Starting phenix.real_space_refine on Fri Aug 7 14:49:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gcc_29930/08_2026/8gcc_29930.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gcc_29930/08_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_29930/08_2026/8gcc_29930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gcc_29930/08_2026/8gcc_29930.map" model { file = "/net/cci-nas-00/data/ceres_data/8gcc_29930/08_2026/8gcc_29930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gcc_29930/08_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-2.2rc3-6140/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: 3.29, per 1000 atoms: 0.15 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: 2.01 Conformation dependent library (CDL) restraints added in 493.7 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: 3.68 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: 4.71 Time building geometry restraints manager: 2.64 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: 39816 1.48 - 2.95: 892 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: 5.290 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: 0.110 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.500 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.920 ------------------------------------------------------------------------------- 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= 0.318 Angle : 0.575 5.931 16582 Z= 0.402 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 0.57538 / 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 : 0.579 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: 0.8847 time to fit residues: 127.8213 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 : 0.409 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.146006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.121566 restraints weight = 36940.300| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.41 r_work: 0.3293 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.0340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12065 Z= 0.164 Angle : 0.541 6.316 16582 Z= 0.312 Chirality : 0.041 0.202 1864 Planarity : 0.004 0.041 1949 Dihedral : 17.814 178.486 2156 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.35 % Allowed : 16.75 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.24), residues: 1402 helix: 2.58 (0.20), residues: 678 sheet: -1.47 (0.45), residues: 154 loop : -0.15 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 978 TYR 0.008 0.001 TYR B 994 PHE 0.012 0.001 PHE B 968 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 0.00347 / 0.16 (12063) covalent geometry : angle 0.54149 / 0.31 (16582) hydrogen bonds : bond 0.05770 / 3.91 ( 630) hydrogen bonds : angle 4.56122 / 3.21 ( 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 145 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 427 ARG cc_start: 0.8179 (mtm110) cc_final: 0.7925 (mtp180) REVERT: B 1140 GLU cc_start: 0.7653 (tp30) cc_final: 0.7287 (tp30) outliers start: 33 outliers final: 20 residues processed: 145 average time/residue: 0.8776 time to fit residues: 140.8319 Evaluate side-chains 129 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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: 0.7980 chunk 70 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.145875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.121473 restraints weight = 37011.234| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.41 r_work: 0.3292 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.0508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12065 Z= 0.169 Angle : 0.525 6.108 16582 Z= 0.302 Chirality : 0.040 0.201 1864 Planarity : 0.004 0.036 1949 Dihedral : 17.776 179.770 2149 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.45 % Allowed : 16.85 % 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: 1.47 (0.24), residues: 1402 helix: 2.56 (0.20), residues: 678 sheet: -1.49 (0.45), residues: 154 loop : -0.22 (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 B 994 PHE 0.017 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 0.00370 / 0.17 (12063) covalent geometry : angle 0.52529 / 0.30 (16582) hydrogen bonds : bond 0.05337 / 3.65 ( 630) hydrogen bonds : angle 4.36179 / 3.07 ( 1726) Misc. bond : bond 0.00120 / 0.06 ( 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 154 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7623 (tm-30) REVERT: A 1044 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.6833 (mp-120) REVERT: B 723 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7659 (tm-30) REVERT: B 1139 ASP cc_start: 0.7831 (m-30) cc_final: 0.7620 (m-30) REVERT: B 1140 GLU cc_start: 0.7641 (tp30) cc_final: 0.7262 (tp30) outliers start: 34 outliers final: 17 residues processed: 153 average time/residue: 1.0805 time to fit residues: 182.3852 Evaluate side-chains 130 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 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: 0.5980 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: 3.