Starting phenix.real_space_refine on Thu Mar 5 14:18:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wgy_32492/03_2026/7wgy_32492_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wgy_32492/03_2026/7wgy_32492.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wgy_32492/03_2026/7wgy_32492_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wgy_32492/03_2026/7wgy_32492_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wgy_32492/03_2026/7wgy_32492.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wgy_32492/03_2026/7wgy_32492.map" } resolution = 4.0 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= 0.003 sd= 0.072 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 101 5.16 5 C 14608 2.51 5 N 3763 2.21 5 O 4442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s 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: 22914 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 8078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8078 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 49, 'TRANS': 983} Chain breaks: 7 Chain: "B" Number of atoms: 6393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 821, 6393 Classifications: {'peptide': 821} Link IDs: {'PTRANS': 37, 'TRANS': 783} Chain breaks: 8 Chain: "C" Number of atoms: 8009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8009 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 49, 'TRANS': 975} Chain breaks: 7 Chain: "D" 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: "E" 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: "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: "I" 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: "J" 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: "K" 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: 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: "C" 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 Time building chain proxies: 5.40, per 1000 atoms: 0.24 Number of scatterers: 22914 At special positions: 0 Unit cell: (141.75, 125.55, 179.55, 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 101 16.00 O 4442 8.00 N 3763 7.00 C 14608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A1301 " - " ASN A 709 " " NAG A1302 " - " ASN A1074 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 343 " " NAG B1301 " - " ASN B 709 " " NAG B1304 " - " ASN B1134 " " NAG C1301 " - " ASN C 709 " " NAG C1302 " - " ASN C1074 " " NAG C1305 " - " ASN C 343 " " NAG D 1 " - " ASN A 717 " " NAG F 1 " - " ASN A1134 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C 801 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 1.1 seconds 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5410 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 43 sheets defined 27.0% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.609A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.203A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.219A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.504A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.808A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.922A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 768 " --> pdb=" O ASN A 764 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 856 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.612A 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 918 removed outlier: 3.948A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.638A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.901A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.885A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.540A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.552A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.938A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 849 through 857 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.594A pdb=" N GLY B 889 " --> 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 918 removed outlier: 3.670A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.537A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.474A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B 961 " --> pdb=" O GLN B 957 " (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 removed outlier: 3.583A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.880A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.590A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.500A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.373A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 removed outlier: 4.124A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.421A 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 737 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 4.168A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.287A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 849 through 856 removed outlier: 3.705A pdb=" N LYS C 854 " --> pdb=" O ILE C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.562A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 941 removed outlier: 3.956A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN C 928 " --> pdb=" O ALA C 924 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER