Starting phenix.real_space_refine on Thu Mar 5 17:51:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l3n_23156/03_2026/7l3n_23156.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l3n_23156/03_2026/7l3n_23156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7l3n_23156/03_2026/7l3n_23156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l3n_23156/03_2026/7l3n_23156.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l3n_23156/03_2026/7l3n_23156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l3n_23156/03_2026/7l3n_23156.map" } resolution = 3.27 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= 0.024 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: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 15370 2.51 5 N 3981 2.21 5 O 4662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24118 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 820, 6383 Classifications: {'peptide': 820} Link IDs: {'PTRANS': 44, 'TRANS': 775} Chain breaks: 9 Chain: "B" Number of atoms: 7813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7813 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 54, 'TRANS': 946} Chain breaks: 8 Chain: "C" Number of atoms: 7847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1005, 7847 Classifications: {'peptide': 1005} Link IDs: {'PTRANS': 54, 'TRANS': 950} Chain breaks: 8 Chain: "D" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 964 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "E" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.95, per 1000 atoms: 0.16 Number of scatterers: 24118 At special positions: 0 Unit cell: (181.131, 138.204, 140.298, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 4662 8.00 N 3981 7.00 C 15370 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1301 " - " ASN A 709 " " NAG A1302 " - " ASN A 801 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A1098 " " NAG A1305 " - " ASN A1134 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B1134 " " NAG B1307 " - " ASN B 717 " " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C1134 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN C 717 " " NAG H 1 " - " ASN C 801 " Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 834.2 milliseconds 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5722 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 50 sheets defined 25.5% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 756 removed outlier: 3.788A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.495A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.579A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.548A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.808A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.319A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.677A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.719A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.572A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.578A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.549A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 4.260A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.653A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.296A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 4.258A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.797A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.136A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.237A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.185A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG B1000 " --> pdb=" O LEU B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.728A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 344 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.556A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.677A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.565A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.014A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.519A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 766 through 783 removed outlier: 3.890A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.562A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.649A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.517A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.649A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.285A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.218A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 102 through 109 removed outlier: 5.106A pdb=" N TYR D 107 " --> pdb=" O ARG D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.692A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.817A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 52 removed outlier: 3.969A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.530A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.976A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.285A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.267A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.267A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.147A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 711 through 715 removed outlier: 