Starting phenix.real_space_refine on Thu Mar 5 21:48:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vhn_32000/03_2026/7vhn_32000.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vhn_32000/03_2026/7vhn_32000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vhn_32000/03_2026/7vhn_32000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vhn_32000/03_2026/7vhn_32000.map" model { file = "/net/cci-nas-00/data/ceres_data/7vhn_32000/03_2026/7vhn_32000.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vhn_32000/03_2026/7vhn_32000.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 117 5.16 5 C 16196 2.51 5 N 4195 2.21 5 O 4895 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 127 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25403 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8323 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 51, 'TRANS': 1012} Chain breaks: 6 Chain: "B" Number of atoms: 8323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8323 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 51, 'TRANS': 1012} Chain breaks: 6 Chain: "C" Number of atoms: 8323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8323 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 51, 'TRANS': 1012} Chain breaks: 6 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.92, per 1000 atoms: 0.23 Number of scatterers: 25403 At special positions: 0 Unit cell: (154.08, 151.94, 201.16, 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 117 16.00 O 4895 8.00 N 4195 7.00 C 16196 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1201 " - " ASN A 61 " " NAG A1202 " - " ASN A 122 " " NAG A1203 " - " ASN A 282 " " NAG A1204 " - " ASN A 331 " " NAG A1205 " - " ASN A 343 " " NAG A1206 " - " ASN A 603 " " NAG A1207 " - " ASN A 616 " " NAG A1208 " - " ASN A 657 " " NAG A1209 " - " ASN A 709 " " NAG A1210 " - " ASN A1074 " " NAG A1211 " - " ASN A 165 " " NAG B1201 " - " ASN B 61 " " NAG B1202 " - " ASN B 122 " " NAG B1203 " - " ASN B 282 " " NAG B1204 " - " ASN B 331 " " NAG B1205 " - " ASN B 343 " " NAG B1206 " - " ASN B 657 " " NAG B1207 " - " ASN B 709 " " NAG B1208 " - " ASN B1074 " " NAG B1209 " - " ASN B 165 " " NAG B1210 " - " ASN B 616 " " NAG C1201 " - " ASN C 282 " " NAG C1202 " - " ASN C 331 " " NAG C1203 " - " ASN C 343 " " NAG C1204 " - " ASN C 616 " " NAG C1205 " - " ASN C 657 " " NAG C1206 " - " ASN C 709 " " NAG C1207 " - " ASN C1074 " " NAG C1208 " - " ASN C 61 " " NAG C1209 " - " ASN C 122 " " NAG C1210 " - " ASN C 165 " Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 963.2 milliseconds 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5976 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 47 sheets defined 23.8% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 406 through 411 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.655A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.624A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 759 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 850 through 855 removed outlier: 3.636A pdb=" N PHE A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.798A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.084A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY A 891 " --> pdb=" O THR A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 891' Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.903A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.900A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.652A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.923A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA A 958 " --> pdb=" O GLN A 954 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR A 961 " --> pdb=" O GLN A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 979 through 983 removed outlier: 3.507A pdb=" N ARG A 983 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1019 removed outlier: 3.930A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 997 " --> pdb=" O ILE A 993 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1032 removed outlier: 3.519A pdb=" N ALA A1026 " --> pdb=" O ALA A1022 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER A1030 " --> pdb=" O ALA A1026 " (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 1148 removed outlier: 4.268A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.932A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.731A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.200A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 removed outlier: 3.954A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.022A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.056A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 852 through 857 removed outlier: 4.176A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY B 857 " --> pdb=" O GLN B 853 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 852 through 857' Processing helix chain 'B' and resid 866 through 884 removed outlier: 4.027A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER B 875 " --> pdb=" O ALA B 871 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.236A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY B 891 " --> pdb=" O THR B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 891' Processing helix chain 'B' and resid 898 through 907 removed outlier: 3.541A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 910 No H-bonds generated for 'chain 'B' and resid 908 through 910' 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 940 removed outlier: 3.829A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 930 " --> pdb=" O GLN B 926 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.628A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN B 960 " --> pdb=" O ALA B 956 " (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 989 through 1015 removed outlier: 3.543A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1018 through 1026 removed outlier: 3.846A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1148 removed outlier: 4.761A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.177A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.666A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.324A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.637A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.581A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.955A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.174A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 850 through 854 removed outlier: 3.656A pdb=" N LYS C 854 " --> pdb=" O ILE C 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 850 through 854' Processing helix chain 'C' and resid 869 through 885 removed outlier: 3.763A pdb=" N SER C 875 " --> pdb=" O ALA C 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 907 removed outlier: 4.030A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.774A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.587A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 944 removed outlier: 4.004A pdb=" N ALA C 944 " --> pdb=" O THR C 941 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 941 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.585A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1018 removed outlier: 3.516A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE C1018 " --> pdb=" O ARG C1014 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1032 removed outlier: 3.532A pdb=" N ASN C1023 " --> pdb=" O ARG C1019 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR C1027 " --> pdb=" O ASN C1023 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.708A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.501A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.703A 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: 5.891A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 135 removed outlier: 6.338A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA6, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 448 through 454 removed outlier: 6.687A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 7.058A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 722 removed outlier: 6.629A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR A1047 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 712 through 722 removed outlier: 6.629A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A1094 " --> pdb=" O THR A1105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 725 through 727 removed outlier: 3.655A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 4.036A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.951A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.755A 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: 11.131A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.110A 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 319 removed outlier: 3.664A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 650 " --> pdb=" O PHE B 643 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 4.147A pdb=" N CYS B 525 " --> pdb=" O CYS B 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 539 through 540 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.767A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD2, first strand: chain 'B' and resid 721 through 727 removed outlier: 3.683A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 721 through 727 removed outlier: 3.683A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 removed outlier: 4.081A pdb=" N SER B 735 " --> pdb=" O ASN B 859 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 5.364A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.612A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.745A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.790A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 11.636A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 10.470A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.926A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 314 removed outlier: 4.064A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 325 through 326 removed outlier: 7.302A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE4, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.600A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C1094 " --> pdb=" O THR C1105 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 718 through 722 removed outlier: 7.080A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR C1047 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 725 through 728 removed outlier: 3.803A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AF2, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 4.130A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) 853 hydrogen bonds defined for protein. 