C 929 " --> pdb=" O ASN C 925 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY C 932 " --> pdb=" O ASN C 928 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER C 937 " --> pdb=" O LYS C 933 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.323A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS C 964 " --> pdb=" O ASN C 960 " (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 987 through 1033 removed outlier: 4.256A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.018A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.061A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.892A 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: 3.533A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 156 through 162 removed outlier: 8.944A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 10.403A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N CYS A 136 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 removed outlier: 4.247A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.502A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.890A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.788A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.534A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.781A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.642A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.371A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.006A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.025A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 49 through 55 removed outlier: 4.289A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.295A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.626A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.237A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.320A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.250A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.947A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 660 removed outlier: 3.544A pdb=" N ALA B 694 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.631A 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 703 removed outlier: 6.182A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.858A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.858A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD2, first strand: chain 'C' and resid 27 through 30 removed outlier: 9.230A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 10.036A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.436A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.653A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.242A pdb=" N LEU C 141 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.044A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AD7, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.550A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 357 removed outlier: 4.707A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.554A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.329A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 714 Processing sheet with id=AE4, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.195A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.570A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.597A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1094 through 1097 960 hydrogen bonds defined for protein. 2637 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: 5.49 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3749 1.31 - 1.44: 6357 1.44 - 1.57: 13176 1.57 - 1.70: 0 1.70 - 1.82: 126 Bond restraints: 23408 Sorted by residual: bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.522 -0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.406 1.521 -0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.521 -0.115 2.00e-02 2.50e+03 3.30e+01 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.520 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.519 -0.113 2.00e-02 2.50e+03 3.21e+01 ... (remaining 23403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 30827 1.93 - 3.86: 829 3.86 - 5.78: 156 5.78 - 7.71: 19 7.71 - 9.64: 9 Bond angle restraints: 31840 Sorted by residual: angle pdb=" C GLU C 619 " pdb=" N VAL C 620 " pdb=" CA VAL C 620 " ideal model delta sigma weight residual 120.33 124.15 -3.82 8.00e-01 1.56e+00 2.28e+01 angle pdb=" N PRO B 621 " pdb=" CA PRO B 621 " pdb=" C PRO B 621 " ideal model delta sigma weight residual 112.47 120.45 -7.98 2.06e+00 2.36e-01 1.50e+01 angle pdb=" CA PRO B 621 " pdb=" N PRO B 621 " pdb=" CD PRO B 621 " ideal model delta sigma weight residual 112.00 106.94 5.06 1.40e+00 5.10e-01 1.31e+01 angle pdb=" CA GLY A 89 " pdb=" C GLY A 89 " pdb=" N VAL A 90 " ideal model delta sigma weight residual 114.73 119.05 -4.32 1.30e+00 5.92e-01 1.10e+01 angle pdb=" C HIS C 207 " pdb=" N THR C 208 " pdb=" CA THR C 208 " ideal model delta sigma weight residual 122.74 114.78 7.96 2.44e+00 1.68e-01 1.06e+01 ... (remaining 31835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.13: 13518 24.13 - 48.26: 591 48.26 - 72.39: 83 72.39 - 96.52: 38 96.52 - 120.65: 35 Dihedral angle restraints: 14265 sinusoidal: 5883 harmonic: 8382 