Starting phenix.real_space_refine on Thu Jun 19 23:32:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wgy_32492/06_2025/7wgy_32492_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wgy_32492/06_2025/7wgy_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wgy_32492/06_2025/7wgy_32492.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wgy_32492/06_2025/7wgy_32492.map" model { file = "/net/cci-nas-00/data/ceres_data/7wgy_32492/06_2025/7wgy_32492_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wgy_32492/06_2025/7wgy_32492_neut.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.63, per 1000 atoms: 0.55 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: 6.80 Conformation dependent library (CDL) restraints added in 2.9 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: 3.39 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: 10.59 Time building geometry restraints manager: 6.99 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 1147 or resid 1301 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.870 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 54.430 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.570 ------------------------------------------------------------------------------- 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 : 7.65 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.024 0.002 TRP C 353 HIS 0.007 0.001 HIS B1058 PHE 0.030 0.002 PHE C 906 TYR 0.023 0.002 TYR A 904 ARG 0.004 0.001 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00510 ( 15) link_NAG-ASN : angle 3.27187 ( 45) link_BETA1-4 : bond 0.00487 ( 8) link_BETA1-4 : angle 1.42247 ( 24) hydrogen bonds : bond 0.15377 ( 946) hydrogen bonds : angle 7.14947 ( 2637) covalent geometry : bond 0.00824 (23408) covalent geometry : angle 0.76864 (31840) Misc. bond : bond 0.00004 ( 1) *********************** 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 : 2.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.7153 (tpp) cc_final: 0.6777 (tpp) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.3450 time to fit residues: 60.5219 Evaluate side-chains 54 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 242 optimal weight: 0.0170 chunk 217 optimal weight: 0.0670 chunk 120 optimal weight: 30.0000 chunk 74 optimal weight: 7.9990 chunk 146 optimal weight: 0.6980 chunk 116 optimal weight: 30.0000 chunk 224 optimal weight: 20.0000 chunk 87 optimal weight: 0.3980 chunk 136 optimal weight: 7.9990 chunk 167 optimal weight: 9.9990 chunk 260 optimal weight: 0.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 C 764 ASN C 901 GLN C 965 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.055383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.040297 restraints weight = 140956.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.041689 restraints weight = 76559.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.042615 restraints weight = 50691.902| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.091 23432 Z= 0.119 Angle : 0.590 11.609 31909 Z= 0.302 Chirality : 0.046 0.309 3732 Planarity : 0.005 0.128 4079 Dihedral : 10.650 115.309 3716 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.75 % Favored : 95.93 % Rotamer: Outliers : 0.32 % Allowed : 4.84 % Favored : 94.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.15), residues: 2829 helix: 1.33 (0.21), residues: 641 sheet: 0.51 (0.19), residues: 654 loop : -1.17 (0.15), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.005 0.001 HIS C 66 PHE 0.015 0.001 PHE A 515 TYR 0.014 0.001 TYR B 265 ARG 0.006 0.000 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00555 ( 15) link_NAG-ASN : angle 3.27512 ( 45) link_BETA1-4 : bond 0.00715 ( 8) link_BETA1-4 : angle 2.06982 ( 24) hydrogen bonds : bond 0.05182 ( 946) hydrogen bonds : angle 5.45379 ( 2637) covalent geometry : bond 0.00247 (23408) covalent geometry : angle 0.57494 (31840) Misc. bond : bond 0.00021 ( 1) *********************** 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 93 