4.050A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.937A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.420A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.738A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.525A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.851A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.078A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.747A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.097A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.288A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC2, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.957A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AC8, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.988A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.332A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.923A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.198A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 34 through 37 removed outlier: 6.169A pdb=" N ARG C 34 " --> pdb=" O SER C 221 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N LEU C 223 " --> pdb=" O ARG C 34 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'C' and resid 47 through 52 removed outlier: 4.102A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.633A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN C 122 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.123A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.529A pdb=" N ILE C 326 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N THR C 573 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ASP C 568 " --> pdb=" O THR C 573 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.889A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.839A pdb=" N PHE C 392 " --> pdb=" O VAL C 524 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.846A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.071A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.071A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 712 through 715 Processing sheet with id=AE6, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.021A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.410A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.804A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF1, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AF2, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.512A pdb=" N ILE D 34 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ARG D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.614A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.490A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'E' and resid 53 through 54 removed outlier: 6.514A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) 1014 hydrogen bonds defined for protein. 2739 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.33 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7740 1.35 - 1.47: 6226 1.47 - 1.60: 10549 1.60 - 1.72: 2 1.72 - 1.85: 133 Bond restraints: 24650 Sorted by residual: bond pdb=" CG PRO B 384 " pdb=" CD PRO B 384 " ideal model delta sigma weight residual 1.503 1.254 0.249 3.40e-02 8.65e+02 5.36e+01 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.503 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C1 NAG B1303 " pdb=" C2 NAG B1303 " ideal model delta sigma weight residual 1.532 1.598 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" N PRO B 384 " pdb=" CD PRO B 384 " ideal model delta sigma weight residual 1.473 1.511 -0.038 1.40e-02 5.10e+03 7.29e+00 bond pdb=" CB PRO B 384 " pdb=" CG PRO B 384 " ideal model delta sigma weight residual 1.492 1.626 -0.134 5.00e-02 4.00e+02 7.22e+00 ... (remaining 24645 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 33277 3.09 - 6.17: 236 6.17 - 9.26: 19 9.26 - 12.35: 3 12.35 - 15.43: 3 Bond angle restraints: 33538 Sorted by residual: angle pdb=" N PRO B 384 " pdb=" CD PRO B 384 " pdb=" CG PRO B 384 " ideal model delta sigma weight residual 103.20 87.77 15.43 1.50e+00 4.44e-01 1.06e+02 angle pdb=" CA PRO B 384 " pdb=" N PRO B 384 " pdb=" CD PRO B 384 " ideal model delta sigma weight residual 112.00 102.51 9.49 1.40e+00 5.10e-01 4.60e+01 angle pdb=" CA CYS C 525 " pdb=" CB CYS C 525 " pdb=" SG CYS C 525 " ideal model delta sigma weight residual 114.40 127.69 -13.29 2.30e+00 1.89e-01 3.34e+01 angle pdb=" C SER E 30 " pdb=" CA SER E 30 " pdb=" CB SER E 30 " ideal model delta sigma weight residual 117.23 109.62 7.61 1.36e+00 5.41e-01 3.13e+01 angle pdb=" CA PRO B 384 " pdb=" CB PRO B 384 " pdb=" CG PRO B 384 " ideal model delta sigma weight residual 104.50 95.28 9.22 1.90e+00 2.77e-01 2.35e+01 ... (remaining 33533 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 13748 17.91 - 35.83: 982 35.83 - 53.74: 207 53.74 - 71.66: 45 71.66 - 89.57: 29 Dihedral angle restraints: 15011 sinusoidal: 6131 harmonic: 8880 Sorted by residual: dihedral pdb=" CB CYS C 743 " pdb=" SG CYS C 743 " pdb=" SG CYS C 749 " pdb=" CB CYS C 749 " ideal model delta sinusoidal sigma weight residual -86.00 -171.22 85.22 1 1.00e+01 1.00e-02 8.80e+01 dihedral pdb=" CB CYS B 743 " pdb=" SG CYS B 743 " pdb=" SG CYS B 749 " pdb=" CB CYS B 749 " ideal model delta sinusoidal sigma weight residual -86.00 -169.08 83.08 1 1.00e+01 1.00e-02 8.44e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -155.11 