Sorted by residual: dihedral pdb=" CA VAL C 620 " pdb=" C VAL C 620 " pdb=" N PRO C 621 " pdb=" CA PRO C 621 " ideal model delta harmonic sigma weight residual 180.00 -149.58 -30.42 0 5.00e+00 4.00e-02 3.70e+01 dihedral pdb=" CA LEU A 517 " pdb=" C LEU A 517 " pdb=" N LEU A 518 " pdb=" CA LEU A 518 " ideal model delta harmonic sigma weight residual 180.00 155.41 24.59 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA VAL A 620 " pdb=" C VAL A 620 " pdb=" N PRO A 621 " pdb=" CA PRO A 621 " ideal model delta harmonic sigma weight residual 180.00 -158.28 -21.72 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 14262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2835 0.053 - 0.106: 725 0.106 - 0.159: 158 0.159 - 0.212: 12 0.212 - 0.265: 2 Chirality restraints: 3732 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.43 0.03 2.00e-02 2.50e+03 2.90e+00 chirality pdb=" CA PRO B 621 " pdb=" N PRO B 621 " pdb=" C PRO B 621 " pdb=" CB PRO B 621 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 282 " 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 1.19e+00 ... (remaining 3729 not shown) Planarity restraints: 4094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 620 " -0.084 5.00e-02 4.00e+02 1.26e-01 2.56e+01 pdb=" N PRO B 621 " 0.219 5.00e-02 4.00e+02 pdb=" CA PRO B 621 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO B 621 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 620 " 0.074 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO C 621 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO C 621 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO C 621 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 620 " -0.066 5.00e-02 4.00e+02 9.87e-02 1.56e+01 pdb=" N PRO A 621 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO A 621 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 621 " -0.053 5.00e-02 4.00e+02 ... (remaining 4091 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 424 2.66 - 3.22: 22164 3.22 - 3.78: 33589 3.78 - 4.34: 45031 4.34 - 4.90: 74335 Nonbonded interactions: 175543 Sorted by model distance: nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.104 3.040 nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 191 " model vdw 2.144 3.040 nonbonded pdb=" O PRO B1053 " pdb=" NE2 GLN B1054 " model vdw 2.163 3.120 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.213 3.040 nonbonded pdb=" O GLY A 889 " pdb=" NZ LYS C1045 " model vdw 2.214 3.120 ... (remaining 175538 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 67 or resid 79 through 143 or resid 156 through \ 828 or resid 848 through 1305)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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 group one per residue 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.210 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 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:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 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 : 0.008 0.116 23432 Z= 0.400 Angle : 0.779 9.638 31909 Z= 0.390 Chirality : 0.049 0.265 3732 Planarity : 0.005 0.126 4079 Dihedral : 15.642 120.655 8855 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.51 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % 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: -0.80 (0.15), residues: 2829 helix: 0.19 (0.20), residues: 635 sheet: 0.38 (0.19), residues: 630 loop : -1.24 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 905 TYR 0.023 0.002 TYR A 904 PHE 0.030 0.002 PHE C 906 TRP 0.024 0.002 TRP C 353 HIS 0.007 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00824 (23408) covalent geometry : angle 0.76864 (31840) hydrogen bonds : bond 0.15377 ( 946) hydrogen bonds : angle 7.14947 ( 2637) Misc. bond : bond 0.00004 ( 1) link_BETA1-4 : bond 0.00487 ( 8) link_BETA1-4 : angle 1.42247 ( 24) link_NAG-ASN : bond 0.00510 ( 15) link_NAG-ASN : angle 3.27187 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.7153 (tpp) cc_final: 0.6858 (tpp) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1532 time to fit residues: 26.7495 Evaluate side-chains 55 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 197 optimal weight: 30.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.0060 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 613 GLN C 764 ASN C 901 GLN C 965 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.054323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.039263 restraints weight = 144471.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.040594 restraints weight = 79599.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.041480 restraints weight = 53334.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.042101 restraints weight = 40170.