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.9014 (tpp) cc_final: 0.8804 (tpp) REVERT: A 869 MET cc_start: 0.9016 (mpp) cc_final: 0.8627 (ptp) REVERT: A 1050 MET cc_start: 0.7626 (ptp) cc_final: 0.7315 (mtm) REVERT: B 697 MET cc_start: 0.8645 (mmm) cc_final: 0.8026 (tpt) REVERT: B 773 GLU cc_start: 0.8966 (tp30) cc_final: 0.8505 (tp30) REVERT: B 774 GLN cc_start: 0.9183 (mm-40) cc_final: 0.8981 (mm-40) REVERT: B 900 MET cc_start: 0.9217 (mtt) cc_final: 0.8937 (mtt) REVERT: B 1029 MET cc_start: 0.8827 (tmm) cc_final: 0.8608 (tmm) REVERT: C 867 ASP cc_start: 0.8727 (p0) cc_final: 0.8441 (p0) REVERT: C 869 MET cc_start: 0.9657 (mtp) cc_final: 0.9261 (ptp) outliers start: 8 outliers final: 4 residues processed: 92 average time/residue: 0.3243 time to fit residues: 50.9844 Evaluate side-chains 62 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU 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 246 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 43 optimal weight: 0.0670 chunk 39 optimal weight: 9.9990 chunk 148 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 278 optimal weight: 0.9980 chunk 257 optimal weight: 0.8980 chunk 248 optimal weight: 7.9990 chunk 218 optimal weight: 10.0000 chunk 195 optimal weight: 0.0020 overall best weight: 1.1928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 613 GLN C 388 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.054943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.039782 restraints weight = 143812.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.041138 restraints weight = 79228.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.042041 restraints weight = 53121.203| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.095 23432 Z= 0.107 Angle : 0.533 10.437 31909 Z= 0.272 Chirality : 0.043 0.289 3732 Planarity : 0.005 0.135 4079 Dihedral : 9.326 114.168 3716 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.78 % Favored : 95.90 % Rotamer: Outliers : 0.60 % Allowed : 6.71 % Favored : 92.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.15), residues: 2829 helix: 1.75 (0.21), residues: 645 sheet: 0.52 (0.19), residues: 664 loop : -1.06 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS A1064 PHE 0.011 0.001 PHE A 400 TYR 0.016 0.001 TYR B1067 ARG 0.002 0.000 ARG C 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 15) link_NAG-ASN : angle 2.85196 ( 45) link_BETA1-4 : bond 0.00488 ( 8) link_BETA1-4 : angle 2.00183 ( 24) hydrogen bonds : bond 0.04445 ( 946) hydrogen bonds : angle 5.08808 ( 2637) covalent geometry : bond 0.00236 (23408) covalent geometry : angle 0.52022 (31840) Misc. bond : bond 0.00027 ( 1) *********************** 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 83 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 3.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 544 ASN cc_start: 0.8825 (OUTLIER) cc_final: 0.8279 (p0) REVERT: A 615 VAL cc_start: 0.8670 (OUTLIER) cc_final: 0.8403 (p) REVERT: A 740 MET cc_start: 0.9110 (tpp) cc_final: 0.8873 (tpp) REVERT: A 869 MET cc_start: 0.9107 (mpp) cc_final: 0.8676 (ptp) REVERT: B 277 LEU cc_start: 0.9638 (mm) cc_final: 0.9331 (tt) REVERT: B 697 MET cc_start: 0.8687 (mmm) cc_final: 0.8085 (tpt) REVERT: B 773 GLU cc_start: 0.9081 (tp30) cc_final: 0.8571 (tp30) REVERT: B 869 MET cc_start: 0.9223 (ptp) cc_final: 0.8856 (ptp) REVERT: C 867 ASP cc_start: 0.8681 (p0) cc_final: 0.8476 (p0) REVERT: C 869 MET cc_start: 0.9693 (mtp) cc_final: 0.9277 (ptp) outliers start: 15 outliers final: 8 residues processed: 81 average time/residue: 0.3324 time to fit residues: 47.0508 Evaluate side-chains 65 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 2.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1130 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain C residue 214 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 209 optimal weight: 20.0000 chunk 148 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 201 optimal weight: 10.0000 chunk 252 optimal weight: 0.0980 chunk 60 optimal weight: 6.9990 chunk 203 optimal weight: 30.0000 chunk 46 optimal weight: 5.9990 chunk 245 optimal weight: 2.