2283 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.62 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5556 1.33 - 1.45: 6794 1.45 - 1.58: 13476 1.58 - 1.71: 0 1.71 - 1.83: 147 Bond restraints: 25973 Sorted by residual: bond pdb=" N ILE A 714 " pdb=" CA ILE A 714 " ideal model delta sigma weight residual 1.458 1.488 -0.030 7.70e-03 1.69e+04 1.55e+01 bond pdb=" N PHE A 329 " pdb=" CA PHE A 329 " ideal model delta sigma weight residual 1.453 1.484 -0.031 8.30e-03 1.45e+04 1.43e+01 bond pdb=" N PHE C 329 " pdb=" CA PHE C 329 " ideal model delta sigma weight residual 1.453 1.488 -0.034 9.20e-03 1.18e+04 1.41e+01 bond pdb=" N ASP B 578 " pdb=" CA ASP B 578 " ideal model delta sigma weight residual 1.453 1.486 -0.033 9.20e-03 1.18e+04 1.28e+01 bond pdb=" N VAL B 126 " pdb=" CA VAL B 126 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.22e-02 6.72e+03 1.01e+01 ... (remaining 25968 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 34213 2.28 - 4.57: 1032 4.57 - 6.85: 67 6.85 - 9.13: 8 9.13 - 11.42: 3 Bond angle restraints: 35323 Sorted by residual: angle pdb=" C LYS C 528 " pdb=" N LYS C 529 " pdb=" CA LYS C 529 " ideal model delta sigma weight residual 121.54 132.96 -11.42 1.91e+00 2.74e-01 3.57e+01 angle pdb=" CA PHE B 133 " pdb=" CB PHE B 133 " pdb=" CG PHE B 133 " ideal model delta sigma weight residual 113.80 118.38 -4.58 1.00e+00 1.00e+00 2.09e+01 angle pdb=" N GLY C 103 " pdb=" CA GLY C 103 " pdb=" C GLY C 103 " ideal model delta sigma weight residual 110.73 119.29 -8.56 1.90e+00 2.77e-01 2.03e+01 angle pdb=" C PHE A 559 " pdb=" CA PHE A 559 " pdb=" CB PHE A 559 " ideal model delta sigma weight residual 113.15 102.57 10.58 2.38e+00 1.77e-01 1.98e+01 angle pdb=" CA THR B 124 " pdb=" C THR B 124 " pdb=" O THR B 124 " ideal model delta sigma weight residual 120.82 116.24 4.58 1.05e+00 9.07e-01 1.91e+01 ... (remaining 35318 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 14383 17.83 - 35.66: 1243 35.66 - 53.49: 212 53.49 - 71.32: 32 71.32 - 89.15: 18 Dihedral angle restraints: 15888 sinusoidal: 6603 harmonic: 9285 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -8.13 -77.87 1 1.00e+01 1.00e-02 7.58e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 169.15 -76.15 1 1.00e+01 1.00e-02 7.30e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -23.81 -62.19 1 1.00e+01 1.00e-02 5.12e+01 ... (remaining 15885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 3780 0.104 - 0.208: 266 0.208 - 0.313: 33 0.313 - 0.417: 4 0.417 - 0.521: 5 Chirality restraints: 4088 Sorted by residual: chirality pdb=" C1 NAG C1203 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG C1203 " pdb=" O5 NAG C1203 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.79e+00 chirality pdb=" C1 NAG C1207 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG C1207 " pdb=" O5 NAG C1207 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.85e+00 chirality pdb=" C1 NAG B1203 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1203 " pdb=" O5 NAG B1203 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.34e+00 ... (remaining 4085 not shown) Planarity restraints: 4568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1205 " 0.349 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C7 NAG B1205 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG B1205 " 0.148 2.00e-02 2.50e+03 pdb=" N2 NAG B1205 " -0.534 2.00e-02 2.50e+03 pdb=" O7 NAG B1205 " 0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1208 " -0.326 2.00e-02 2.50e+03 2.82e-01 9.95e+02 pdb=" C7 NAG C1208 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG C1208 " -0.045 2.00e-02 2.50e+03 pdb=" N2 NAG C1208 " 0.495 2.00e-02 2.50e+03 pdb=" O7 NAG C1208 " -0.199 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1208 " -0.316 2.00e-02 2.50e+03 2.76e-01 9.53e+02 pdb=" C7 NAG B1208 " 0.067 2.00e-02 2.50e+03 pdb=" C8 NAG B1208 " -0.082 2.00e-02 2.50e+03 pdb=" N2 NAG B1208 " 0.494 2.00e-02 2.50e+03 pdb=" O7 NAG B1208 " -0.162 2.00e-02 2.50e+03 ... (remaining 4565 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.16: 4 2.16 - 2.84: 9031 2.84 - 3.53: 33847 3.53 - 4.21: 55697 4.21 - 4.90: 95836 Nonbonded interactions: 194415 Sorted by model distance: nonbonded pdb=" ND2 ASN A 164 " pdb=" C1 NAG A1211 " model vdw 1.473 3.550 nonbonded pdb=" O GLU C 661 " pdb=" OH TYR C 695 " model vdw 2.029 3.040 nonbonded pdb=" OG1 THR A 393 " pdb=" O GLU A 516 " model vdw 2.128 3.040 nonbonded pdb=" OG1 THR B 22 " pdb=" O LYS B 77 " model vdw 2.147 3.040 nonbonded pdb=" O ASP C 442 " pdb=" ND2 ASN C 448 " model vdw 2.172 3.120 ... (remaining 194410 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 14 through 1210) selection = chain 'B' selection = chain 'C' } 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: 2.100 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: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 24.060 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 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 : 0.006 0.066 26046 Z= 0.357 Angle : 0.888 12.540 35500 Z= 0.528 Chirality : 0.062 0.521 4088 Planarity : 0.015 0.300 4537 Dihedral : 13.367 89.150 9786 Min Nonbonded Distance : 1.473 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.71 % Favored : 92.22 % Rotamer: Outliers : 0.72 % Allowed : 1.47 % Favored : 97.81 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.13), residues: 3150 helix: -1.45 (0.19), residues: 639 sheet: -1.15 (0.19), residues: 646 loop : -2.54 (0.13), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 815 TYR 0.023 0.002 TYR A 453 PHE 0.029 0.002 PHE B 201 TRP 0.026 0.002 TRP A 64 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00607 (25973) covalent geometry : angle 0.84573 (35323) SS BOND : bond 0.00426 ( 42) SS BOND : angle 1.44841 ( 84) hydrogen bonds : bond 0.21830 ( 837) hydrogen bonds : angle 8.83993 ( 2283) link_NAG-ASN : bond 0.01499 ( 31) link_NAG-ASN : angle 5.23912 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 193 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.8205 (m-80) cc_final: 0.7616 (m-80) REVERT: A 374 PHE cc_start: 0.5230 (m-80) cc_final: 0.4899 (m-80) REVERT: A 855 PHE cc_start: 0.8341 (m-10) cc_final: 0.8103 (m-80) REVERT: B 118 LEU cc_start: 0.8960 (tt) cc_final: 0.8319 (mp) REVERT: B 129 LYS cc_start: 0.7421 (mttt) cc_final: 0.7040 (mttt) REVERT: B 177 MET cc_start: -0.0844 (tpp) cc_final: -0.1841 (ttp) REVERT: B 708 SER cc_start: 0.9021 (OUTLIER) cc_final: 0.8809 (p) REVERT: B 900 MET cc_start: 0.8416 (mtt) cc_final: 0.8215 (mtt) REVERT: B 1029 MET cc_start: 0.9359 (tpp) cc_final: 0.9047 (tpp) REVERT: C 904 TYR cc_start: 0.7625 (m-10) cc_final: 0.7328 (m-10) REVERT: C 1050 MET cc_start: 0.8370 (ptm) cc_final: 0.8137 (ptm) outliers start: 20 outliers final: 7 residues processed: 207 average time/residue: 0.1667 time to fit residues: 55.6772 Evaluate side-chains 131 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 709 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.0980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN B 66 HIS B 125 ASN B 134 GLN B 655 HIS B 774 GLN B 859 ASN B 901 GLN C 81 ASN C 134 GLN C 872 GLN C 957 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.108568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.078993 restraints weight = 66355.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.078100 restraints weight = 42454.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.078540 restraints weight = 51773.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.079012 restraints weight = 34843.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.079720 restraints weight = 30125.725| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26046 Z= 0.131 Angle : 0.660 11.118 35500 Z= 0.334 Chirality : 0.046 0.331 4088 Planarity : 0.004 0.051 4537 Dihedral : 5.937 57.592 4078 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.97 % Allowed : 6.96 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.14), residues: 3150 helix: -0.47 (0.20), residues: 651 sheet: -0.88 (0.19), residues: 641 loop : -2.33 (0.13), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 21 TYR 0.018 0.001 TYR C 204 PHE 0.029 0.001 PHE B 338 TRP 0.025 0.001 TRP B 436 HIS 0.006 0.001 HIS C1118 Details of bonding type rmsd covalent geometry : bond 0.00282 (25973) covalent geometry : angle 0.64492 (35323) SS BOND : bond 0.00481 ( 42) SS BOND : angle 1.41651 ( 84) hydrogen bonds : bond 0.05450 ( 837) hydrogen bonds : angle 6.21008 ( 2283) link_NAG-ASN : bond 0.00490 ( 31) link_NAG-ASN : angle 2.53282 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7307 (m-10) cc_final: 0.6115 (m-10) REVERT: A 135 PHE cc_start: 0.7964 (m-80) cc_final: 0.7243 (m-80) REVERT: A 570 ASP cc_start: 0.8011 (p0) cc_final: 0.7619 (p0) REVERT: B 118 LEU cc_start: 0.8876 (tt) cc_final: 0.8234 (mp) REVERT: B 129 LYS cc_start: 0.7207 (mttt) cc_final: 0.6851 (mttt) REVERT: B 177 MET cc_start: -0.0455 (tpp) cc_final: -0.2143 (mtm) REVERT: B 1029 MET cc_start: 0.9347 (tpp) cc_final: 0.9000 (tpp) REVERT: C 238 PHE cc_start: 0.8448 (p90) cc_final: 0.7948 (p90) REVERT: C 327 VAL cc_start: 0.9278 (OUTLIER) cc_final: 0.9063 (t) REVERT: C 529 LYS cc_start: 0.6665 (mmmt) cc_final: 0.6379 (mmmt) REVERT: C 773 GLU cc_start: 0.7579 (tp30) cc_final: 0.7285 (tp30) REVERT: C 904 TYR cc_start: 0.7591 (m-10) cc_final: 0.7045 (m-10) outliers start: 27 outliers final: 19 residues processed: 180 average time/residue: 0.1469 time to fit residues: 44.0923 Evaluate side-chains 147 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 93 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 312 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 166 optimal weight: 8.9990 chunk 170 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN B 859 ASN C 30 ASN C 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.105629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.075905 restraints weight = 66676.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.074761 restraints weight = 45397.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.075294 restraints weight = 55538.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.075789 restraints weight = 37633.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.076354 restraints weight = 32906.257| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 26046 Z= 0.254 Angle : 0.703 11.353 35500 Z= 0.357 Chirality : 0.047 0.287 4088 Planarity : 0.005 0.059 4537 Dihedral : 6.008 59.438 4075 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.46 % Favored : 92.51 % Rotamer: Outliers : 1.58 % Allowed : 10.55 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.14), residues: 3150 helix: -0.45 (0.20), residues: 644 sheet: -1.00 (0.19), residues: 666 loop : -2.31 (0.13), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 509 TYR 0.018 0.002 TYR C 204 PHE 0.024 0.002 PHE C 429 TRP 0.039 0.002 TRP B 436 HIS 0.005 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00596 (25973) covalent geometry : angle 0.69076 (35323) SS BOND : bond 0.00372 ( 42) SS BOND : angle 1.51571 ( 84) hydrogen bonds : bond 0.05675 ( 837) hydrogen bonds : angle 6.05043 ( 2283) link_NAG-ASN : bond 0.00358 ( 31) link_NAG-ASN : angle 2.31920 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 136 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.8159 (m-80) cc_final: 0.7514 (m-80) REVERT: A 529 LYS cc_start: 0.7919 (tppt) cc_final: 0.7651 (tppt) REVERT: A 570 ASP cc_start: 0.8148 (p0) cc_final: 0.7893 (p0) REVERT: B 129 LYS cc_start: 0.7071 (mttt) cc_final: 0.6860 (mttt) REVERT: B 177 MET cc_start: -0.0463 (tpp) cc_final: -0.1712 (mtm) REVERT: B 515 