Starting phenix.real_space_refine on Sat Jul 4 17:10:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gcc_29930/07_2026/8gcc_29930.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gcc_29930/07_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_29930/07_2026/8gcc_29930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gcc_29930/07_2026/8gcc_29930.map" model { file = "/net/cci-nas-00/data/ceres_data/8gcc_29930/07_2026/8gcc_29930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gcc_29930/07_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-6108/lib/python3.11/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: 3.82, per 1000 atoms: 0.17 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: 2.20 Conformation dependent library (CDL) restraints added in 562.8 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: 3.97 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: 5.41 Time building geometry restraints manager: 2.97 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: 39817 1.48 - 2.95: 891 2.95 - 4.43: 101 4.43 - 5.91: 9 5.91 - 7.38: 4 Bond angle restraints: 40822 Sorted by residual: angle pdb=" O4' DT C 19 " pdb=" C4' DT C 19 " pdb=" C3' DT C 19 " ideal model delta sigma weight residual 106.00 102.72 3.28 6.00e-01 2.78e+00 2.98e+01 angle pdb=" O4' DG C 11 " pdb=" C4' DG C 11 " pdb=" C3' DG C 11 " ideal model delta sigma weight residual 106.00 103.26 2.74 6.00e-01 2.78e+00 2.09e+01 angle pdb=" O4' DT C 19 " pdb=" C1' DT C 19 " pdb=" N1 DT C 19 " ideal model delta sigma weight residual 108.00 111.11 -3.11 7.00e-01 2.04e+00 1.97e+01 angle pdb=" O4' DC D 7 " pdb=" C4' DC D 7 " pdb=" C3' DC D 7 " ideal model delta sigma weight residual 106.00 103.36 2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" O4' DG D 11 " pdb=" C4' DG D 11 " pdb=" C3' DG D 11 " ideal model delta sigma weight residual 106.00 103.44 2.56 6.00e-01 2.78e+00 1.82e+01 ... (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 - 0.038: 1362 0.038 - 0.076: 344 0.076 - 0.113: 92 0.113 - 0.151: 50 0.151 - 0.189: 16 Chirality restraints: 1864 Sorted by residual: chirality pdb=" C3' DT D 10 " pdb=" C4' DT D 10 " pdb=" O3' DT D 10 " pdb=" C2' DT D 10 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.93e-01 chirality pdb=" C3' DA D 6 " pdb=" C4' DA D 6 " pdb=" O3' DA D 6 " pdb=" C2' DA D 6 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.21e-01 chirality pdb=" C3' DT D 18 " pdb=" C4' DT D 18 " pdb=" O3' DT D 18 " pdb=" C2' DT D 18 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.65e-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: 3.820 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: 0.150 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 25.380 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 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= 0.317 Angle : 0.574 5.931 16582 Z= 0.400 Chirality : 0.044 0.189 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/Z covalent geometry : bond 0.00527 / 0.32 (12063) covalent geometry : angle 0.57371 / 0.40 (16582) hydrogen bonds : bond 0.12672 / 8.71 ( 630) hydrogen bonds : angle 5.14221 / 3.66 ( 1726) Misc. bond : bond 0.00040 / 0.02 ( 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 : 0.588 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: 1.0407 time to fit residues: 151.0135 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 : 0.584 ------------------------------------------------------------------------------- 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... 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 = 0.3686 r_free = 0.3686 target = 0.146079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.121612 restraints weight = 36919.569| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.41 r_work: 0.3295 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.0316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12065 Z= 0.165 Angle : 0.542 6.090 16582 Z= 0.313 Chirality : 0.041 0.190 1864 Planarity : 0.004 0.041 1949 Dihedral : 17.839 178.884 2156 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.35 % Allowed : 16.65 % Favored : 80.00 % 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: 2.57 (0.20), residues: 678 sheet: -1.48 (0.45), residues: 154 loop : -0.15 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 978 TYR 0.008 0.001 TYR B 994 PHE 0.011 0.001 PHE B 968 TRP 0.009 0.001 TRP A 642 HIS 0.002 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (12063) covalent geometry : angle 0.54166 / 0.31 (16582) hydrogen bonds : bond 0.05756 / 3.90 ( 630) hydrogen bonds : angle 4.58998 / 3.23 ( 1726) Misc. bond : bond 0.00085 / 0.04 ( 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 143 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 427 ARG cc_start: 0.8163 (mtm110) cc_final: 0.7909 (mtp180) REVERT: B 1140 GLU cc_start: 0.7653 (tp30) cc_final: 0.7288 (tp30) outliers start: 33 outliers final: 20 residues processed: 143 average time/residue: 1.0965 time to fit residues: 172.7566 Evaluate side-chains 131 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 479 GLU Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 565 SER 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 634 ASP 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 1123 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 116 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3678 r_free = 0.3678 target = 0.145301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.120870 restraints weight = 37041.965| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.41 r_work: 0.3274 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.0487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12065 Z= 0.190 Angle : 0.536 6.358 16582 Z= 0.308 Chirality : 0.041 0.185 1864 Planarity : 0.004 0.037 1949 Dihedral : 17.810 179.935 2149 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.55 % Allowed : 16.65 % 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: 1.39 (0.24), residues: 1402 helix: 2.49 (0.20), residues: 678 sheet: -1.55 (0.45), residues: 154 loop : -0.25 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 978 TYR 0.009 0.001 TYR A 994 PHE 0.016 0.001 PHE A 968 TRP 0.009 0.002 TRP B 861 HIS 0.002 0.001 HIS B 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (12063) covalent geometry : angle 0.53567 / 0.31 (16582) hydrogen bonds : bond 0.05463 / 3.73 ( 630) hydrogen bonds : angle 4.42043 / 3.11 ( 1726) Misc. bond : bond 0.00142 / 0.07 ( 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: 35 poor density : 121 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7631 (tm-30) REVERT: A 1044 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.6867 (mp-120) REVERT: B 723 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7668 (tm-30) REVERT: B 1140 GLU cc_start: 0.7641 (tp30) cc_final: 0.7260 (tp30) outliers start: 35 outliers final: 19 residues processed: 156 average time/residue: 1.0728 time to fit residues: 184.4436 Evaluate side-chains 134 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 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 519 ILE Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain B residue 723 GLU 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 894 THR 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: 0.9990 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3666 r_free = 0.3666 target = 0.144127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.119837 restraints weight = 37199.112| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.39 r_work: 0.3280 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.0586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12065 Z= 0.202 Angle : 0.543 6.551 16582 Z= 0.311 Chirality : 0.041 0.182 1864 Planarity : 0.004 0.036 1949 Dihedral : 17.766 179.844 2144 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.45 % Allowed : 16.45 % 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: 1.31 (0.24), residues: 1402 helix: 2.40 (0.20), residues: 680 sheet: -1.58 (0.45), residues: 154 loop : -0.26 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 451 TYR 0.010 0.001 TYR B 994 PHE 0.016 0.001 PHE B 968 TRP 0.009 0.002 TRP B 861 HIS 0.003 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 (12063) covalent geometry : angle 0.54346 / 0.31 (16582) hydrogen bonds : bond 0.05451 / 3.72 ( 630) hydrogen bonds : angle 4.34188 / 3.06 ( 1726) Misc. bond : bond 0.00084 / 0.04 ( 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 150 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: A 723 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7615 (tm-30) REVERT: A 1044 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.6844 (mp-120) REVERT: B 723 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7644 (tm-30) REVERT: B 1044 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.6890 (mp-120) REVERT: B 1140 GLU cc_start: 0.7582 (tp30) cc_final: 0.7361 (tp30) outliers start: 34 outliers final: 16 residues processed: 149 average time/residue: 1.0813 time to fit residues: 177.3365 Evaluate side-chains 128 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 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 519 ILE Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 793 ASP 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: 0.6980 chunk 142 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.146359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.122017 restraints weight = 36710.114| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.40 r_work: 0.3279 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.0622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12065 Z= 0.151 Angle : 0.515 5.920 16582 Z= 0.297 Chirality : 0.040 0.183 1864 Planarity : 0.004 0.032 1949 Dihedral : 17.734 179.520 2141 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.15 % Allowed : 16.85 % Favored : 80.00 % 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: 1.47 (0.24), residues: 1402 helix: 2.55 (0.20), residues: 680 sheet: -1.53 (0.45), residues: 154 loop : -0.21 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 978 TYR 0.008 0.001 TYR B 994 PHE 0.011 0.001 PHE A 968 TRP 0.008 0.001 TRP A 642 HIS 0.002 0.001 HIS B 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (12063) covalent geometry : angle 0.51481 / 0.30 (16582) hydrogen bonds : bond 0.05207 / 3.54 ( 630) hydrogen bonds : angle 4.24368 / 2.99 ( 1726) Misc. bond : bond 0.00054 / 0.03 ( 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 151 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 723 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: A 1044 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.6852 (mp-120) REVERT: B 723 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: B 1140 GLU cc_start: 0.7641 (tp30) cc_final: 0.7242 (tp30) outliers start: 31 outliers final: 17 residues processed: 151 average time/residue: 1.0667 time to fit residues: 177.4633 Evaluate side-chains 134 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 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 984 LEU 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 688 VAL Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 778 THR 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 1123 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 119 optimal weight: 0.0470 chunk 127 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3688 r_free = 0.3688 target = 0.146201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.121773 restraints weight = 36984.655| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.40 r_work: 0.3287 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.0676 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= 0.162 Angle : 0.521 6.227 16582 Z= 0.299 Chirality : 0.040 0.180 1864 Planarity : 0.004 0.040 1949 Dihedral : 17.705 179.246 2135 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.45 % Allowed : 16.45 % 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: 1.46 (0.24), residues: 1402 helix: 2.57 (0.20), residues: 680 sheet: -1.55 (0.45), residues: 154 loop : -0.24 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 978 TYR 0.009 0.001 TYR A 994 PHE 0.015 0.001 PHE A 968 TRP 0.008 0.001 TRP A 642 HIS 0.002 0.001 HIS B 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (12063) covalent geometry : angle 0.52094 / 0.30 (16582) hydrogen bonds : bond 0.05171 / 3.54 ( 630) hydrogen bonds : angle 4.18591 / 2.95 ( 1726) Misc. bond : bond 0.00047 / 0.02 ( 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 155 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 723 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7650 (tm-30) REVERT: A 807 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8155 (pp20) REVERT: A 1044 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.6817 (mp-120) REVERT: B 723 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7673 (tm-30) REVERT: B 1044 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.6873 (mp-120) REVERT: B 1140 GLU cc_start: 0.7571 (tp30) cc_final: 0.7199 (tp30) outliers start: 34 outliers final: 21 residues processed: 154 average time/residue: 1.0168 time to fit residues: 172.5472 Evaluate side-chains 140 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 479 GLU 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 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 984 LEU 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 723 GLU 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 894 THR Chi-restraints excluded: chain B residue 1044 GLN 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: 1.9990 chunk 71 optimal weight: 6.9990 chunk 134 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 143 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3696 r_free = 0.3696 target = 0.146847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.122391 restraints weight = 36877.726| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.41 r_work: 0.3296 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.0735 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= 0.141 Angle : 0.508 5.820 16582 Z= 0.293 Chirality : 0.039 0.179 1864 Planarity : 0.003 0.032 1949 Dihedral : 17.697 179.103 2135 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.84 % Allowed : 16.75 % Favored : 80.41 % 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: 2.70 (0.20), residues: 680 sheet: -1.49 (0.46), residues: 154 loop : -0.19 (0.27), residues: 568 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 0.014 0.001 PHE B 968 TRP 0.008 0.001 TRP A 642 HIS 0.002 0.000 HIS B 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (12063) covalent geometry : angle 0.50761 / 0.29 (16582) hydrogen bonds : bond 0.05048 / 3.45 ( 630) hydrogen bonds : angle 4.11026 / 2.89 ( 1726) Misc. bond : bond 0.00039 / 0.02 ( 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 149 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 723 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7623 (tm-30) REVERT: A 958 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7689 (tt0) REVERT: A 1044 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.6828 (mp-120) REVERT: B 723 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7652 (tm-30) REVERT: B 1044 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.6857 (mp-120) REVERT: B 1140 GLU cc_start: 0.7548 (tp30) cc_final: 0.7188 (tp30) outliers start: 28 outliers final: 21 residues processed: 149 average time/residue: 1.0112 time to fit residues: 165.7313 Evaluate side-chains 141 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 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 984 LEU 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 778 THR Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1044 GLN 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: 3.9990 chunk 132 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 116 optimal weight: 0.0270 chunk 21 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3700 r_free = 0.3700 target = 0.147225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122777 restraints weight = 36757.985| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.41 r_work: 0.3301 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.0780 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= 0.132 Angle : 0.506 5.790 16582 Z= 0.292 Chirality : 0.039 0.177 1864 Planarity : 0.004 0.034 1949 Dihedral : 17.688 178.850 2135 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.15 % Allowed : 16.55 % Favored : 80.30 % 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: 1.69 (0.24), residues: 1402 helix: 2.78 (0.20), residues: 680 sheet: -1.45 (0.46), residues: 154 loop : -0.16 (0.28), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 978 TYR 0.007 0.001 TYR A 530 PHE 0.010 0.001 PHE B 676 TRP 0.009 0.001 TRP A 642 HIS 0.002 0.000 HIS A 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (12063) covalent geometry : angle 0.50607 / 0.29 (16582) hydrogen bonds : bond 0.04975 / 3.41 ( 630) hydrogen bonds : angle 4.05866 / 2.86 ( 1726) Misc. bond : bond 0.00031 / 0.02 ( 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 152 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7620 (tm-30) REVERT: A 958 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7699 (tt0) REVERT: A 1044 GLN cc_start: 0.7398 (OUTLIER) cc_final: 0.6833 (mp-120) REVERT: B 723 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7639 (tm-30) REVERT: B 1044 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.6886 (mp-120) REVERT: B 1140 GLU cc_start: 0.7557 (tp30) cc_final: 0.7198 (tp30) outliers start: 31 outliers final: 20 residues processed: 152 average time/residue: 1.0758 time to fit residues: 179.6547 Evaluate side-chains 140 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 723 GLU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 806 VAL 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 984 LEU Chi-restraints excluded: chain A residue 1044 GLN Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain B residue 433 