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- 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 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 = 0.3272 r_free = 0.3272 target = 0.052715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.037809 restraints weight = 147272.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.039099 restraints weight = 81912.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.039963 restraints weight = 55033.426| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 23432 Z= 0.216 Angle : 0.613 11.506 31909 Z= 0.313 Chirality : 0.044 0.272 3732 Planarity : 0.005 0.140 4079 Dihedral : 8.347 117.255 3716 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.63 % Favored : 95.05 % Rotamer: Outliers : 1.07 % Allowed : 8.61 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.15), residues: 2829 helix: 1.64 (0.20), residues: 652 sheet: 0.52 (0.20), residues: 613 loop : -1.16 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 64 HIS 0.004 0.001 HIS C1064 PHE 0.015 0.001 PHE A 92 TYR 0.022 0.001 TYR C 904 ARG 0.005 0.000 ARG B 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00510 ( 15) link_NAG-ASN : angle 3.03766 ( 45) link_BETA1-4 : bond 0.00494 ( 8) link_BETA1-4 : angle 2.23080 ( 24) hydrogen bonds : bond 0.04600 ( 946) hydrogen bonds : angle 5.29139 ( 2637) covalent geometry : bond 0.00474 (23408) covalent geometry : angle 0.60003 (31840) Misc. bond : bond 0.00010 ( 1) *********************** 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 79 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 52 time to evaluate : 2.562 Fit side-chains REVERT: A 615 VAL cc_start: 0.8899 (OUTLIER) cc_final: 0.8633 (p) REVERT: A 740 MET cc_start: 0.9165 (tpp) cc_final: 0.8909 (tpp) REVERT: A 869 MET cc_start: 0.9040 (mpp) cc_final: 0.8762 (ptp) REVERT: B 277 LEU cc_start: 0.9634 (mm) cc_final: 0.9225 (tt) REVERT: B 697 MET cc_start: 0.8670 (mmm) cc_final: 0.8058 (tpt) REVERT: B 731 MET cc_start: 0.9056 (ptp) cc_final: 0.8705 (ppp) REVERT: B 773 GLU cc_start: 0.9083 (tp30) cc_final: 0.8700 (tm-30) REVERT: B 869 MET cc_start: 0.9282 (OUTLIER) cc_final: 0.8932 (ptp) REVERT: C 214 ARG cc_start: 0.6367 (OUTLIER) cc_final: 0.5364 (tpm170) REVERT: C 867 ASP cc_start: 0.8650 (p0) cc_final: 0.8391 (p0) outliers start: 27 outliers final: 14 residues processed: 77 average time/residue: 0.3028 time to fit residues: 41.5274 Evaluate side-chains 65 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER 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 785 VAL Chi-restraints excluded: chain A residue 856 ASN 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 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 858 LEU Chi-restraints excluded: chain C residue 1034 LEU 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 160 optimal weight: 3.9990 chunk 272 optimal weight: 0.4980 chunk 223 optimal weight: 30.0000 chunk 77 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 193 optimal weight: 5.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.052286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.037428 restraints weight = 147051.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.038718 restraints weight = 81060.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.039591 restraints weight = 54222.871| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2425 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= 0.197 Angle : 0.593 12.083 31909 Z= 0.303 Chirality : 0.044 0.282 3732 Planarity : 0.005 0.140 4079 Dihedral : 7.394 117.228 3716 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.38 % Favored : 95.30 % Rotamer: Outliers : 1.19 % Allowed : 10.64 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 2829 helix: 1.74 (0.20), residues: 652 sheet: 0.41 (0.20), residues: 635 loop : -1.20 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 64 HIS 