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.042521 restraints weight = 32735.528| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 23432 Z= 0.143 Angle : 0.596 10.442 31909 Z= 0.308 Chirality : 0.045 0.304 3732 Planarity : 0.005 0.130 4079 Dihedral : 10.806 116.172 3716 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.14 % Favored : 95.55 % Rotamer: Outliers : 0.48 % Allowed : 4.88 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.15), residues: 2829 helix: 1.23 (0.21), residues: 645 sheet: 0.40 (0.19), residues: 647 loop : -1.19 (0.15), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 319 TYR 0.015 0.001 TYR C 904 PHE 0.014 0.001 PHE A 338 TRP 0.014 0.001 TRP C 64 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00308 (23408) covalent geometry : angle 0.58102 (31840) hydrogen bonds : bond 0.05310 ( 946) hydrogen bonds : angle 5.58822 ( 2637) Misc. bond : bond 0.00001 ( 1) link_BETA1-4 : bond 0.00673 ( 8) link_BETA1-4 : angle 2.17380 ( 24) link_NAG-ASN : bond 0.00471 ( 15) link_NAG-ASN : angle 3.28011 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.9019 (tpp) cc_final: 0.8815 (tpp) REVERT: A 1050 MET cc_start: 0.7742 (ptp) cc_final: 0.7389 (mtm) REVERT: B 275 PHE cc_start: 0.8444 (m-80) cc_final: 0.7528 (m-80) REVERT: B 697 MET cc_start: 0.8630 (mmm) cc_final: 0.8011 (tpt) REVERT: B 773 GLU cc_start: 0.8982 (tp30) cc_final: 0.8596 (tp30) REVERT: B 1029 MET cc_start: 0.8914 (tmm) cc_final: 0.8665 (tmm) REVERT: C 214 ARG cc_start: 0.6110 (OUTLIER) cc_final: 0.5064 (tpm170) REVERT: C 867 ASP cc_start: 0.8734 (p0) cc_final: 0.8473 (p0) REVERT: C 869 MET cc_start: 0.9614 (mtp) cc_final: 0.9169 (ptp) outliers start: 12 outliers final: 5 residues processed: 81 average time/residue: 0.1346 time to fit residues: 18.8492 Evaluate side-chains 62 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 734 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 153 optimal weight: 0.1980 chunk 204 optimal weight: 10.0000 chunk 246 optimal weight: 0.0770 chunk 159 optimal weight: 10.0000 chunk 277 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 175 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 209 optimal weight: 9.9990 chunk 240 optimal weight: 10.0000 overall best weight: 2.4544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.053603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.038609 restraints weight = 145713.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.039924 restraints weight = 80618.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.040787 restraints weight = 54106.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.041392 restraints weight = 40905.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.041801 restraints weight = 33405.906| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 23432 Z= 0.148 Angle : 0.563 11.051 31909 Z= 0.288 Chirality : 0.044 0.282 3732 Planarity : 0.005 0.137 4079 Dihedral : 9.477 115.636 3716 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.42 % Favored : 95.26 % Rotamer: Outliers : 0.91 % Allowed : 7.30 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.15), residues: 2829 helix: 1.68 (0.21), residues: 654 sheet: 0.52 (0.20), residues: 603 loop : -1.21 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 273 TYR 0.016 0.001 TYR C 904 PHE 0.011 0.001 PHE A 817 TRP 0.008 0.001 TRP A 64 HIS 0.002 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00328 (23408) covalent geometry : angle 0.55012 (31840) hydrogen bonds : bond 0.04636 ( 946) hydrogen bonds : angle 5.26252 ( 2637) Misc. bond : bond 0.00009 ( 1) link_BETA1-4 : bond 0.00472 ( 8) link_BETA1-4 : angle 2.10902 ( 24) link_NAG-ASN : bond 0.00397 ( 15) link_NAG-ASN : angle 2.94210 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 59 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 615 VAL cc_start: 0.8885 (OUTLIER) cc_final: 0.8630 (p) REVERT: A 740 MET cc_start: 0.9152 (tpp) cc_final: 0.8912 (tpp) REVERT: B 697 MET cc_start: 0.8635 (mmm) cc_final: 0.8024 (tpt) REVERT: B 773 GLU cc_start: 0.9044 (tp30) cc_final: 0.8590 (tp30) REVERT: B 869 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8851 (ptp) REVERT: C 867 ASP cc_start: 0.8583 (p0) cc_final: 0.8333 (p0) REVERT: C 869 MET cc_start: 0.9642 (mtp) cc_final: 0.9207 (ptp) outliers start: 23 outliers final: 14 residues processed: 78 average time/residue: 0.1393 time to fit residues: 18.7638 Evaluate side-chains 68 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 858 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 211 optimal weight: 9.9990 chunk 95 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 175 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 856 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.052074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.037237 restraints weight = 148736.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.038497 restraints weight = 82644.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.039342 restraints weight = 55557.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.039930 restraints weight = 42034.