misc. bond : bond 0.00031 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7545 (tm-30) REVERT: A 958 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7419 (mt-10) REVERT: A 1044 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.6813 (mp-120) REVERT: B 723 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7564 (tm-30) REVERT: B 1139 ASP cc_start: 0.7726 (m-30) cc_final: 0.7374 (m-30) REVERT: B 1140 GLU cc_start: 0.7590 (tp30) cc_final: 0.7247 (tp30) outliers start: 29 outliers final: 12 residues processed: 155 average time/residue: 1.0842 time to fit residues: 183.6605 Evaluate side-chains 137 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 1044 GLN Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 1123 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 141 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 21 optimal weight: 0.0980 chunk 79 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 137 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN B1166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.147559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.123260 restraints weight = 36833.417| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.41 r_work: 0.3307 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12065 Z= 0.134 Angle : 0.493 4.727 16582 Z= 0.278 Chirality : 0.039 0.140 1864 Planarity : 0.003 0.036 1949 Dihedral : 17.400 174.322 2123 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.83 % Allowed : 18.27 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.24), residues: 1402 helix: 2.91 (0.20), residues: 680 sheet: -1.70 (0.49), residues: 124 loop : -0.16 (0.27), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 978 TYR 0.007 0.001 TYR A 994 PHE 0.010 0.001 PHE A 676 TRP 0.008 0.001 TRP A 642 HIS 0.002 0.000 HIS B 724 Details of bonding type rmsd covalent geometry : bond 0.00309 (12063) covalent geometry : angle 0.49344 (16582) hydrogen bonds : bond 0.04717 ( 630) hydrogen bonds : angle 3.91782 ( 1726) Misc. bond : bond 0.00029 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 723 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7590 (tm-30) REVERT: A 958 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7461 (mt-10) REVERT: A 1044 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.6824 (mp-120) REVERT: B 723 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7611 (tm-30) REVERT: B 1044 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.6858 (mp-120) outliers start: 18 outliers final: 12 residues processed: 143 average time/residue: 1.1611 time to fit residues: 180.5072 Evaluate side-chains 132 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 1044 GLN Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 1044 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 89 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 38 optimal weight: 0.0970 chunk 111 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 77 optimal weight: 0.3980 chunk 84 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 920 GLN A1166 ASN B1166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.148549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.124269 restraints weight = 36924.122| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.41 r_work: 0.3319 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12065 Z= 0.122 Angle : 0.487 4.680 16582 Z= 0.274 Chirality : 0.038 0.141 1864 Planarity : 0.003 0.032 1949 Dihedral : 17.373 174.436 2123 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.42 % Allowed : 18.88 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.24), residues: 1402 helix: 2.99 (0.20), residues: 680 sheet: -1.63 (0.49), residues: 124 loop : -0.15 (0.27), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 978 TYR 0.007 0.001 TYR A 591 PHE 0.009 0.001 PHE B 968 TRP 0.008 0.001 TRP A 642 HIS 0.002 0.000 HIS A 724 Details of bonding type rmsd covalent geometry : bond 0.00280 (12063) covalent geometry : angle 0.48663 (16582) hydrogen bonds : bond 0.04609 ( 630) hydrogen bonds : angle 3.85818 ( 1726) Misc. bond : bond 0.00023 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.550 Fit side-chains REVERT: A 418 ASN cc_start: 0.8209 (m-40) cc_final: 0.7997 (m-40) REVERT: A 958 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7457 (mt-10) REVERT: A 1044 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.6900 (mp-120) outliers start: 14 outliers final: 10 residues processed: 136 average time/residue: 1.2768 time to fit residues: 187.8487 Evaluate side-chains 127 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 1044 GLN Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 823 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 56 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN B1166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.146979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.122614 restraints weight = 37099.857| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.41 r_work: 0.3296 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12065 Z= 0.158 Angle : 0.507 4.738 16582 Z= 0.285 Chirality : 0.039 0.142 1864 Planarity : 0.004 0.038 1949 Dihedral : 17.384 173.703 2123 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.73 % Allowed : 18.68 % Favored : 79.59 % 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: 1.77 (0.24), residues: 1402 helix: 2.87 (0.20), residues: 680 sheet: -1.39 (0.46), residues: 144 loop : -0.19 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 978 TYR 0.009 0.001 TYR A 994 PHE 0.010 0.001 PHE A 676 TRP 0.009 0.001 TRP A 642 HIS 0.002 0.001 HIS A 724 Details of bonding type rmsd covalent geometry : bond 0.00370 (12063) covalent geometry : angle 0.50667 (16582) hydrogen bonds : bond 0.04763 ( 630) hydrogen bonds : angle 3.90960 ( 1726) Misc. bond : bond 0.00034 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 418 ASN cc_start: 0.8212 (m-40) cc_final: 0.8004 (m-40) REVERT: A 958 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7478 (mt-10) REVERT: A 1044 GLN cc_start: 0.7434 (OUTLIER) cc_final: 0.6835 (mp-120) outliers start: 17 outliers final: 9 residues processed: 136 average time/residue: 1.1978 time to fit residues: 176.9313 Evaluate side-chains 129 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 1044 GLN Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 823 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 124 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN B1166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.146789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.122307 restraints weight = 36976.262| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.41 r_work: 0.3291 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12065 Z= 0.160 Angle : 0.511 4.719 16582 Z= 0.287 Chirality : 0.039 0.141 1864 Planarity : 0.004 0.035 1949 Dihedral : 17.389 173.715 2123 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.12 % Allowed : 19.39 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.24), residues: 1402 helix: 2.83 (0.20), residues: 680 sheet: -1.40 (0.46), residues: 144 loop : -0.19 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 978 TYR 0.008 0.001 TYR A 994 PHE 0.010 0.001 PHE A 676 TRP 0.007 0.001 TRP A 642 HIS 0.002 0.000 HIS B 724 Details of bonding type rmsd covalent geometry : bond 0.00372 (12063) covalent geometry : angle 0.51058 (16582) hydrogen bonds : bond 0.04774 ( 630) hydrogen bonds : angle 3.91062 ( 1726) Misc. bond : bond 0.00038 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6682.41 seconds wall clock time: 113 minutes 28.49 seconds (6808.49 seconds total)