0.004 0.001 HIS C1048 PHE 0.014 0.001 PHE A 92 TYR 0.019 0.001 TYR C 904 ARG 0.004 0.000 ARG C 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 15) link_NAG-ASN : angle 2.88406 ( 45) link_BETA1-4 : bond 0.00285 ( 8) link_BETA1-4 : angle 2.26518 ( 24) hydrogen bonds : bond 0.04480 ( 946) hydrogen bonds : angle 5.29754 ( 2637) covalent geometry : bond 0.00432 (23408) covalent geometry : angle 0.57990 (31840) Misc. bond : bond 0.00037 ( 1) *********************** 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 84 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 54 time to evaluate : 2.584 Fit side-chains revert: symmetry clash REVERT: A 615 VAL cc_start: 0.8970 (OUTLIER) cc_final: 0.8720 (p) REVERT: A 740 MET cc_start: 0.9173 (tpp) cc_final: 0.8926 (tpp) REVERT: A 869 MET cc_start: 0.9027 (mpp) cc_final: 0.8741 (ptp) REVERT: A 1122 VAL cc_start: 0.9041 (OUTLIER) cc_final: 0.8816 (p) REVERT: B 277 LEU cc_start: 0.9641 (mm) cc_final: 0.9226 (tt) REVERT: B 697 MET cc_start: 0.8799 (mmm) cc_final: 0.8516 (tpt) REVERT: B 731 MET cc_start: 0.9062 (ptp) cc_final: 0.8726 (ppp) REVERT: B 773 GLU cc_start: 0.9144 (tp30) cc_final: 0.8811 (tm-30) REVERT: B 869 MET cc_start: 0.9287 (OUTLIER) cc_final: 0.8957 (ptp) REVERT: C 214 ARG cc_start: 0.6613 (OUTLIER) cc_final: 0.5544 (tpm170) REVERT: C 421 TYR cc_start: 0.9053 (m-10) cc_final: 0.8834 (m-10) REVERT: C 867 ASP cc_start: 0.8727 (p0) cc_final: 0.8449 (p0) outliers start: 30 outliers final: 20 residues processed: 82 average time/residue: 0.2949 time to fit residues: 43.3061 Evaluate side-chains 75 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 51 time to evaluate : 2.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 361 CYS 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 856 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE 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 126 VAL Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 531 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 1034 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 5 optimal weight: 9.9990 chunk 172 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 253 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 275 optimal weight: 7.9990 chunk 251 optimal weight: 0.8980 chunk 10 optimal weight: 20.0000 chunk 106 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.052357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.037480 restraints weight = 146581.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.038778 restraints weight = 80764.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.039648 restraints weight = 54025.439| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2564 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= 0.171 Angle : 0.568 11.908 31909 Z= 0.290 Chirality : 0.043 0.283 3732 Planarity : 0.005 0.140 4079 Dihedral : 7.068 115.674 3716 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.45 % Favored : 95.23 % Rotamer: Outliers : 1.27 % Allowed : 11.71 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.16), residues: 2829 helix: 1.90 (0.21), residues: 646 sheet: 0.33 (0.20), residues: 642 loop : -1.18 (0.15), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.003 0.001 HIS A 207 PHE 0.013 0.001 PHE A 92 TYR 0.019 0.001 TYR C 904 ARG 0.004 0.000 ARG C 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 15) link_NAG-ASN : angle 2.85906 ( 45) link_BETA1-4 : bond 0.00352 ( 8) link_BETA1-4 : angle 2.28342 ( 24) hydrogen bonds : bond 0.04338 ( 946) hydrogen bonds : angle 5.22795 ( 2637) covalent geometry : bond 0.00377 (23408) covalent geometry : angle 0.55451 (31840) Misc. bond : bond 0.00005 ( 1) *********************** 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 86 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 54 time to evaluate : 2.496 Fit side-chains REVERT: A 615 VAL cc_start: 0.8936 (OUTLIER) cc_final: 0.8666 (p) REVERT: A 740 MET cc_start: 0.9180 (tpp) cc_final: 0.8944 (tpp) REVERT: A 869 MET cc_start: 0.9028 (mpp) cc_final: 0.8740 (ptp) REVERT: A 1122 VAL cc_start: 0.9039 (OUTLIER) cc_final: 0.8824 (p) REVERT: B 132 GLU cc_start: 0.8451 (mp0) cc_final: 0.8246 (mp0) REVERT: B 277 LEU cc_start: 0.9645 (mm) cc_final: 0.9230 (tt) REVERT: B 697 MET cc_start: 0.8788 (mmm) cc_final: 0.8502 (tpt) REVERT: B 731 MET cc_start: 0.8961 (ptp) cc_final: 0.8755 (ppp) REVERT: B 773 GLU cc_start: 0.9159 (tp30) cc_final: 0.8877 (tm-30) REVERT: B 869 MET cc_start: 0.9313 (OUTLIER) cc_final: 0.8971 (ptp) REVERT: C 214 ARG cc_start: 0.6758 (OUTLIER) cc_final: 0.5757 (tpm170) REVERT: C 867 ASP cc_start: 0.8723 (p0) cc_final: 0.8438 (p0) outliers start: 32 outliers final: 17 residues processed: 83 average time/residue: 0.2844 time to fit residues: 42.1179 Evaluate side-chains 73 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER 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 785 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1034 LEU 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 126 VAL 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 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1034 LEU 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 96 optimal weight: 8.9990 chunk 120 optimal weight: 9.9990 chunk 72 optimal weight: 0.4980 chunk 54 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 188 optimal weight: 6.9990 chunk 248 optimal weight: 0.9990 chunk 269 optimal weight: 0.8980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** 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 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.053073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.038169 restraints weight = 145469.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.039485 restraints weight = 80076.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.040365 restraints weight = 53468.608| |-----------------------------------------------------------------------------| r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 23432 Z= 0.116 Angle : 0.528 12.806 31909 Z= 0.268 Chirality : 0.043 0.289 3732 Planarity : 0.004 0.139 4079 Dihedral : 6.525 113.279 3716 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.03 % Favored : 95.69 % Rotamer: Outliers : 1.15 % Allowed : 11.91 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.16), residues: 2829 helix: 2.16 (0.21), residues: 644 sheet: 0.42 (0.20), residues: 642 loop : -1.12 (0.15), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.003 0.001 HIS C1048 PHE 0.013 0.001 PHE A 192 TYR 0.014 0.001 TYR B 265 ARG 0.005 0.000 ARG C 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00370 ( 15) link_NAG-ASN : angle 2.73198 ( 45) link_BETA1-4 : bond 0.00451 ( 8) link_BETA1-4 : angle 2.18926 ( 24) hydrogen bonds : bond 0.03946 ( 946) hydrogen bonds : angle 4.99421 ( 2637) covalent geometry : bond 0.00264 (23408) covalent geometry : angle 0.51479 (31840) Misc. bond : bond 0.00002 ( 1) *********************** 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 86 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 57 time to evaluate : 2.792 Fit side-chains REVERT: A 740 MET cc_start: 0.9151 (tpp) cc_final: 0.8942 (tpp) REVERT: A 869 MET cc_start: 0.9027 (mpp) cc_final: 0.8763 (ptp) REVERT: A 1122 VAL cc_start: 0.9036 (OUTLIER) cc_final: 0.8823 (p) REVERT: B 277 LEU cc_start: 0.9627 (mm) cc_final: 0.9276 (tp) REVERT: B 697 MET cc_start: 0.8775 (mmm) cc_final: 0.8477 (tpt) REVERT: B 773 GLU cc_start: 0.9179 (tp30) cc_final: 0.8892 (tm-30) REVERT: B 869 MET cc_start: 0.9303 (OUTLIER) cc_final: 0.8965 (ptp) REVERT: C 214 ARG cc_start: 0.6646 (OUTLIER) cc_final: 0.5815 (tpm170) REVERT: C 421 TYR cc_start: 0.9274 (m-80) cc_final: 0.9005 (m-80) REVERT: C 867 ASP cc_start: 0.8707 (p0) cc_final: 0.8441 (p0) outliers start: 29 outliers final: 21 residues processed: 84 average time/residue: 0.3220 time to fit residues: 50.1111 Evaluate side-chains 76 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 52 time to evaluate : 2.