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.7919 (p90) REVERT: B 1029 MET cc_start: 0.9295 (tpp) cc_final: 0.8916 (tpp) REVERT: C 238 PHE cc_start: 0.8596 (p90) cc_final: 0.8394 (p90) REVERT: C 342 PHE cc_start: 0.6241 (OUTLIER) cc_final: 0.5420 (t80) REVERT: C 378 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7622 (ttmt) REVERT: C 519 HIS cc_start: 0.6161 (OUTLIER) cc_final: 0.5898 (m90) REVERT: C 529 LYS cc_start: 0.6765 (mmmt) cc_final: 0.6548 (mmmt) REVERT: C 904 TYR cc_start: 0.7621 (m-10) cc_final: 0.7096 (m-10) outliers start: 44 outliers final: 26 residues processed: 170 average time/residue: 0.1559 time to fit residues: 43.9355 Evaluate side-chains 158 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 174 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 301 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 57 optimal weight: 0.2980 chunk 81 optimal weight: 0.9990 chunk 238 optimal weight: 4.9990 chunk 148 optimal weight: 9.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.108191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.078782 restraints weight = 65910.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.077283 restraints weight = 43676.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.077940 restraints weight = 53596.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.078150 restraints weight = 38163.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.078786 restraints weight = 33171.614| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26046 Z= 0.115 Angle : 0.600 13.107 35500 Z= 0.301 Chirality : 0.044 0.303 4088 Planarity : 0.004 0.063 4537 Dihedral : 5.532 57.653 4073 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.83 % Allowed : 11.84 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.14), residues: 3150 helix: -0.02 (0.20), residues: 663 sheet: -0.73 (0.20), residues: 633 loop : -2.17 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 983 TYR 0.014 0.001 TYR C 204 PHE 0.019 0.001 PHE A 456 TRP 0.013 0.001 TRP B 436 HIS 0.005 0.001 HIS C1118 Details of bonding type rmsd covalent geometry : bond 0.00259 (25973) covalent geometry : angle 0.58807 (35323) SS BOND : bond 0.00325 ( 42) SS BOND : angle 1.35902 ( 84) hydrogen bonds : bond 0.04283 ( 837) hydrogen bonds : angle 5.48825 ( 2283) link_NAG-ASN : bond 0.00331 ( 31) link_NAG-ASN : angle 2.05150 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 149 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7358 (m-80) cc_final: 0.6467 (m-10) REVERT: A 529 LYS cc_start: 0.7901 (tppt) cc_final: 0.7565 (tppt) REVERT: A 570 ASP cc_start: 0.8174 (p0) cc_final: 0.7696 (p0) REVERT: A 878 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8974 (mp) REVERT: B 177 MET cc_start: -0.0795 (tpp) cc_final: -0.2157 (mtm) REVERT: B 515 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.7773 (p90) REVERT: B 1029 MET cc_start: 0.9323 (tpp) cc_final: 0.8951 (tpp) REVERT: C 21 ARG cc_start: 0.3833 (OUTLIER) cc_final: 0.3595 (mtt180) REVERT: C 238 PHE cc_start: 0.8515 (p90) cc_final: 0.7989 (p90) REVERT: C 327 VAL cc_start: 0.9148 (OUTLIER) cc_final: 0.8918 (t) REVERT: C 378 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7589 (ttmt) REVERT: C 773 GLU cc_start: 0.7536 (tp30) cc_final: 0.7226 (tp30) REVERT: C 858 LEU cc_start: 0.9185 (mp) cc_final: 0.8646 (pp) REVERT: C 904 TYR cc_start: 0.7460 (m-10) cc_final: 0.7054 (m-10) outliers start: 51 outliers final: 29 residues processed: 192 average time/residue: 0.1593 time to fit residues: 50.0783 Evaluate side-chains 161 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1066 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 241 optimal weight: 0.8980 chunk 8 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 3 optimal weight: 0.0980 chunk 99 optimal weight: 3.9990 chunk 273 optimal weight: 4.9990 chunk 311 optimal weight: 0.8980 chunk 250 optimal weight: 0.0030 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 144 optimal weight: 7.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 859 ASN C 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.108141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.078826 restraints weight = 66057.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.077192 restraints weight = 43979.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.077875 restraints weight = 54863.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.078081 restraints weight = 38863.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.078738 restraints weight = 33670.413| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26046 Z= 0.119 Angle : 0.583 11.129 35500 Z= 0.292 Chirality : 0.044 0.280 4088 Planarity : 0.004 0.063 4537 Dihedral : 5.344 58.234 4071 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.01 % Allowed : 13.02 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.14), residues: 3150 helix: 0.25 (0.20), residues: 652 sheet: -0.62 (0.19), residues: 644 loop : -2.10 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 983 TYR 0.039 0.001 TYR A 473 PHE 0.026 0.001 PHE A 456 TRP 0.042 0.001 TRP B 436 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00270 (25973) covalent geometry : angle 0.57322 (35323) SS BOND : bond 0.00281 ( 42) SS BOND : angle 1.15527 ( 84) hydrogen bonds : bond 0.04095 ( 837) hydrogen bonds : angle 5.31030 ( 2283) link_NAG-ASN : bond 0.00289 ( 31) link_NAG-ASN : angle 1.96242 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 146 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7326 (m-80) cc_final: 0.6447 (m-10) REVERT: A 158 ARG cc_start: 0.6986 (ttm110) cc_final: 0.6596 (tpp80) REVERT: A 529 LYS cc_start: 0.7836 (tppt) cc_final: 0.7537 (tppt) REVERT: A 570 ASP cc_start: 0.8181 (p0) cc_final: 0.7656 (p0) REVERT: B 118 LEU cc_start: 0.9105 (tt) cc_final: 0.8375 (mp) REVERT: B 177 MET cc_start: -0.0854 (tpp) cc_final: -0.2170 (mtm) REVERT: B 324 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8143 (pm20) REVERT: B 515 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.7768 (p90) REVERT: B 1029 MET cc_start: 0.9348 (tpp) cc_final: 0.9031 (tpp) REVERT: C 238 PHE cc_start: 0.8542 (p90) cc_final: 0.8041 (p90) REVERT: C 327 VAL cc_start: 0.9118 (OUTLIER) cc_final: 0.8903 (t) REVERT: C 378 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7397 (ttmt) REVERT: C 773 GLU cc_start: 0.7659 (tp30) cc_final: 0.7398 (tp30) REVERT: C 904 TYR cc_start: 0.7433 (m-10) cc_final: 0.7034 (m-10) REVERT: C 974 SER cc_start: 0.8724 (OUTLIER) cc_final: 0.8419 (m) outliers start: 56 outliers final: 36 residues processed: 193 average time/residue: 0.1583 time to fit residues: 50.2248 Evaluate side-chains 170 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 129 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 52 optimal weight: 3.9990 chunk 252 optimal weight: 8.9990 chunk 291 optimal weight: 3.9990 chunk 300 optimal weight: 3.9990 chunk 271 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 126 optimal weight: 6.9990 chunk 213 optimal weight: 3.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN B 859 ASN C 81 ASN C 774 GLN C 872 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.104734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.069372 restraints weight = 66784.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.071256 restraints weight = 39646.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.072513 restraints weight = 28133.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.073349 restraints weight = 22552.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.073781 restraints weight = 19572.924| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 26046 Z= 0.279 Angle : 0.705 10.698 35500 Z= 0.359 Chirality : 0.047 0.275 4088 Planarity : 0.005 0.064 4537 Dihedral : 5.955 59.555 4071 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.84 % Favored : 92.10 % Rotamer: Outliers : 2.62 % Allowed : 14.10 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.14), residues: 3150 helix: -0.11 (0.20), residues: 654 sheet: -0.85 (0.19), residues: 652 loop : -2.22 (0.13), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 983 TYR 0.028 0.002 TYR A 473 PHE 0.034 0.002 PHE C 133 TRP 0.013 0.002 TRP B 436 HIS 0.006 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00652 (25973) covalent geometry : angle 0.69411 (35323) SS BOND : bond 0.00356 ( 42) SS BOND : angle 1.40765 ( 84) hydrogen bonds : bond 0.05562 ( 837) hydrogen bonds : angle 5.76496 ( 2283) link_NAG-ASN : bond 0.00329 ( 31) link_NAG-ASN : angle 2.25321 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 126 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7284 (m-80) cc_final: 0.6181 (m-10) REVERT: A 135 PHE cc_start: 0.8140 (m-80) cc_final: 0.7470 (m-80) REVERT: A 392 PHE cc_start: 0.6858 (m-10) cc_final: 0.6382 (m-10) REVERT: A 570 ASP cc_start: 0.8084 (p0) cc_final: 0.7572 (p0) REVERT: A 878 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9149 (mp) REVERT: A 1031 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: B 118 LEU cc_start: 0.9092 (tt) cc_final: 0.8353 (mp) REVERT: B 177 MET cc_start: -0.0618 (tpp) cc_final: -0.1973 (mtm) REVERT: B 324 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7932 (pm20) REVERT: B 396 TYR cc_start: 0.7890 (m-80) cc_final: 0.7282 (m-80) REVERT: B 515 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.7961 (p90) REVERT: B 1029 MET cc_start: 0.9390 (tpp) cc_final: 0.9018 (tpp) REVERT: C 21 ARG cc_start: 0.3980 (OUTLIER) cc_final: 0.3617 (mtt180) REVERT: C 238 PHE cc_start: 0.8695 (p90) cc_final: 0.8271 (p90) REVERT: C 315 THR cc_start: 0.8610 (p) cc_final: 0.8398 (p) REVERT: C 378 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7658 (ttmt) REVERT: C 455 LEU cc_start: 0.8119 (tp) cc_final: 0.7612 (mp) REVERT: C 904 TYR cc_start: 0.7683 (m-10) cc_final: 0.7269 (m-10) outliers start: 73 outliers final: 47 residues processed: 189 average time/residue: 0.1515 time to fit residues: 48.1285 Evaluate side-chains 173 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 120 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 249 optimal weight: 7.9990 chunk 239 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 46 optimal weight: 0.0980 chunk 230 optimal weight: 2.9990 chunk 305 optimal weight: 0.8980 chunk 121 optimal weight: 9.9990 chunk 139 optimal weight: 9.9990 chunk 140 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B 859 ASN C 872 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.106798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.076994 restraints weight = 65994.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.076020 restraints weight = 43768.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.076539 restraints weight = 51975.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.076946 restraints weight = 36046.