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.145333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.120849 restraints weight = 37061.238| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.41 r_work: 0.3273 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.0593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12065 Z= 0.201 Angle : 0.545 6.759 16582 Z= 0.311 Chirality : 0.041 0.197 1864 Planarity : 0.004 0.037 1949 Dihedral : 17.705 179.989 2140 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.45 % Allowed : 16.75 % 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: 1.36 (0.24), residues: 1402 helix: 2.45 (0.20), residues: 680 sheet: -1.55 (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 A 994 PHE 0.015 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 0.00455 / 0.20 (12063) covalent geometry : angle 0.54538 / 0.31 (16582) hydrogen bonds : bond 0.05426 / 3.71 ( 630) hydrogen bonds : angle 4.31393 / 3.04 ( 1726) Misc. bond : bond 0.00088 / 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 : 0.579 Fit side-chains revert: symmetry clash REVERT: A 723 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7643 (tm-30) REVERT: A 1044 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.6812 (mp-120) REVERT: A 1139 ASP cc_start: 0.7866 (m-30) cc_final: 0.7451 (m-30) REVERT: B 723 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: B 1139 ASP cc_start: 0.7825 (m-30) cc_final: 0.7564 (m-30) REVERT: B 1140 GLU cc_start: 0.7641 (tp30) cc_final: 0.7261 (tp30) outliers start: 34 outliers final: 17 residues processed: 149 average time/residue: 1.0309 time to fit residues: 169.4613 Evaluate side-chains 129 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 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 634 ASP Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 894 THR 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: 0.5980 chunk 142 optimal weight: 5.9990 chunk 125 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 6 optimal weight: 0.0770 chunk 51 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.147300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.122896 restraints weight = 36679.615| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.41 r_work: 0.3303 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 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 : 0.003 0.025 12065 Z= 0.127 Angle : 0.502 5.582 16582 Z= 0.290 Chirality : 0.039 0.198 1864 Planarity : 0.003 0.032 1949 Dihedral : 17.659 179.497 2137 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.35 % Allowed : 16.45 % 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: 1.63 (0.24), residues: 1402 helix: 2.68 (0.20), residues: 680 sheet: -1.41 (0.46), residues: 154 loop : -0.15 (0.28), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 978 TYR 0.007 0.001 TYR B 994 PHE 0.010 0.001 PHE A 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 0.00262 / 0.13 (12063) covalent geometry : angle 0.50179 / 0.29 (16582) hydrogen bonds : bond 0.05085 / 3.46 ( 630) hydrogen bonds : angle 4.18336 / 2.94 ( 1726) Misc. bond : bond 0.00013 / 0.01 ( 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 158 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.718 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: 0.7615 (tm-30) REVERT: A 1044 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.6842 (mp-120) REVERT: B 723 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7651 (tm-30) REVERT: B 1044 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.6841 (mp-120) REVERT: B 1139 ASP cc_start: 0.7825 (m-30) cc_final: 0.7523 (m-30) REVERT: B 1140 GLU cc_start: 0.7636 (tp30) cc_final: 0.7267 (tp30) outliers start: 33 outliers final: 18 residues processed: 158 average time/residue: 1.0690 time to fit residues: 186.4541 Evaluate side-chains 138 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 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 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 806 VAL Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 1044 GLN Chi-restraints excluded: chain B residue 1123 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 119 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 68 optimal weight: 0.0050 chunk 78 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- 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 = 0.146251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.121812 restraints weight = 37008.080| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.41 r_work: 0.3288 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.0690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12065 Z= 0.166 Angle : 0.523 6.405 16582 Z= 0.299 Chirality : 0.040 0.193 1864 Planarity : 0.004 0.039 1949 Dihedral : 17.659 179.330 2135 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.84 % Allowed : 17.06 % 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: 1.56 (0.24), residues: 1402 helix: 2.65 (0.20), residues: 680 sheet: -1.47 (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 0.013 0.001 PHE B 968 TRP 0.008 0.001 TRP B 861 HIS 0.002 0.001 HIS B 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (12063) covalent geometry : angle 0.52265 / 0.30 (16582) hydrogen bonds : bond 0.05134 / 3.52 ( 630) hydrogen bonds : angle 4.14770 / 2.92 ( 1726) Misc. bond : bond 0.00031 / 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 147 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 723 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7657 (tm-30) REVERT: A 807 