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.040317 restraints weight = 34358.436| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 23432 Z= 0.227 Angle : 0.637 12.025 31909 Z= 0.324 Chirality : 0.044 0.272 3732 Planarity : 0.005 0.141 4079 Dihedral : 8.399 118.471 3716 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.98 % Favored : 94.70 % Rotamer: Outliers : 1.31 % Allowed : 9.92 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.15), residues: 2829 helix: 1.49 (0.20), residues: 663 sheet: 0.29 (0.19), residues: 635 loop : -1.27 (0.15), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 273 TYR 0.025 0.002 TYR C 904 PHE 0.014 0.002 PHE A 92 TRP 0.010 0.002 TRP A 64 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00496 (23408) covalent geometry : angle 0.62396 (31840) hydrogen bonds : bond 0.04686 ( 946) hydrogen bonds : angle 5.46215 ( 2637) Misc. bond : bond 0.00021 ( 1) link_BETA1-4 : bond 0.00425 ( 8) link_BETA1-4 : angle 2.34736 ( 24) link_NAG-ASN : bond 0.00549 ( 15) link_NAG-ASN : angle 3.09915 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 54 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 615 VAL cc_start: 0.8966 (OUTLIER) cc_final: 0.8718 (p) REVERT: A 740 MET cc_start: 0.9143 (tpp) cc_final: 0.8892 (tpp) REVERT: A 1122 VAL cc_start: 0.9000 (OUTLIER) cc_final: 0.8774 (p) REVERT: B 697 MET cc_start: 0.8790 (mmm) cc_final: 0.8442 (tpt) REVERT: B 773 GLU cc_start: 0.9119 (tp30) cc_final: 0.8872 (tp30) REVERT: B 869 MET cc_start: 0.9283 (OUTLIER) cc_final: 0.8931 (ptp) REVERT: C 214 ARG cc_start: 0.6378 (OUTLIER) cc_final: 0.5548 (tpm170) REVERT: C 421 TYR cc_start: 0.9158 (m-10) cc_final: 0.8918 (m-10) REVERT: C 867 ASP cc_start: 0.8705 (p0) cc_final: 0.8426 (p0) REVERT: C 869 MET cc_start: 0.9656 (mtp) cc_final: 0.9230 (ptp) outliers start: 33 outliers final: 18 residues processed: 83 average time/residue: 0.1264 time to fit residues: 18.4242 Evaluate side-chains 74 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 52 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 270 optimal weight: 5.9990 chunk 205 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 151 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 280 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 277 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 199 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 755 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.051657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.036874 restraints weight = 148272.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.038134 restraints weight = 81715.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.038981 restraints weight = 54799.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.039559 restraints weight = 41294.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.039965 restraints weight = 33834.092| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 23432 Z= 0.242 Angle : 0.641 11.957 31909 Z= 0.326 Chirality : 0.044 0.281 3732 Planarity : 0.005 0.142 4079 Dihedral : 7.801 118.070 3716 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.34 % Favored : 94.34 % Rotamer: Outliers : 1.31 % Allowed : 11.95 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.15), residues: 2829 helix: 1.53 (0.20), residues: 659 sheet: 0.14 (0.19), residues: 648 loop : -1.32 (0.15), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 273 TYR 0.024 0.002 TYR C 904 PHE 0.017 0.001 PHE A 92 TRP 0.009 0.001 TRP A 64 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00526 (23408) covalent geometry : angle 0.62763 (31840) hydrogen bonds : bond 0.04728 ( 946) hydrogen bonds : angle 5.55287 ( 2637) Misc. bond : bond 0.00033 ( 1) link_BETA1-4 : bond 0.00330 ( 8) link_BETA1-4 : angle 2.40781 ( 24) link_NAG-ASN : bond 0.00543 ( 15) link_NAG-ASN : angle 3.02288 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 57 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: A 615 VAL cc_start: 0.9032 (OUTLIER) cc_final: 0.8777 (p) REVERT: A 740 MET cc_start: 0.9170 (tpp) cc_final: 0.8954 (tpp) REVERT: B 65 PHE cc_start: 0.9222 (m-80) cc_final: 0.8996 (m-80) REVERT: B 697 MET cc_start: 0.8776 (mmm) cc_final: 0.8430 (tpt) REVERT: B 773 GLU cc_start: 0.9116 (tp30) cc_final: 0.8668 (tp30) REVERT: B 869 MET cc_start: 0.9294 (OUTLIER) cc_final: 0.8958 (ptp) REVERT: C 214 ARG cc_start: 0.6575 (OUTLIER) cc_final: 0.5538 (tpm170) REVERT: C 867 ASP cc_start: 0.8725 (p0) cc_final: 0.8431 (p0) outliers start: 33 outliers final: 22 residues processed: 85 average time/residue: 0.1265 time to fit residues: 19.0701 Evaluate side-chains 80 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 55 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 42 optimal weight: 20.0000 chunk 140 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 197 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 228 optimal weight: 20.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN ** C 211 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 = 0.3243 r_free = 0.3243 target = 0.051738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.036950 restraints weight = 148208.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.038204 restraints weight = 82465.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.039039 restraints weight = 55464.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.039632 restraints weight = 41981.