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 433 VAL Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 62 VAL 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 126 VAL Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1034 LEU 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 231 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 277 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 270 optimal weight: 9.9990 chunk 283 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 275 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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** ** B 280 ASN ** 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 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 = 0.3281 r_free = 0.3281 target = 0.053019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.038148 restraints weight = 144953.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.039441 restraints weight = 80201.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.040319 restraints weight = 53724.332| |-----------------------------------------------------------------------------| r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2791 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= 0.122 Angle : 0.531 12.236 31909 Z= 0.269 Chirality : 0.042 0.281 3732 Planarity : 0.005 0.139 4079 Dihedral : 6.367 112.574 3716 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.07 % Favored : 95.65 % Rotamer: Outliers : 1.19 % Allowed : 12.31 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.16), residues: 2829 helix: 2.17 (0.21), residues: 646 sheet: 0.47 (0.20), residues: 640 loop : -1.08 (0.15), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.003 0.001 HIS C1048 PHE 0.022 0.001 PHE B 65 TYR 0.015 0.001 TYR C 904 ARG 0.003 0.000 ARG C 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00382 ( 15) link_NAG-ASN : angle 2.73722 ( 45) link_BETA1-4 : bond 0.00525 ( 8) link_BETA1-4 : angle 2.20275 ( 24) hydrogen bonds : bond 0.03869 ( 946) hydrogen bonds : angle 4.94691 ( 2637) covalent geometry : bond 0.00277 (23408) covalent geometry : angle 0.51769 (31840) Misc. bond : bond 0.00003 ( 1) *********************** 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 84 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 54 time to evaluate : 2.550 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.7299 (tpt) cc_final: 0.7012 (tpt) REVERT: A 615 VAL cc_start: 0.8745 (OUTLIER) cc_final: 0.8499 (p) REVERT: A 740 MET cc_start: 0.9155 (tpp) cc_final: 0.8938 (tpp) REVERT: A 869 MET cc_start: 0.9028 (mpp) cc_final: 0.8773 (ptp) REVERT: A 1122 VAL cc_start: 0.9003 (OUTLIER) cc_final: 0.8790 (p) REVERT: B 277 LEU cc_start: 0.9626 (mm) cc_final: 0.9269 (tp) REVERT: B 697 MET cc_start: 0.8814 (mmm) cc_final: 0.8526 (tpt) REVERT: B 773 GLU cc_start: 0.9207 (tp30) cc_final: 0.8902 (tm-30) REVERT: B 869 MET cc_start: 0.9304 (OUTLIER) cc_final: 0.8962 (ptp) REVERT: C 214 ARG cc_start: 0.6652 (OUTLIER) cc_final: 0.5852 (tpm170) REVERT: C 421 TYR cc_start: 0.9314 (m-80) cc_final: 0.8999 (m-80) REVERT: C 867 ASP cc_start: 0.8702 (p0) cc_final: 0.8465 (p0) REVERT: C 869 MET cc_start: 0.9607 (mtp) cc_final: 0.9364 (ptp) outliers start: 30 outliers final: 22 residues processed: 82 average time/residue: 0.2878 time to fit residues: 42.1825 Evaluate side-chains 79 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 53 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1034 LEU Chi-restraints excluded: chain A residue 1122 VAL 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 126 VAL Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 267 VAL 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 1034 LEU 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 221 optimal weight: 5.9990 chunk 171 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 222 optimal weight: 20.0000 chunk 254 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 245 optimal weight: 7.9990 chunk 271 optimal weight: 9.9990 chunk 205 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN C 211 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.053622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.038713 restraints weight = 145755.