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8164 (pp20) REVERT: A 958 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7712 (tt0) REVERT: A 1044 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.6851 (mp-120) REVERT: B 723 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7674 (tm-30) REVERT: B 1139 ASP cc_start: 0.7826 (m-30) cc_final: 0.7489 (m-30) REVERT: B 1140 GLU cc_start: 0.7643 (tp30) cc_final: 0.7262 (tp30) outliers start: 28 outliers final: 19 residues processed: 147 average time/residue: 1.0987 time to fit residues: 178.3331 Evaluate side-chains 137 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 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 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 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 984 LEU Chi-restraints excluded: chain B residue 1123 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 125 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.146748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.122312 restraints weight = 36891.588| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.41 r_work: 0.3294 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.0737 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= 0.150 Angle : 0.514 6.038 16582 Z= 0.295 Chirality : 0.040 0.191 1864 Planarity : 0.003 0.032 1949 Dihedral : 17.663 179.371 2135 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.94 % Allowed : 16.75 % 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: 1.63 (0.24), residues: 1402 helix: 2.72 (0.20), residues: 680 sheet: -1.46 (0.46), residues: 154 loop : -0.18 (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 B 994 PHE 0.010 0.001 PHE A 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 0.00326 / 0.15 (12063) covalent geometry : angle 0.51376 / 0.30 (16582) hydrogen bonds : bond 0.05063 / 3.46 ( 630) hydrogen bonds : angle 4.09670 / 2.88 ( 1726) Misc. bond : bond 0.00037 / 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 148 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 723 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7629 (tm-30) REVERT: A 958 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7699 (tt0) REVERT: A 1044 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.6834 (mp-120) REVERT: B 723 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7655 (tm-30) REVERT: B 1044 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.6857 (mp-120) REVERT: B 1139 ASP cc_start: 0.7822 (m-30) cc_final: 0.7451 (m-30) REVERT: B 1140 GLU cc_start: 0.7596 (tp30) cc_final: 0.7236 (tp30) outliers start: 29 outliers final: 19 residues processed: 147 average time/residue: 1.0842 time to fit residues: 175.5101 Evaluate side-chains 138 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 8 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 40 optimal weight: 0.0980 chunk 11 optimal weight: 0.9980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.147409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.123017 restraints weight = 36733.506| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.40 r_work: 0.3304 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.0791 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= 0.133 Angle : 0.507 5.879 16582 Z= 0.291 Chirality : 0.039 0.190 1864 Planarity : 0.003 0.032 1949 Dihedral : 17.660 179.091 2135 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.64 % Allowed : 16.95 % 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: 1.73 (0.24), residues: 1402 helix: 2.81 (0.20), residues: 680 sheet: -1.40 (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 0.008 0.001 TYR A 591 PHE 0.010 0.001 PHE A 676 TRP 0.008 0.001 TRP A 642 HIS 0.002 0.000 HIS A 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (12063) covalent geometry : angle 0.50690 / 0.29 (16582) hydrogen bonds : bond 0.04961 / 3.40 ( 630) hydrogen bonds : angle 4.03154 / 2.84 ( 1726) Misc. bond : bond 0.00041 / 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 151 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7598 (tm-30) REVERT: A 807 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8152 (pp20) REVERT: A 958 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7691 (tt0) REVERT: A 1044 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.6831 (mp-120) REVERT: B 723 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7632 (tm-30) REVERT: B 1044 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.6848 (mp-120) REVERT: B 1139 ASP cc_start: 0.7798 (m-30) cc_final: 0.7401 (m-30) REVERT: B 1140 GLU cc_start: 0.7613 (tp30) cc_final: 0.7254 (tp30) outliers start: 26 outliers final: 16 residues processed: 151 average time/residue: 0.9915 time to fit residues: 165.4146 Evaluate side-chains 137 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 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 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 688 VAL Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 894 THR 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: 0.9980 chunk 111 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 113 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.147117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.122702 restraints weight = 36902.215| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.41 