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.040039 restraints weight = 34330.390| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 23432 Z= 0.204 Angle : 0.602 12.206 31909 Z= 0.307 Chirality : 0.043 0.284 3732 Planarity : 0.005 0.141 4079 Dihedral : 7.342 115.829 3716 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.88 % Favored : 94.80 % Rotamer: Outliers : 1.63 % Allowed : 12.86 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % 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: -0.36 (0.15), residues: 2829 helix: 1.67 (0.20), residues: 658 sheet: 0.04 (0.19), residues: 659 loop : -1.28 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 273 TYR 0.021 0.001 TYR C 904 PHE 0.014 0.001 PHE A 92 TRP 0.008 0.001 TRP A 64 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00449 (23408) covalent geometry : angle 0.58864 (31840) hydrogen bonds : bond 0.04505 ( 946) hydrogen bonds : angle 5.47059 ( 2637) Misc. bond : bond 0.00011 ( 1) link_BETA1-4 : bond 0.00436 ( 8) link_BETA1-4 : angle 2.41766 ( 24) link_NAG-ASN : bond 0.00469 ( 15) link_NAG-ASN : angle 2.95109 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 59 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: A 615 VAL cc_start: 0.8964 (OUTLIER) cc_final: 0.8734 (p) REVERT: A 740 MET cc_start: 0.9151 (tpp) cc_final: 0.8926 (tpp) REVERT: A 869 MET cc_start: 0.9167 (ptp) cc_final: 0.8930 (ptp) REVERT: B 697 MET cc_start: 0.8791 (mmm) cc_final: 0.8538 (tpt) REVERT: B 773 GLU cc_start: 0.9117 (tp30) cc_final: 0.8690 (tp30) REVERT: B 869 MET cc_start: 0.9286 (OUTLIER) cc_final: 0.8943 (ptp) REVERT: C 214 ARG cc_start: 0.6522 (OUTLIER) cc_final: 0.5699 (tpm170) REVERT: C 421 TYR cc_start: 0.9479 (m-80) cc_final: 0.9045 (m-80) REVERT: C 867 ASP cc_start: 0.8701 (p0) cc_final: 0.8417 (p0) outliers start: 41 outliers final: 26 residues processed: 96 average time/residue: 0.1325 time to fit residues: 22.2939 Evaluate side-chains 82 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 53 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 138 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 143 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 244 optimal weight: 9.9990 chunk 229 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 chunk 240 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 115 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.052118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.037310 restraints weight = 146805.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.038577 restraints weight = 81189.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.039443 restraints weight = 54355.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.040036 restraints weight = 40978.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.040439 restraints weight = 33461.319| |-----------------------------------------------------------------------------| r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 23432 Z= 0.163 Angle : 0.574 12.365 31909 Z= 0.292 Chirality : 0.043 0.286 3732 Planarity : 0.005 0.141 4079 Dihedral : 6.998 114.983 3716 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.81 % Favored : 94.87 % Rotamer: Outliers : 1.59 % Allowed : 13.66 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % 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: -0.28 (0.16), residues: 2829 helix: 1.78 (0.21), residues: 663 sheet: 0.08 (0.19), residues: 662 loop : -1.26 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 273 TYR 0.017 0.001 TYR C 904 PHE 0.028 0.001 PHE B 65 TRP 0.006 0.001 TRP A 64 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00363 (23408) covalent geometry : angle 0.56071 (31840) hydrogen bonds : bond 0.04327 ( 946) hydrogen bonds : angle 5.34974 ( 2637) Misc. bond : bond 0.00002 ( 1) link_BETA1-4 : bond 0.00387 ( 8) link_BETA1-4 : angle 2.32073 ( 24) link_NAG-ASN : bond 0.00421 ( 15) link_NAG-ASN : angle 2.86354 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 56 time to evaluate : 0.946 Fit side-chains REVERT: A 615 VAL cc_start: 0.8873 (OUTLIER) cc_final: 0.8629 (p) REVERT: A 740 MET cc_start: 0.9137 (tpp) cc_final: 0.8925 (tpp) REVERT: A 869 MET cc_start: 0.9157 (ptp) cc_final: 0.8892 (ptp) REVERT: B 277 LEU cc_start: 0.9580 (mm) cc_final: 0.9167 (tp) REVERT: B 697 MET cc_start: 0.8779 (mmm) cc_final: 0.8507 (tpt) REVERT: B 773 GLU cc_start: 0.9122 (tp30) cc_final: 0.8700 (tp30) REVERT: B 869 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.8943 (ptp) REVERT: C 214 ARG cc_start: 0.6588 (OUTLIER) cc_final: 0.5754 (tpm170) REVERT: C 421 TYR cc_start: 0.9432 (m-80) cc_final: 0.9171 (m-80) REVERT: C 867 ASP cc_start: 0.8732 (p0) cc_final: 0.8454 (p0) outliers start: 40 outliers final: 25 residues processed: 92 average time/residue: 0.1309 time to fit residues: 21.2827 Evaluate side-chains 82 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 54 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 276 optimal weight: 3.9990 chunk 133 optimal weight: 8.9990 chunk 260 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 167 optimal weight: 9.9990 chunk 249 optimal weight: 0.9990 chunk 234 optimal weight: 10.0000 chunk 157 optimal weight: 0.9990 chunk 165 optimal weight: 6.9990 chunk 257 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN ** C 544 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 = 0.3265 r_free = 0.3265 target = 0.052565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.037738 restraints weight = 146190.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.039018 restraints weight = 80776.