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.040041 restraints weight = 80254.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.040922 restraints weight = 53645.576| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.098 23432 Z= 0.097 Angle : 0.513 13.113 31909 Z= 0.259 Chirality : 0.042 0.285 3732 Planarity : 0.004 0.137 4079 Dihedral : 5.969 111.139 3716 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.85 % Favored : 95.86 % Rotamer: Outliers : 1.23 % Allowed : 12.23 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.16), residues: 2829 helix: 2.25 (0.21), residues: 652 sheet: 0.58 (0.20), residues: 637 loop : -1.01 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C1102 HIS 0.003 0.001 HIS C1048 PHE 0.022 0.001 PHE B 65 TYR 0.013 0.001 TYR B 265 ARG 0.002 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00382 ( 15) link_NAG-ASN : angle 2.66685 ( 45) link_BETA1-4 : bond 0.00563 ( 8) link_BETA1-4 : angle 2.12061 ( 24) hydrogen bonds : bond 0.03583 ( 946) hydrogen bonds : angle 4.79190 ( 2637) covalent geometry : bond 0.00225 (23408) covalent geometry : angle 0.49983 (31840) Misc. bond : bond 0.00051 ( 1) *********************** 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 88 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 57 time to evaluate : 2.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7178 (tpt) cc_final: 0.6908 (tpt) REVERT: A 740 MET cc_start: 0.9140 (tpp) cc_final: 0.8936 (tpp) REVERT: A 869 MET cc_start: 0.8998 (mpp) cc_final: 0.8752 (ptp) REVERT: A 900 MET cc_start: 0.9059 (mmt) cc_final: 0.8712 (mmp) REVERT: A 1122 VAL cc_start: 0.8982 (OUTLIER) cc_final: 0.8774 (p) REVERT: B 277 LEU cc_start: 0.9599 (mm) cc_final: 0.9269 (tp) REVERT: B 697 MET cc_start: 0.8801 (mmm) cc_final: 0.8508 (tpt) REVERT: B 731 MET cc_start: 0.8876 (ppp) cc_final: 0.8042 (ppp) REVERT: B 773 GLU cc_start: 0.9167 (tp30) cc_final: 0.8853 (tm-30) REVERT: B 900 MET cc_start: 0.9148 (mtt) cc_final: 0.8904 (mtt) REVERT: C 211 ASN cc_start: 0.5078 (OUTLIER) cc_final: 0.4405 (p0) REVERT: C 214 ARG cc_start: 0.6569 (OUTLIER) cc_final: 0.6345 (tpm170) REVERT: C 421 TYR cc_start: 0.9301 (m-80) cc_final: 0.8990 (m-80) REVERT: C 478 THR cc_start: 0.3786 (OUTLIER) cc_final: 0.3510 (p) REVERT: C 867 ASP cc_start: 0.8717 (p0) cc_final: 0.8458 (p0) REVERT: C 869 MET cc_start: 0.9597 (mtp) cc_final: 0.9377 (ptp) outliers start: 31 outliers final: 17 residues processed: 86 average time/residue: 0.3460 time to fit residues: 55.3617 Evaluate side-chains 74 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 2.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1122 VAL 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 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 1034 LEU 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 45 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 274 optimal weight: 0.9980 chunk 234 optimal weight: 2.9990 chunk 279 optimal weight: 0.8980 chunk 256 optimal weight: 4.9990 chunk 103 optimal weight: 20.0000 chunk 217 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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** ** B 949 GLN ** 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 = 0.3295 r_free = 0.3295 target = 0.053505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.038613 restraints weight = 144933.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.039926 restraints weight = 79856.