r_work: 0.3299 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.0810 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 : 0.515 6.093 16582 Z= 0.296 Chirality : 0.039 0.188 1864 Planarity : 0.003 0.032 1949 Dihedral : 17.660 179.010 2134 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.34 % Allowed : 17.66 % 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: 1.70 (0.24), residues: 1402 helix: 2.79 (0.20), residues: 680 sheet: -1.41 (0.46), residues: 154 loop : -0.18 (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 B 994 PHE 0.012 0.001 PHE A 968 TRP 0.008 0.001 TRP B 642 HIS 0.002 0.000 HIS B 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (12063) covalent geometry : angle 0.51498 / 0.30 (16582) hydrogen bonds : bond 0.04972 / 3.42 ( 630) hydrogen bonds : angle 4.02246 / 2.83 ( 1726) Misc. bond : bond 0.00042 / 0.02 ( 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 140 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7600 (tm-30) REVERT: A 958 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7698 (tt0) REVERT: A 1044 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.6841 (mp-120) REVERT: B 723 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7631 (tm-30) REVERT: B 1139 ASP cc_start: 0.7800 (m-30) cc_final: 0.7396 (m-30) REVERT: B 1140 GLU cc_start: 0.7618 (tp30) cc_final: 0.7258 (tp30) outliers start: 23 outliers final: 17 residues processed: 140 average time/residue: 1.0110 time to fit residues: 156.0023 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 : 0.560 ------------------------------------------------------------------------------- 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 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 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 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: 0.6980 chunk 42 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 113 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.146999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.122530 restraints weight = 36990.606| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.41 r_work: 0.3287 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12065 Z= 0.149 Angle : 0.514 6.125 16582 Z= 0.295 Chirality : 0.039 0.186 1864 Planarity : 0.003 0.032 1949 Dihedral : 17.669 179.131 2133 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.34 % Allowed : 17.97 % 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: 1.70 (0.24), residues: 1402 helix: 2.79 (0.20), residues: 680 sheet: -1.41 (0.45), residues: 154 loop : -0.17 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 978 TYR 0.008 0.001 TYR B 994 PHE 0.010 0.001 PHE A 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 0.00324 / 0.15 (12063) covalent geometry : angle 0.51444 / 0.30 (16582) hydrogen bonds : bond 0.04961 / 3.41 ( 630) hydrogen bonds : angle 4.00941 / 2.82 ( 1726) Misc. bond : bond 0.00038 / 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 140 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7567 (tm-30) REVERT: A 807 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8143 (pp20) REVERT: A 958 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7433 (mt-10) REVERT: A 1044 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.6782 (mp-120) REVERT: B 723 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7610 (tm-30) REVERT: B 1139 ASP cc_start: 0.7780 (m-30) cc_final: 0.7367 (m-30) REVERT: B 1140 GLU cc_start: 0.7605 (tp30) cc_final: 0.7256 (tp30) outliers start: 23 outliers final: 18 residues processed: 140 average time/residue: 0.9705 time to fit residues: 150.6047 Evaluate side-chains 139 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 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 433 THR Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 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 124 optimal weight: 0.9990 chunk 116 optimal weight: 0.0060 chunk 120 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 39 optimal weight: 0.1980 chunk 48 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.147917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.123523 restraints weight = 36813.207| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.40 r_work: 0.3309 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.0871 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= 0.126 Angle : 0.502 5.733 16582 Z= 0.289 Chirality : 0.039 0.187 1864 Planarity : 0.003 0.046 1949 Dihedral : 17.656 178.975 2133 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.93 % Allowed : 18.27 % 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: 1.80 (0.24), residues: 1402 helix: 2.87 (0.20), residues: 680 sheet: -1.36 (0.46), residues: 154 loop : -0.13 (0.28), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 978 TYR 0.007 0.001 TYR A 530 PHE 0.010 0.001 PHE B 968 TRP 0.009 0.001 TRP B 642 HIS 0.002 0.000 HIS B 724 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (12063) covalent geometry : angle 0.50192 / 0.29 (16582) hydrogen bonds : bond 0.04863 / 3.34 ( 630) hydrogen bonds : angle 3.97995 / 2.80 ( 1726) Misc. bond : bond 0.00027 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6383.93 seconds wall clock time: 108 minutes 41.89 seconds (6521.89 seconds total)