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.039878 restraints weight = 54101.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.040460 restraints weight = 40749.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.040872 restraints weight = 33379.148| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 23432 Z= 0.132 Angle : 0.554 12.461 31909 Z= 0.281 Chirality : 0.043 0.285 3732 Planarity : 0.005 0.140 4079 Dihedral : 6.711 113.413 3716 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.70 % Favored : 95.02 % Rotamer: Outliers : 1.47 % Allowed : 13.97 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % 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: -0.14 (0.16), residues: 2829 helix: 1.93 (0.21), residues: 658 sheet: 0.24 (0.19), residues: 651 loop : -1.20 (0.16), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 273 TYR 0.016 0.001 TYR C 904 PHE 0.011 0.001 PHE A 377 TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00299 (23408) covalent geometry : angle 0.54099 (31840) hydrogen bonds : bond 0.04102 ( 946) hydrogen bonds : angle 5.20612 ( 2637) Misc. bond : bond 0.00012 ( 1) link_BETA1-4 : bond 0.00500 ( 8) link_BETA1-4 : angle 2.28876 ( 24) link_NAG-ASN : bond 0.00384 ( 15) link_NAG-ASN : angle 2.80895 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 55 time to evaluate : 0.802 Fit side-chains REVERT: A 615 VAL cc_start: 0.8793 (OUTLIER) cc_final: 0.8555 (p) REVERT: A 740 MET cc_start: 0.9127 (tpp) cc_final: 0.8910 (tpp) REVERT: A 900 MET cc_start: 0.9173 (mmt) cc_final: 0.8866 (mmp) REVERT: B 277 LEU cc_start: 0.9563 (mm) cc_final: 0.9149 (tp) REVERT: B 697 MET cc_start: 0.8807 (mmm) cc_final: 0.8534 (tpt) REVERT: B 773 GLU cc_start: 0.9144 (tp30) cc_final: 0.8733 (tp30) REVERT: B 869 MET cc_start: 0.9298 (OUTLIER) cc_final: 0.8958 (ptp) REVERT: C 211 ASN cc_start: 0.4743 (OUTLIER) cc_final: 0.3994 (p0) REVERT: C 214 ARG cc_start: 0.6663 (OUTLIER) cc_final: 0.5927 (tpm170) REVERT: C 421 TYR cc_start: 0.9437 (m-80) cc_final: 0.9157 (m-80) REVERT: C 867 ASP cc_start: 0.8714 (p0) cc_final: 0.8437 (p0) outliers start: 37 outliers final: 23 residues processed: 88 average time/residue: 0.1287 time to fit residues: 19.9291 Evaluate side-chains 79 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 52 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 75 optimal weight: 3.9990 chunk 264 optimal weight: 4.9990 chunk 261 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 225 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 237 optimal weight: 4.9990 chunk 193 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.052316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.037513 restraints weight = 147331.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.038792 restraints weight = 81508.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.039652 restraints weight = 54648.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.040243 restraints weight = 41184.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.040656 restraints weight = 33653.664| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 23432 Z= 0.156 Angle : 0.582 15.704 31909 Z= 0.292 Chirality : 0.043 0.280 3732 Planarity : 0.005 0.140 4079 Dihedral : 6.621 112.759 3716 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.84 % Favored : 94.87 % Rotamer: Outliers : 1.51 % Allowed : 14.01 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % 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 (0.16), residues: 2829 helix: 1.93 (0.21), residues: 658 sheet: 0.24 (0.19), residues: 647 loop : -1.21 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 273 TYR 0.019 0.001 TYR C 904 PHE 0.012 0.001 PHE A 92 TRP 0.006 0.001 TRP A 64 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00348 (23408) covalent geometry : angle 0.56952 (31840) hydrogen bonds : bond 0.04119 ( 946) hydrogen bonds : angle 5.21294 ( 2637) Misc. bond : bond 0.00008 ( 1) link_BETA1-4 : bond 0.00525 ( 8) link_BETA1-4 : angle 2.30839 ( 24) link_NAG-ASN : bond 0.00408 ( 15) link_NAG-ASN : angle 2.83584 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 53 time to evaluate : 0.935 Fit side-chains REVERT: A 615 VAL cc_start: 0.8696 (OUTLIER) cc_final: 0.8450 (p) REVERT: A 740 MET cc_start: 0.9145 (tpp) cc_final: 0.8929 (tpp) REVERT: A 869 MET cc_start: 0.9139 (ptp) cc_final: 0.8893 (ptp) REVERT: B 277 LEU cc_start: 0.9569 (mm) cc_final: 0.9152 (tp) REVERT: B 697 MET cc_start: 0.8774 (mmm) cc_final: 0.8506 (tpt) REVERT: B 773 GLU cc_start: 0.9170 (tp30) cc_final: 0.8766 (tp30) REVERT: B 869 MET cc_start: 0.9296 (OUTLIER) cc_final: 0.8948 (ptp) REVERT: C 214 ARG cc_start: 0.6681 (OUTLIER) cc_final: 0.5890 (tpm170) REVERT: C 421 TYR cc_start: 0.9439 (m-80) cc_final: 0.9184 (m-80) REVERT: C 478 THR cc_start: 0.3836 (OUTLIER) cc_final: 0.3559 (p) REVERT: C 867 ASP cc_start: 0.8725 (p0) cc_final: 0.8455 (p0) outliers start: 38 outliers final: 26 residues processed: 87 average time/residue: 0.1253 time to fit residues: 19.5664 Evaluate side-chains 83 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 53 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 12 optimal weight: 30.0000 chunk 171 optimal weight: 0.9980 chunk 252 optimal weight: 2.9990 chunk 202 optimal weight: 10.0000 chunk 46 optimal weight: 20.0000 chunk 69 optimal weight: 5.9990 chunk 235 optimal weight: 5.9990 chunk 241 optimal weight: 10.0000 chunk 151 optimal weight: 0.0470 chunk 148 optimal weight: 0.5980 chunk 50 optimal weight: 9.9990 overall best weight: 2.