69.11 1 1.00e+01 1.00e-02 6.18e+01 ... (remaining 15008 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 3618 0.097 - 0.195: 273 0.195 - 0.292: 2 0.292 - 0.389: 0 0.389 - 0.487: 1 Chirality restraints: 3894 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.92e+00 chirality pdb=" CA CYS C 525 " pdb=" N CYS C 525 " pdb=" C CYS C 525 " pdb=" CB CYS C 525 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 3891 not shown) Planarity restraints: 4331 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 383 " -0.080 5.00e-02 4.00e+02 1.15e-01 2.10e+01 pdb=" N PRO B 384 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO B 384 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO B 384 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.75e+01 pdb=" N PRO A 987 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 94 " 0.047 5.00e-02 4.00e+02 7.17e-02 8.23e+00 pdb=" N PRO E 95 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO E 95 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 95 " 0.038 5.00e-02 4.00e+02 ... (remaining 4328 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 231 2.61 - 3.18: 20956 3.18 - 3.76: 35111 3.76 - 4.33: 49335 4.33 - 4.90: 83109 Nonbonded interactions: 188742 Sorted by model distance: nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.041 3.040 nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.108 3.040 nonbonded pdb=" OG1 THR A 323 " pdb=" OE1 GLU A 324 " model vdw 2.134 3.040 nonbonded pdb=" OG1 THR A 108 " pdb=" O ASN A 234 " model vdw 2.142 3.040 nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.147 3.040 ... (remaining 188737 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 'B' and (resid 27 through 95 or resid 99 through 140 or resid 157 through \ 620 or resid 641 through 1304)) selection = (chain 'C' and (resid 27 through 66 or resid 81 through 209 or resid 217 through \ 243 or resid 264 through 1304)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 7.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 20.460 Find NCS groups from input model: 0.260 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 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 0.249 24709 Z= 0.206 Angle : 0.775 15.433 33678 Z= 0.411 Chirality : 0.051 0.487 3894 Planarity : 0.006 0.115 4312 Dihedral : 13.498 89.573 9178 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.04 % Allowed : 0.19 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % 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: -0.76 (0.14), residues: 2996 helix: -0.33 (0.18), residues: 628 sheet: 0.59 (0.18), residues: 733 loop : -1.09 (0.14), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.004 ARG C 509 TYR 0.047 0.002 TYR B 453 PHE 0.030 0.002 PHE A 140 TRP 0.022 0.002 TRP B 886 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00489 (24650) covalent geometry : angle 0.75545 (33538) SS BOND : bond 0.00464 ( 37) SS BOND : angle 1.72339 ( 74) hydrogen bonds : bond 0.12769 ( 1014) hydrogen bonds : angle 6.96490 ( 2739) link_BETA1-4 : bond 0.00861 ( 3) link_BETA1-4 : angle 3.19528 ( 9) link_NAG-ASN : bond 0.00518 ( 19) link_NAG-ASN : angle 3.68091 ( 57) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 535 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 TRP cc_start: 0.5248 (m-90) cc_final: 0.5038 (m-90) REVERT: B 172 SER cc_start: 0.6837 (t) cc_final: 0.6625 (p) REVERT: C 882 ILE cc_start: 0.8679 (mt) cc_final: 0.8393 (mt) REVERT: D 20 VAL cc_start: 0.9013 (t) cc_final: 0.8784 (t) REVERT: D 107 TYR cc_start: 0.5519 (p90) cc_final: 0.5279 (p90) outliers start: 1 outliers final: 0 residues processed: 535 average time/residue: 0.1555 time to fit residues: 133.4011 Evaluate side-chains 277 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.2980 chunk 298 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 872 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN B 481 ASN B 493 GLN B 644 GLN B 703 ASN B 926 GLN B 965 GLN B1010 GLN B1083 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN C1010 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.098405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.067916 restraints weight = 73868.594| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.72 r_work: 0.3053 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 24709 Z= 0.158 Angle : 0.698 11.562 33678 Z= 0.358 Chirality : 0.049 0.414 3894 Planarity : 0.005 0.052 4312 Dihedral : 6.403 59.071 3720 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.99 % Allowed : 10.34 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % 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: -0.04 (0.15), residues: 2996 helix: 0.64 (0.20), residues: 654 sheet: 0.79 (0.18), residues: 708 loop : -0.65 (0.14), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 408 TYR 0.029 0.002 TYR B 204 PHE 0.034 0.002 PHE A 329 TRP 0.014 0.001 TRP B 353 HIS 0.005 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00355 (24650) covalent geometry : angle 0.68034 (33538) SS BOND : bond 0.00964 ( 37) SS BOND : angle 1.26483 ( 74) hydrogen bonds : bond 0.04122 ( 1014) hydrogen bonds : angle 5.83549 ( 2739) link_BETA1-4 : bond 0.00676 ( 3) link_BETA1-4 : angle 3.01691 ( 9) link_NAG-ASN : bond 0.00624 ( 19) link_NAG-ASN : angle 3.51469 ( 57) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 292 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 756 TYR cc_start: 0.8544 (OUTLIER) cc_final: 0.8028 (t80) REVERT: A 904 TYR cc_start: 0.8374 (t80) cc_final: 0.8102 (t80) REVERT: A 990 GLU cc_start: 0.8406 (tm-30) cc_final: 0.7955 (mm-30) REVERT: B 104 TRP cc_start: 0.6186 (m-90) cc_final: 0.5638 (m-90) REVERT: B 229 LEU cc_start: 0.7388 (mp) cc_final: 0.7031 (mp) REVERT: B 758 SER cc_start: 0.8961 (OUTLIER) cc_final: 0.8429 (t) REVERT: B 1077 THR cc_start: 0.7651 (t) cc_final: 0.7386 (t) REVERT: C 392 PHE cc_start: 0.7497 (m-10) cc_final: 0.6888 (m-10) REVERT: C 439 ASN cc_start: 0.8124 (p0) cc_final: 0.7906 (p0) REVERT: C 878 LEU cc_start: 0.8571 (mt) cc_final: 0.8284 (mt) REVERT: C 882 ILE cc_start: 0.9151 (mt) cc_final: 0.8928 (mt) REVERT: C 904 TYR cc_start: 0.8070 (t80) cc_final: 0.7780 (t80) REVERT: C 1037 SER cc_start: 0.8233 (t) cc_final: 0.7643 (p) REVERT: D 104 ARG cc_start: 0.7138 (tpp80) cc_final: 0.6772 (tpp80) outliers start: 53 outliers final: 28 residues processed: 322 average time/residue: 0.1410 time to fit residues: 75.0293 Evaluate side-chains 258 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 228 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1065 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 158 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 294 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 209 optimal weight: 10.0000 chunk 279 optimal weight: 4.9990 chunk 150 optimal weight: 0.0370 chunk 179 optimal weight: 0.0020 chunk 60 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 overall best weight: 0.4866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 493 GLN C 762 GLN C1010 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.103425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.071907 restraints weight = 70769.463| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 4.01 r_work: 0.3051 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 24709 Z= 0.122 Angle : 0.616 10.660 33678 Z= 0.312 Chirality : 0.047 0.401 3894 Planarity : 0.004 0.054 4312 Dihedral : 5.766 56.419 3720 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.13 % Allowed : 12.73 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % 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: 0.15 (0.15), residues: 2996 helix: 0.97 (0.20), residues: 653 sheet: 0.83 (0.18), residues: 709 loop : -0.57 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 357 TYR 0.025 0.001 TYR D 80 PHE 0.025 0.001 PHE C 392 TRP 0.011 0.001 TRP B 353 HIS 0.002 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00272 (24650) covalent geometry : angle 0.60207 (33538) SS BOND : bond 0.00269 ( 37) SS BOND : angle 0.90455 ( 74) hydrogen bonds : bond 0.03760 ( 1014) hydrogen bonds : angle 5.49955 ( 2739) link_BETA1-4 : bond 0.01212 ( 3) link_BETA1-4 : angle 2.39303 ( 9) link_NAG-ASN : bond 0.00512 ( 19) link_NAG-ASN : angle 3.03759 ( 57) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 243 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7918 (m-90) cc_final: 0.7403 (m-90) REVERT: A 612 TYR cc_start: 0.8015 (m-80) cc_final: 0.7794 (m-80) REVERT: A 756 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.8391 (t80) REVERT: A 762 GLN cc_start: 0.8807 (mt0) cc_final: 0.8423 (mt0) REVERT: A 904 TYR cc_start: 0.8487 (t80) cc_final: 0.8257 (t80) REVERT: A 969 ASN cc_start: 0.7442 (m-40) cc_final: 0.6931 (t0) REVERT: B 104 TRP cc_start: 0.6288 (m-90) cc_final: 0.5715 (m-90) REVERT: B 1027 THR cc_start: 0.9338 (m) cc_final: 0.9126 (t) REVERT: C 878 LEU cc_start: 0.8694 (mt) cc_final: 0.8390 (mt) REVERT: C 882 ILE cc_start: 0.9212 (mt) cc_final: 0.8987 (mt) REVERT: C 904 TYR cc_start: 0.8230 (t80) cc_final: 0.7945 (t80) REVERT: C 1037 SER cc_start: 0.8708 (t) cc_final: 0.8057 (p) REVERT: D 34 ILE cc_start: 0.8083 (mm) cc_final: 0.7842 (mt) REVERT: D 121 VAL cc_start: 0.7198 (OUTLIER) cc_final: 0.6901 (p) REVERT: E 35 TRP cc_start: 0.8023 (m100) cc_final: 0.7532 (m100) outliers start: 57 outliers final: 27 residues processed: 282 average time/residue: 0.1475 time to fit residues: 68.3170 Evaluate side-chains 236 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 207 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 121 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 227 optimal weight: 1.9990 chunk 197 optimal weight: 0.7980 chunk 196 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 290 optimal weight: 9.9990 chunk 137 optimal weight: 0.0270 chunk 35 optimal weight: 5.9990 overall best weight: 1.