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 778 THR Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1044 GLN Chi-restraints excluded: chain B residue 1123 THR 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: 0.9980 chunk 72 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 chunk 111 optimal weight: 0.9980 chunk 23 optimal weight: 0.0670 chunk 77 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.147536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.123125 restraints weight = 36856.552| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.41 r_work: 0.3305 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.0801 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= 0.131 Angle : 0.503 5.738 16582 Z= 0.291 Chirality : 0.039 0.176 1864 Planarity : 0.003 0.032 1949 Dihedral : 17.643 178.688 2132 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.44 % Allowed : 17.36 % 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: 1.75 (0.24), residues: 1402 helix: 2.83 (0.20), residues: 680 sheet: -1.42 (0.46), residues: 154 loop : -0.14 (0.28), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 978 TYR 0.007 0.001 TYR A 530 PHE 0.012 0.001 PHE A 968 TRP 0.007 0.001 TRP A 642 HIS 0.002 0.000 HIS B 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (12063) covalent geometry : angle 0.50324 / 0.29 (16582) hydrogen bonds : bond 0.04930 / 3.38 ( 630) hydrogen bonds : angle 4.02774 / 2.84 ( 1726) Misc. bond : bond 0.00028 / 0.01 ( 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 142 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7600 (tm-30) REVERT: A 958 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7458 (mt-10) REVERT: A 1044 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.6836 (mp-120) REVERT: B 723 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7628 (tm-30) REVERT: B 1140 GLU cc_start: 0.7551 (tp30) cc_final: 0.7197 (tp30) outliers start: 24 outliers final: 17 residues processed: 142 average time/residue: 1.0960 time to fit residues: 170.8992 Evaluate side-chains 136 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 723 GLU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 806 VAL 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 519 ILE 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 793 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 56 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 95 optimal weight: 0.4980 chunk 113 optimal weight: 0.5980 chunk 96 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3701 r_free = 0.3701 target = 0.147276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.122814 restraints weight = 36974.129| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.41 r_work: 0.3301 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.0832 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= 0.141 Angle : 0.510 5.994 16582 Z= 0.293 Chirality : 0.039 0.173 1864 Planarity : 0.003 0.032 1949 Dihedral : 17.640 178.730 2130 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.13 % Allowed : 17.87 % Favored : 80.00 % 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: 1.74 (0.24), residues: 1402 helix: 2.83 (0.20), residues: 680 sheet: -1.41 (0.47), residues: 144 loop : -0.17 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 978 TYR 0.008 0.001 TYR B 994 PHE 0.010 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/Z covalent geometry : bond 0.00304 / 0.14 (12063) covalent geometry : angle 0.51014 / 0.29 (16582) hydrogen bonds : bond 0.04922 / 3.39 ( 630) hydrogen bonds : angle 4.00675 / 2.82 ( 1726) Misc. bond : bond 0.00030 / 0.02 ( 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 142 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 723 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7570 (tm-30) REVERT: A 958 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7457 (mt-10) REVERT: A 1044 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.6845 (mp-120) REVERT: B 723 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7611 (tm-30) REVERT: B 1140 GLU cc_start: 0.7636 (tp30) cc_final: 0.7283 (tp30) outliers start: 21 outliers final: 13 residues processed: 142 average time/residue: 1.1087 time to fit residues: 172.3854 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 : 0.518 ------------------------------------------------------------------------------- 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 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 519 ILE 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 1123 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: 0.9980 chunk 120 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 39 optimal weight: 0.0970 chunk 48 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 overall best weight: 0.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3700 r_free = 0.3700 target = 0.147236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.122839 restraints weight = 36850.157| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.40 r_work: 0.3299 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.0846 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= 0.146 Angle : 0.512 5.970 16582 Z= 0.294 Chirality : 0.039 0.173 1864 Planarity : 0.004 0.043 1949 Dihedral : 17.641 178.897 2129 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.52 % Allowed : 18.78 % 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: 1.74 (0.24), residues: 1402 helix: 2.82 (0.20), residues: 680 sheet: -1.41 (0.47), residues: 144 loop : -0.16 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 978 TYR 0.008 0.001 TYR B 994 PHE 0.012 0.001 PHE B 968 TRP 0.008 0.001 TRP A 642 HIS 0.002 0.000 HIS B 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (12063) covalent geometry : angle 0.51182 / 0.29 (16582) hydrogen bonds : bond 0.04914 / 3.38 ( 630) hydrogen bonds : angle 4.00169 / 2.82 ( 1726) Misc. bond : bond 0.00035 / 0.02 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6462.87 seconds wall clock time: 110 minutes 4.06 seconds (6604.06 seconds total)