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN ** C 544 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 = 0.3269 r_free = 0.3269 target = 0.052700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.037858 restraints weight = 147374.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.039149 restraints weight = 81072.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.040021 restraints weight = 54154.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.040615 restraints weight = 40689.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.041029 restraints weight = 33213.158| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 23432 Z= 0.128 Angle : 0.556 12.602 31909 Z= 0.280 Chirality : 0.043 0.282 3732 Planarity : 0.005 0.139 4079 Dihedral : 6.386 111.796 3716 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.42 % Favored : 95.30 % Rotamer: Outliers : 1.23 % Allowed : 14.21 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % 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: -0.05 (0.16), residues: 2829 helix: 2.07 (0.21), residues: 652 sheet: 0.31 (0.19), residues: 647 loop : -1.16 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 273 TYR 0.018 0.001 TYR C 904 PHE 0.009 0.001 PHE A 92 TRP 0.006 0.001 TRP B 104 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00292 (23408) covalent geometry : angle 0.54345 (31840) hydrogen bonds : bond 0.03952 ( 946) hydrogen bonds : angle 5.10672 ( 2637) Misc. bond : bond 0.00015 ( 1) link_BETA1-4 : bond 0.00566 ( 8) link_BETA1-4 : angle 2.23761 ( 24) link_NAG-ASN : bond 0.00384 ( 15) link_NAG-ASN : angle 2.78518 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5658 Ramachandran restraints generated. 2829 Oldfield, 0 Emsley, 2829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 53 time to evaluate : 0.922 Fit side-chains REVERT: A 615 VAL cc_start: 0.8698 (OUTLIER) cc_final: 0.8456 (p) REVERT: A 740 MET cc_start: 0.9124 (tpp) cc_final: 0.8909 (tpp) REVERT: A 869 MET cc_start: 0.9139 (ptp) cc_final: 0.8897 (ptp) REVERT: B 277 LEU cc_start: 0.9557 (mm) cc_final: 0.9140 (tp) REVERT: B 697 MET cc_start: 0.8796 (mmm) cc_final: 0.8520 (tpt) REVERT: B 773 GLU cc_start: 0.9177 (tp30) cc_final: 0.8772 (tp30) REVERT: B 869 MET cc_start: 0.9278 (OUTLIER) cc_final: 0.8903 (ptp) REVERT: C 211 ASN cc_start: 0.4982 (OUTLIER) cc_final: 0.4103 (p0) REVERT: C 214 ARG cc_start: 0.6604 (OUTLIER) cc_final: 0.5646 (tpm170) REVERT: C 421 TYR cc_start: 0.9428 (m-80) cc_final: 0.9174 (m-80) REVERT: C 478 THR cc_start: 0.3799 (OUTLIER) cc_final: 0.3520 (p) REVERT: C 867 ASP cc_start: 0.8698 (p0) cc_final: 0.8438 (p0) outliers start: 31 outliers final: 25 residues processed: 80 average time/residue: 0.1305 time to fit residues: 18.7004 Evaluate side-chains 82 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 52 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 181 optimal weight: 0.9980 chunk 129 optimal weight: 0.0030 chunk 223 optimal weight: 4.9990 chunk 205 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 203 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 266 optimal weight: 3.9990 chunk 167 optimal weight: 0.0970 chunk 123 optimal weight: 9.9990 overall best weight: 2.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.052655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.037816 restraints weight = 146506.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.039104 restraints weight = 80916.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.039972 restraints weight = 54151.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.040564 restraints weight = 40706.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.040989 restraints weight = 33225.226| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.205 23432 Z= 0.162 Angle : 0.711 59.145 31909 Z= 0.389 Chirality : 0.046 1.031 3732 Planarity : 0.005 0.138 4079 Dihedral : 6.393 111.641 3716 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.35 % Favored : 95.33 % Rotamer: Outliers : 1.23 % Allowed : 14.17 % Favored : 84.60 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % 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 (0.16), residues: 2829 helix: 2.07 (0.21), residues: 652 sheet: 0.31 (0.20), residues: 647 loop : -1.16 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 273 TYR 0.018 0.001 TYR C 904 PHE 0.010 0.001 PHE A 92 TRP 0.006 0.001 TRP C 436 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00345 (23408) covalent geometry : angle 0.70174 (31840) hydrogen bonds : bond 0.03953 ( 946) hydrogen bonds : angle 5.10647 ( 2637) Misc. bond : bond 0.00015 ( 1) link_BETA1-4 : bond 0.00515 ( 8) link_BETA1-4 : angle 2.25350 ( 24) link_NAG-ASN : bond 0.00385 ( 15) link_NAG-ASN : angle 2.78495 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3075.24 seconds wall clock time: 54 minutes 26.81 seconds (3266.81 seconds total)