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 751 ASN B 901 GLN B 955 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 439 ASN C 493 GLN C 901 GLN C1010 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN E 100 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.095080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.064033 restraints weight = 75257.129| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.74 r_work: 0.2988 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.5217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 24709 Z= 0.243 Angle : 0.713 11.049 33678 Z= 0.367 Chirality : 0.050 0.440 3894 Planarity : 0.005 0.071 4312 Dihedral : 5.744 55.917 3720 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.45 % Allowed : 13.30 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % 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: -0.07 (0.15), residues: 2996 helix: 0.68 (0.20), residues: 656 sheet: 0.61 (0.18), residues: 734 loop : -0.64 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 403 TYR 0.046 0.002 TYR C 369 PHE 0.046 0.002 PHE C 392 TRP 0.018 0.002 TRP B 64 HIS 0.007 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00565 (24650) covalent geometry : angle 0.70146 (33538) SS BOND : bond 0.00494 ( 37) SS BOND : angle 1.35354 ( 74) hydrogen bonds : bond 0.04442 ( 1014) hydrogen bonds : angle 5.69913 ( 2739) link_BETA1-4 : bond 0.00648 ( 3) link_BETA1-4 : angle 3.01481 ( 9) link_NAG-ASN : bond 0.00372 ( 19) link_NAG-ASN : angle 2.71900 ( 57) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 184 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6842 (m-80) cc_final: 0.6592 (m-80) REVERT: A 173 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8598 (tm-30) REVERT: A 324 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.5576 (pm20) REVERT: A 762 GLN cc_start: 0.9016 (mt0) cc_final: 0.8646 (mt0) REVERT: A 969 ASN cc_start: 0.8273 (m-40) cc_final: 0.7789 (t0) REVERT: A 974 SER cc_start: 0.8773 (m) cc_final: 0.8568 (t) REVERT: A 1125 ASN cc_start: 0.8071 (OUTLIER) cc_final: 0.7707 (p0) REVERT: B 104 TRP cc_start: 0.6486 (m-90) cc_final: 0.5998 (m-90) REVERT: B 855 PHE cc_start: 0.7415 (m-80) cc_final: 0.7068 (m-80) REVERT: B 1130 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.9114 (mt) REVERT: C 189 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8448 (pt) REVERT: C 226 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7907 (mt) REVERT: C 904 TYR cc_start: 0.8491 (t80) cc_final: 0.8226 (t80) REVERT: C 984 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8737 (tt) REVERT: C 988 GLU cc_start: 0.9332 (OUTLIER) cc_final: 0.9028 (pm20) REVERT: C 1005 GLN cc_start: 0.9323 (mm110) cc_final: 0.9122 (mt0) REVERT: D 34 ILE cc_start: 0.8011 (mm) cc_final: 0.7762 (mt) REVERT: D 121 VAL cc_start: 0.7445 (OUTLIER) cc_final: 0.6849 (p) outliers start: 92 outliers final: 50 residues processed: 262 average time/residue: 0.1530 time to fit residues: 64.4272 Evaluate side-chains 211 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 152 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 123 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 63 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 92 optimal weight: 0.0010 chunk 45 optimal weight: 0.9990 chunk 141 optimal weight: 0.1980 chunk 162 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 481 ASN B 901 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1135 ASN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.098162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.067994 restraints weight = 74399.325| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.58 r_work: 0.3070 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.5417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 24709 Z= 0.117 Angle : 0.601 11.344 33678 Z= 0.303 Chirality : 0.046 0.432 3894 Planarity : 0.004 0.057 4312 Dihedral : 5.296 55.442 3720 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.28 % Allowed : 15.28 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.16 (0.15), residues: 2996 helix: 1.09 (0.20), residues: 663 sheet: 0.63 (0.18), residues: 710 loop : -0.52 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 319 TYR 0.021 0.001 TYR D 80 PHE 0.015 0.001 PHE D 64 TRP 0.028 0.002 TRP E 35 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00264 (24650) covalent geometry : angle 0.58620 (33538) SS BOND : bond 0.00367 ( 37) SS BOND : angle 1.48109 ( 74) hydrogen bonds : bond 0.03677 ( 1014) hydrogen bonds : angle 5.38770 ( 2739) link_BETA1-4 : bond 0.01112 ( 3) link_BETA1-4 : angle 2.63588 ( 9) link_NAG-ASN : bond 0.00469 ( 19) link_NAG-ASN : angle 2.71797 ( 57) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 168 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.5988 (pm20) REVERT: A 542 ASN cc_start: 0.8788 (t0) cc_final: 0.8258 (p0) REVERT: A 756 TYR cc_start: 0.8928 (OUTLIER) cc_final: 0.8412 (t80) REVERT: A 969 ASN cc_start: 0.8164 (m-40) cc_final: 0.7798 (t0) REVERT: A 1002 GLN cc_start: 0.8869 (tm-30) cc_final: 0.8668 (tp-100) REVERT: B 370 ASN cc_start: 0.8676 (m-40) cc_final: 0.8271 (p0) REVERT: B 990 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8338 (tp30) REVERT: C 189 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8406 (pt) REVERT: D 34 ILE cc_start: 0.8250 (mm) cc_final: 0.8012 (mt) REVERT: D 121 VAL cc_start: 0.7111 (OUTLIER) cc_final: 0.6781 (p) outliers start: 61 outliers final: 37 residues processed: 218 average time/residue: 0.1553 time to fit residues: 55.4049 Evaluate side-chains 191 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 121 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 284 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 chunk 165 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 267 optimal weight: 0.9980 chunk 186 optimal weight: 0.0970 chunk 114 optimal weight: 6.9990 chunk 44 optimal weight: 0.2980 