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.040804 restraints weight = 53439.955| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 23432 Z= 0.107 Angle : 0.530 16.581 31909 Z= 0.265 Chirality : 0.043 0.278 3732 Planarity : 0.004 0.136 4079 Dihedral : 5.898 110.812 3716 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.89 % Favored : 95.83 % Rotamer: Outliers : 0.83 % Allowed : 12.62 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.16), residues: 2829 helix: 2.26 (0.21), residues: 652 sheet: 0.61 (0.20), residues: 631 loop : -1.00 (0.16), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.003 0.001 HIS B1048 PHE 0.027 0.001 PHE B 65 TYR 0.013 0.001 TYR C 904 ARG 0.002 0.000 ARG C 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 15) link_NAG-ASN : angle 2.69092 ( 45) link_BETA1-4 : bond 0.00588 ( 8) link_BETA1-4 : angle 2.09437 ( 24) hydrogen bonds : bond 0.03600 ( 946) hydrogen bonds : angle 4.77624 ( 2637) covalent geometry : bond 0.00250 (23408) covalent geometry : angle 0.51735 (31840) Misc. bond : bond 0.00005 ( 1) ********************** 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 75 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 54 time to evaluate : 3.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6992 (tpt) cc_final: 0.6719 (tpt) REVERT: A 740 MET cc_start: 0.9147 (tpp) cc_final: 0.8946 (tpp) REVERT: A 869 MET cc_start: 0.9012 (mpp) cc_final: 0.8758 (ptp) REVERT: A 900 MET cc_start: 0.9085 (mmt) cc_final: 0.8738 (mmp) REVERT: A 1122 VAL cc_start: 0.8981 (OUTLIER) cc_final: 0.8775 (p) REVERT: B 277 LEU cc_start: 0.9589 (mm) cc_final: 0.9244 (tp) REVERT: B 697 MET cc_start: 0.8793 (mmm) cc_final: 0.8507 (tpt) REVERT: B 731 MET cc_start: 0.8858 (ppp) cc_final: 0.7983 (ppp) REVERT: B 773 GLU cc_start: 0.9181 (tp30) cc_final: 0.8856 (tm-30) REVERT: B 900 MET cc_start: 0.9292 (mtt) cc_final: 0.9020 (mtt) REVERT: C 214 ARG cc_start: 0.6575 (OUTLIER) cc_final: 0.5546 (tpm170) REVERT: C 421 TYR cc_start: 0.9312 (m-80) cc_final: 0.9033 (m-80) REVERT: C 478 THR cc_start: 0.3786 (OUTLIER) cc_final: 0.3512 (p) REVERT: C 867 ASP cc_start: 0.8724 (p0) cc_final: 0.8490 (p0) REVERT: C 869 MET cc_start: 0.9599 (mtp) cc_final: 0.9383 (ptp) outliers start: 21 outliers final: 17 residues processed: 74 average time/residue: 0.3527 time to fit residues: 46.8870 Evaluate side-chains 73 residues out of total 2519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 3.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1122 VAL 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 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 1034 LEU 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 185 optimal weight: 20.0000 chunk 194 optimal weight: 30.0000 chunk 277 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 12 optimal weight: 0.8980 chunk 286 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.052766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.037841 restraints weight = 146651.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.039150 restraints weight = 80393.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.040027 restraints weight = 53717.524| |-----------------------------------------------------------------------------| r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3037 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= 0.153 Angle : 0.554 12.431 31909 Z= 0.280 Chirality : 0.042 0.271 3732 Planarity : 0.005 0.137 4079 Dihedral : 6.055 110.617 3716 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.56 % Favored : 95.16 % Rotamer: Outliers : 1.03 % Allowed : 12.62 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.16), residues: 2829 helix: 2.18 (0.21), residues: 652 sheet: 0.57 (0.20), residues: 628 loop : -1.05 (0.15), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 104 HIS 0.004 0.001 HIS C1064 PHE 0.026 0.001 PHE B 65 TYR 0.018 0.001 TYR C 904 ARG 0.004 0.000 ARG C 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00422 ( 15) link_NAG-ASN : angle 2.78638 ( 45) link_BETA1-4 : bond 0.00540 ( 8) link_BETA1-4 : angle 2.14184 ( 24) hydrogen bonds : bond 0.03898 ( 946) hydrogen bonds : angle 4.91817 ( 2637) covalent geometry : bond 0.00343 (23408) covalent geometry : angle 0.54144 (31840) Misc. bond : bond 0.00026 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6143.03 seconds wall clock time: 111 minutes 29.09 seconds (6689.09 seconds total)