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.077476 restraints weight = 31624.023| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26046 Z= 0.135 Angle : 0.601 10.964 35500 Z= 0.303 Chirality : 0.044 0.285 4088 Planarity : 0.004 0.065 4537 Dihedral : 5.572 58.698 4071 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.08 % Allowed : 15.46 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.14), residues: 3150 helix: 0.21 (0.20), residues: 651 sheet: -0.67 (0.19), residues: 649 loop : -2.11 (0.13), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 983 TYR 0.014 0.001 TYR C 204 PHE 0.023 0.001 PHE C1052 TRP 0.049 0.002 TRP B 436 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00309 (25973) covalent geometry : angle 0.58952 (35323) SS BOND : bond 0.00300 ( 42) SS BOND : angle 1.26053 ( 84) hydrogen bonds : bond 0.04471 ( 837) hydrogen bonds : angle 5.42286 ( 2283) link_NAG-ASN : bond 0.00302 ( 31) link_NAG-ASN : angle 2.06764 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 132 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7387 (m-80) cc_final: 0.6074 (m-10) REVERT: A 135 PHE cc_start: 0.8074 (m-80) cc_final: 0.7377 (m-80) REVERT: A 158 ARG cc_start: 0.6973 (tpp-160) cc_final: 0.6378 (tpp80) REVERT: A 392 PHE cc_start: 0.6670 (m-10) cc_final: 0.6247 (m-10) REVERT: A 570 ASP cc_start: 0.8180 (p0) cc_final: 0.7641 (p0) REVERT: A 878 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9028 (mp) REVERT: A 1031 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: B 118 LEU cc_start: 0.9122 (tt) cc_final: 0.8457 (mp) REVERT: B 324 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8012 (pm20) REVERT: B 396 TYR cc_start: 0.7908 (m-80) cc_final: 0.7399 (m-80) REVERT: B 515 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.7783 (p90) REVERT: B 1029 MET cc_start: 0.9262 (tpp) cc_final: 0.8979 (tpp) REVERT: C 238 PHE cc_start: 0.8660 (p90) cc_final: 0.8107 (p90) REVERT: C 455 LEU cc_start: 0.8082 (tp) cc_final: 0.7619 (mp) REVERT: C 773 GLU cc_start: 0.7543 (tp30) cc_final: 0.7297 (tp30) REVERT: C 904 TYR cc_start: 0.7548 (m-10) cc_final: 0.7138 (m-10) REVERT: C 974 SER cc_start: 0.8704 (m) cc_final: 0.8420 (m) outliers start: 58 outliers final: 40 residues processed: 184 average time/residue: 0.1591 time to fit residues: 48.8356 Evaluate side-chains 166 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 122 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 238 optimal weight: 4.9990 chunk 72 optimal weight: 0.0050 chunk 55 optimal weight: 6.9990 chunk 224 optimal weight: 10.0000 chunk 193 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 156 optimal weight: 0.5980 overall best weight: 2.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.105698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.069354 restraints weight = 67020.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.071344 restraints weight = 38734.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.072665 restraints weight = 27143.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.073461 restraints weight = 21630.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.074049 restraints weight = 18770.259| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 26046 Z= 0.189 Angle : 0.622 10.957 35500 Z= 0.316 Chirality : 0.045 0.276 4088 Planarity : 0.004 0.064 4537 Dihedral : 5.640 58.893 4071 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.22 % Allowed : 15.50 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.14), residues: 3150 helix: 0.19 (0.20), residues: 647 sheet: -0.71 (0.19), residues: 647 loop : -2.08 (0.13), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 983 TYR 0.025 0.001 TYR A 473 PHE 0.020 0.002 PHE C1052 TRP 0.032 0.001 TRP B 436 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00443 (25973) covalent geometry : angle 0.61092 (35323) SS BOND : bond 0.00347 ( 42) SS BOND : angle 1.31815 ( 84) hydrogen bonds : bond 0.04691 ( 837) hydrogen bonds : angle 5.46480 ( 2283) link_NAG-ASN : bond 0.00292 ( 31) link_NAG-ASN : angle 2.09065 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 125 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7412 (m-80) cc_final: 0.6101 (m-10) REVERT: A 135 PHE cc_start: 0.8150 (m-80) cc_final: 0.7432 (m-80) REVERT: A 158 ARG cc_start: 0.6941 (tpp-160) cc_final: 0.6344 (tpp80) REVERT: A 392 PHE cc_start: 0.6877 (m-10) cc_final: 0.6407 (m-10) REVERT: A 570 ASP cc_start: 0.8104 (p0) cc_final: 0.7544 (p0) REVERT: A 878 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9069 (mp) REVERT: A 1031 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: B 118 LEU cc_start: 0.9086 (tt) cc_final: 0.8392 (mp) REVERT: B 324 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7972 (pm20) REVERT: B 396 TYR cc_start: 0.7893 (m-80) cc_final: 0.7295 (m-80) REVERT: B 515 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.7821 (p90) REVERT: B 1029 MET cc_start: 0.9383 (tpp) cc_final: 0.9024 (tpp) REVERT: C 238 PHE cc_start: 0.8772 (p90) cc_final: 0.8141 (p90) REVERT: C 455 LEU cc_start: 0.8118 (tp) cc_final: 0.7654 (mp) REVERT: C 773 GLU cc_start: 0.7647 (tp30) cc_final: 0.7403 (tp30) REVERT: C 904 TYR cc_start: 0.7645 (m-10) cc_final: 0.7215 (m-10) REVERT: C 974 SER cc_start: 0.8737 (OUTLIER) cc_final: 0.8429 (m) outliers start: 62 outliers final: 46 residues processed: 178 average time/residue: 0.1490 time to fit residues: 44.3566 Evaluate side-chains 174 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 123 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 44 optimal weight: 2.9990 chunk 278 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 249 optimal weight: 7.9990 chunk 258 optimal weight: 4.9990 chunk 302 optimal weight: 3.9990 chunk 317 optimal weight: 0.0010 chunk 276 optimal weight: 2.9990 chunk 226 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.106419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.070029 restraints weight = 66991.