chunk 279 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.098251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.068983 restraints weight = 74655.838| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.76 r_work: 0.3060 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.5662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24709 Z= 0.118 Angle : 0.590 10.908 33678 Z= 0.296 Chirality : 0.046 0.440 3894 Planarity : 0.004 0.058 4312 Dihedral : 5.143 55.232 3720 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.51 % Allowed : 15.96 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.30 (0.15), residues: 2996 helix: 1.29 (0.21), residues: 664 sheet: 0.72 (0.19), residues: 702 loop : -0.48 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 319 TYR 0.020 0.001 TYR D 80 PHE 0.019 0.001 PHE C 392 TRP 0.044 0.002 TRP E 35 HIS 0.003 0.000 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00271 (24650) covalent geometry : angle 0.57590 (33538) SS BOND : bond 0.00414 ( 37) SS BOND : angle 1.41725 ( 74) hydrogen bonds : bond 0.03483 ( 1014) hydrogen bonds : angle 5.23650 ( 2739) link_BETA1-4 : bond 0.00735 ( 3) link_BETA1-4 : angle 2.64498 ( 9) link_NAG-ASN : bond 0.00417 ( 19) link_NAG-ASN : angle 2.62549 ( 57) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 163 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9208 (tt) cc_final: 0.8584 (mp) REVERT: A 189 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7372 (mt) REVERT: A 324 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6127 (pm20) REVERT: A 542 ASN cc_start: 0.8968 (t0) cc_final: 0.8358 (p0) REVERT: A 902 MET cc_start: 0.8829 (tpp) cc_final: 0.8619 (tpt) REVERT: A 969 ASN cc_start: 0.8212 (m-40) cc_final: 0.7839 (t0) REVERT: A 974 SER cc_start: 0.8712 (t) cc_final: 0.8330 (p) REVERT: A 1002 GLN cc_start: 0.8877 (tm-30) cc_final: 0.8558 (tp-100) REVERT: B 370 ASN cc_start: 0.8698 (m-40) cc_final: 0.8292 (p0) REVERT: B 900 MET cc_start: 0.9002 (mtm) cc_final: 0.8683 (mtm) REVERT: C 189 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8427 (pt) REVERT: D 34 ILE cc_start: 0.8058 (mm) cc_final: 0.7832 (mt) REVERT: D 121 VAL cc_start: 0.7113 (OUTLIER) cc_final: 0.6652 (p) outliers start: 67 outliers final: 45 residues processed: 219 average time/residue: 0.1474 time to fit residues: 53.0431 Evaluate side-chains 200 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 151 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 121 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 57 optimal weight: 0.4980 chunk 232 optimal weight: 7.9990 chunk 247 optimal weight: 0.5980 chunk 52 optimal weight: 0.0030 chunk 19 optimal weight: 5.9990 chunk 190 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 197 optimal weight: 0.9980 chunk 205 optimal weight: 3.9990 chunk 155 optimal weight: 0.2980 chunk 92 optimal weight: 8.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.098453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.068509 restraints weight = 74291.183| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 3.51 r_work: 0.3087 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.5834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24709 Z= 0.107 Angle : 0.578 10.985 33678 Z= 0.289 Chirality : 0.046 0.434 3894 Planarity : 0.004 0.058 4312 Dihedral : 5.040 55.345 3720 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.32 % Allowed : 16.40 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.38 (0.15), residues: 2996 helix: 1.44 (0.21), residues: 662 sheet: 0.81 (0.19), residues: 691 loop : -0.46 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 98 TYR 0.018 0.001 TYR C1067 PHE 0.020 0.001 PHE A 65 TRP 0.029 0.002 TRP A 104 HIS 0.003 0.000 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00244 (24650) covalent geometry : angle 0.56228 (33538) SS BOND : bond 0.00290 ( 37) SS BOND : angle 1.58430 ( 74) hydrogen bonds : bond 0.03324 ( 1014) hydrogen bonds : angle 5.15672 ( 2739) link_BETA1-4 : bond 0.01103 ( 3) link_BETA1-4 : angle 2.64621 ( 9) link_NAG-ASN : bond 0.00447 ( 19) link_NAG-ASN : angle 2.59232 ( 57) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 161 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.8222 (t80) REVERT: A 118 LEU cc_start: 0.9226 (tt) cc_final: 0.8586 (mp) REVERT: A 189 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7375 (mt) REVERT: A 324 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6191 (pm20) REVERT: A 542 ASN cc_start: 0.8981 (t0) cc_final: 0.8253 (p0) REVERT: A 969 ASN cc_start: 0.8230 (m-40) cc_final: 0.7854 (t0) REVERT: A 974 SER cc_start: 0.8852 (OUTLIER) cc_final: 0.8478 (p) REVERT: A 1002 GLN cc_start: 0.8846 (tm-30) cc_final: 0.8462 (tp-100) REVERT: B 370 ASN cc_start: 0.8643 (m-40) cc_final: 0.8299 (p0) REVERT: B 378 LYS cc_start: 0.8326 (tptp) cc_final: 0.8091 (tppt) REVERT: C 189 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8437 (pt) REVERT: C 984 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8799 (tt) REVERT: D 34 ILE cc_start: 0.8159 (mm) cc_final: 0.7936 (mt) REVERT: D 65 GLN cc_start: 0.8859 (tp40) cc_final: 0.8260 (mt0) outliers start: 62 outliers final: 42 residues processed: 212 average time/residue: 0.1600 time to fit residues: 54.4820 Evaluate side-chains 198 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 150 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain E residue 30 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 160 optimal weight: 2.9990 chunk 135 optimal weight: 0.0050 chunk 80 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 216 optimal weight: 0.7980 chunk 274 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 230 optimal weight: 3.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.096147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.066437 restraints weight = 74632.256| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 3.66 r_work: 0.3000 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.6345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 24709 Z= 0.182 Angle : 0.618 10.759 33678 Z= 0.312 Chirality : 0.047 0.443 3894 Planarity : 0.004 0.057 4312 Dihedral : 5.157 55.636 3720 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.47 % Allowed : 16.48 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.26 (0.15), residues: 2996 helix: 1.29 (0.21), residues: 661 sheet: 0.63 (0.19), residues: 708 loop : -0.47 (0.15), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 408 TYR 0.022 0.002 TYR E 49 PHE 0.022 0.001 PHE B 927 TRP 0.018 0.002 TRP A 104 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00427 (24650) covalent geometry : angle 0.60327 (33538) SS BOND : bond 0.00540 ( 37) SS BOND : angle 1.65501 ( 74) hydrogen bonds : bond 0.03691 ( 1014) hydrogen bonds : angle 5.25632 ( 2739) link_BETA1-4 : bond 0.00843 ( 3) link_BETA1-4 : angle 2.73131 ( 9) link_NAG-ASN : bond 0.00323 ( 19) link_NAG-ASN : angle 2.54197 ( 57) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 155 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.9024 (OUTLIER) cc_final: 0.8129 (t80) REVERT: A 189 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7537 (mt) REVERT: A 969 ASN cc_start: 0.8427 (m-40) cc_final: 0.8072 (t0) REVERT: A 974 SER cc_start: 0.8696 (OUTLIER) cc_final: 0.8375 (p) REVERT: A 1002 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8610 (tp-100) REVERT: B 370 ASN cc_start: 0.8638 (m-40) cc_final: 0.8329 (p0) REVERT: C 189 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8447 (pt) REVERT: C 525 CYS cc_start: 0.4798 (OUTLIER) cc_final: 0.4498 (p) REVERT: C 984 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8921 (tt) REVERT: D 34 ILE cc_start: 0.8153 (mm) cc_final: 0.7917 (mt) REVERT: D 64 PHE cc_start: 0.6687 (m-80) cc_final: 0.6344 (m-80) REVERT: D 65 GLN cc_start: 0.8958 (tp40) cc_final: 0.8361 (mt0) REVERT: D 67 ARG cc_start: 0.6765 (ptm160) cc_final: 0.6427 (ttt-90) REVERT: D 117 GLN cc_start: 0.7627 (pm20) cc_final: 0.7416 (pm20) outliers start: 66 outliers final: 46 residues processed: 211 average time/residue: 0.1472 time to fit residues: 50.9818 Evaluate side-chains 197 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 145 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 142 optimal weight: 0.9990 chunk 192 optimal weight: 8.9990 chunk 172 optimal weight: 3.9990 chunk 275 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 226 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 217 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 ASN B 965 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.097341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.067601 restraints weight = 73718.504| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.60 r_work: 0.3073 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.6666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 24709 Z= 0.160 Angle : 0.607 11.253 33678 Z= 0.305 Chirality : 0.047 0.444 3894 Planarity : 0.004 0.057 4312 Dihedral : 5.135 55.189 3720 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.32 % Allowed : 17.08 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.28 (0.15), residues: 2996 helix: 1.27 (0.21), residues: 669 sheet: 0.64 (0.19), residues: 693 loop : -0.44 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 98 TYR 0.019 0.001 TYR D 80 PHE 0.031 0.001 PHE B 133 TRP 0.022 0.002 TRP A 886 HIS 0.002 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00378 (24650) covalent geometry : angle 0.59284 (33538) SS BOND : bond 0.00368 ( 37) SS BOND : angle 1.46722 ( 74) hydrogen bonds : bond 0.03535 ( 1014) hydrogen bonds : angle 5.21057 ( 2739) link_BETA1-4 : bond 0.00976 ( 3) link_BETA1-4 : angle 2.62528 ( 9) link_NAG-ASN : bond 0.00362 ( 19) link_NAG-ASN : angle 2.59472 ( 57) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 158 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8215 (t80) REVERT: A 118 LEU cc_start: 0.9316 (tt) cc_final: 0.8637 (mp) REVERT: A 189 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7778 (mt) REVERT: A 969 ASN cc_start: 0.8517 (m-40) cc_final: 0.8158 (t0) REVERT: A 974 SER cc_start: 0.8800 (OUTLIER) cc_final: 0.8520 (p) REVERT: A 1002 GLN cc_start: 0.8840 (tm-30) cc_final: 0.8459 (tp-100) REVERT: B 370 ASN cc_start: 0.8651 (m-40) cc_final: 0.8366 (p0) REVERT: B 378 LYS cc_start: 0.8478 (tptp) cc_final: 0.8253 (tppt) REVERT: C 189 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8524 (pt) REVERT: C 525 CYS cc_start: 0.4908 (OUTLIER) cc_final: 0.4471 (p) REVERT: C 786 LYS cc_start: 0.8227 (pptt) cc_final: 0.7887 (mtmm) REVERT: C 984 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8828 (tt) REVERT: D 34 ILE cc_start: 0.8161 (mm) cc_final: 0.7931 (mt) REVERT: D 67 ARG cc_start: 0.6943 (ptm160) cc_final: 0.6689 (ttt-90) REVERT: E 100 GLN cc_start: 0.8408 (pm20) cc_final: 0.8093 (pm20) outliers start: 62 outliers final: 46 residues processed: 211 average time/residue: 0.1540 time to fit residues: 52.5035 Evaluate side-chains 196 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 144 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 157 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 chunk 125 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 150 optimal weight: 0.5980 chunk 222 optimal weight: 0.1980 chunk 72 optimal weight: 0.6980 chunk 167 optimal weight: 3.9990 chunk 180 optimal weight: 0.0670 chunk 192 optimal weight: 9.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.098471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.068272 restraints weight = 73532.402| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 3.51 r_work: 0.3115 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.6811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24709 Z= 0.111 Angle : 0.600 11.127 33678 Z= 0.301 Chirality : 0.046 0.435 3894 Planarity : 0.004 0.058 4312 Dihedral : 5.023 55.272 3720 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.95 % Allowed : 17.45 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.40 (0.15), residues: 2996 helix: 1.46 (0.21), residues: 664 sheet: 0.73 (0.19), residues: 687 loop : -0.41 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 408 TYR 0.024 0.001 TYR E 49 PHE 0.027 0.001 PHE B 133 TRP 0.021 0.002 TRP A 104 HIS 0.002 0.000 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00256 (24650) covalent geometry : angle 0.58694 (33538) SS BOND : bond 0.00444 ( 37) SS BOND : angle 1.41641 ( 74) hydrogen bonds : bond 0.03312 ( 1014) hydrogen bonds : angle 5.13666 ( 2739) link_BETA1-4 : bond 0.01040 ( 3) link_BETA1-4 : angle 2.60613 ( 9) link_NAG-ASN : bond 0.00430 ( 19) link_NAG-ASN : angle 2.52356 ( 57) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 156 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.8189 (t80) REVERT: A 118 LEU cc_start: 0.9288 (tt) cc_final: 0.8653 (mp) REVERT: A 189 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7787 (mt) REVERT: A 969 ASN cc_start: 0.8512 (m-40) cc_final: 0.8220 (t0) REVERT: A 974 SER cc_start: 0.8775 (OUTLIER) cc_final: 0.8542 (p) REVERT: A 1002 GLN cc_start: 0.8745 (tm-30) cc_final: 0.8443 (tp40) REVERT: B 370 ASN cc_start: 0.8622 (m-40) cc_final: 0.8375 (p0) REVERT: B 378 LYS cc_start: 0.8537 (tptp) cc_final: 0.8312 (tppt) REVERT: B 754 LEU cc_start: 0.9636 (mt) cc_final: 0.9435 (mt) REVERT: C 189 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8506 (pt) REVERT: C 525 CYS cc_start: 0.4737 (OUTLIER) cc_final: 0.4418 (p) REVERT: C 786 LYS cc_start: 0.8130 (pptt) cc_final: 0.7782 (mtmm) REVERT: C 984 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8793 (tt) REVERT: D 34 ILE cc_start: 0.8213 (mm) cc_final: 0.8006 (mt) REVERT: D 65 GLN cc_start: 0.8886 (tp40) cc_final: 0.8264 (mt0) REVERT: D 67 ARG cc_start: 0.6777 (ptm160) cc_final: 0.6486 (ttt-90) REVERT: E 100 GLN cc_start: 0.8389 (pm20) cc_final: 0.8068 (pm20) outliers start: 52 outliers final: 39 residues processed: 199 average time/residue: 0.1516 time to fit residues: 49.8143 Evaluate side-chains 189 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 144 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain E residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 94 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 149 optimal weight: 0.0670 chunk 115 optimal weight: 5.9990 chunk 239 optimal weight: 0.0670 chunk 199 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 284 optimal weight: 0.9980 overall best weight: 0.8058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.098022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.067818 restraints weight = 73361.854| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 3.48 r_work: 0.3083 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.6926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24709 Z= 0.125 Angle : 0.590 10.714 33678 Z= 0.296 Chirality : 0.046 0.433 3894 Planarity : 0.004 0.058 4312 Dihedral : 4.984 55.216 3720 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.95 % Allowed : 17.64 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.42 (0.15), residues: 2996 helix: 1.50 (0.21), residues: 665 sheet: 0.75 (0.19), residues: 675 loop : -0.40 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 319 TYR 0.021 0.001 TYR B 170 PHE 0.027 0.001 PHE B 133 TRP 0.024 0.002 TRP A 104 HIS 0.002 0.000 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00294 (24650) covalent geometry : angle 0.57678 (33538) SS BOND : bond 0.00503 ( 37) SS BOND : angle 1.38549 ( 74) hydrogen bonds : bond 0.03325 ( 1014) hydrogen bonds : angle 5.09041 ( 2739) link_BETA1-4 : bond 0.00974 ( 3) link_BETA1-4 : angle 2.60954 ( 9) link_NAG-ASN : bond 0.00378 ( 19) link_NAG-ASN : angle 2.46451 ( 57) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6557.71 seconds wall clock time: 112 minutes 51.20 seconds (6771.20 seconds total)