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.072031 restraints weight = 38532.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.073309 restraints weight = 27034.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.074138 restraints weight = 21548.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.074717 restraints weight = 18785.363| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 26046 Z= 0.153 Angle : 0.609 10.968 35500 Z= 0.307 Chirality : 0.045 0.279 4088 Planarity : 0.004 0.077 4537 Dihedral : 5.553 58.312 4071 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.15 % Allowed : 15.68 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.14), residues: 3150 helix: 0.31 (0.20), residues: 648 sheet: -0.61 (0.19), residues: 677 loop : -2.02 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 983 TYR 0.039 0.001 TYR A 473 PHE 0.024 0.001 PHE C 133 TRP 0.029 0.001 TRP B 436 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00358 (25973) covalent geometry : angle 0.59681 (35323) SS BOND : bond 0.00321 ( 42) SS BOND : angle 1.58542 ( 84) hydrogen bonds : bond 0.04389 ( 837) hydrogen bonds : angle 5.38858 ( 2283) link_NAG-ASN : bond 0.00329 ( 31) link_NAG-ASN : angle 2.05066 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 127 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7261 (m-80) cc_final: 0.5963 (m-10) REVERT: A 135 PHE cc_start: 0.8077 (m-80) cc_final: 0.7417 (m-80) REVERT: A 158 ARG cc_start: 0.6955 (tpp-160) cc_final: 0.6391 (tpp80) REVERT: A 392 PHE cc_start: 0.6859 (m-10) cc_final: 0.6387 (m-10) REVERT: A 421 TYR cc_start: 0.3923 (m-80) cc_final: 0.3497 (m-10) REVERT: A 570 ASP cc_start: 0.8129 (p0) cc_final: 0.7589 (p0) REVERT: A 878 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.9045 (mp) REVERT: A 1031 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: B 118 LEU cc_start: 0.9046 (tt) cc_final: 0.8404 (mp) REVERT: B 177 MET cc_start: -0.2754 (mtm) cc_final: -0.3195 (tpp) REVERT: B 324 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7930 (pm20) REVERT: B 396 TYR cc_start: 0.7859 (m-80) cc_final: 0.7256 (m-80) REVERT: B 515 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.7665 (p90) REVERT: B 1029 MET cc_start: 0.9370 (tpp) cc_final: 0.9030 (tpp) REVERT: C 238 PHE cc_start: 0.8754 (p90) cc_final: 0.8137 (p90) REVERT: C 773 GLU cc_start: 0.7607 (tp30) cc_final: 0.7346 (tp30) REVERT: C 904 TYR cc_start: 0.7661 (m-10) cc_final: 0.7257 (m-10) REVERT: C 974 SER cc_start: 0.8696 (m) cc_final: 0.8395 (m) outliers start: 60 outliers final: 45 residues processed: 176 average time/residue: 0.1558 time to fit residues: 45.8411 Evaluate side-chains 173 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 124 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 248 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 292 optimal weight: 3.9990 chunk 287 optimal weight: 0.9990 chunk 281 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 250 optimal weight: 8.9990 chunk 243 optimal weight: 0.4980 chunk 167 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.106337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.069911 restraints weight = 66552.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.071990 restraints weight = 37532.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.073368 restraints weight = 25986.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.074115 restraints weight = 20529.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.074772 restraints weight = 17847.204| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26046 Z= 0.158 Angle : 0.612 10.886 35500 Z= 0.308 Chirality : 0.044 0.275 4088 Planarity : 0.004 0.064 4537 Dihedral : 5.525 58.623 4071 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 1.76 % Allowed : 16.11 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.14), residues: 3150 helix: 0.33 (0.20), residues: 655 sheet: -0.60 (0.19), residues: 675 loop : -2.00 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 983 TYR 0.036 0.001 TYR A 421 PHE 0.032 0.001 PHE C 429 TRP 0.026 0.001 TRP B 436 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00370 (25973) covalent geometry : angle 0.59918 (35323) SS BOND : bond 0.00330 ( 42) SS BOND : angle 1.60300 ( 84) hydrogen bonds : bond 0.04359 ( 837) hydrogen bonds : angle 5.35042 ( 2283) link_NAG-ASN : bond 0.00293 ( 31) link_NAG-ASN : angle 2.04342 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 129 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7249 (m-80) cc_final: 0.6246 (m-10) REVERT: A 158 ARG cc_start: 0.7000 (tpp-160) cc_final: 0.6424 (tpp80) REVERT: A 392 PHE cc_start: 0.6863 (m-10) cc_final: 0.6396 (m-10) REVERT: A 421 TYR cc_start: 0.3845 (m-80) cc_final: 0.3628 (m-10) REVERT: A 570 ASP cc_start: 0.8152 (p0) cc_final: 0.7625 (p0) REVERT: A 878 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9027 (mp) REVERT: A 1031 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: B 118 LEU cc_start: 0.9065 (tt) cc_final: 0.8444 (mp) REVERT: B 177 MET cc_start: -0.2918 (mtm) cc_final: -0.3416 (tpp) REVERT: B 324 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7938 (pm20) REVERT: B 396 TYR cc_start: 0.7905 (m-80) cc_final: 0.7301 (m-80) REVERT: B 515 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.7697 (p90) REVERT: B 1029 MET cc_start: 0.9381 (tpp) cc_final: 0.9056 (tpp) REVERT: C 21 ARG cc_start: 0.3370 (OUTLIER) cc_final: 0.3040 (mtt180) REVERT: C 238 PHE cc_start: 0.8755 (p90) cc_final: 0.8168 (p90) REVERT: C 773 GLU cc_start: 0.7664 (tp30) cc_final: 0.7393 (tp30) REVERT: C 904 TYR cc_start: 0.7649 (m-10) cc_final: 0.7232 (m-10) REVERT: C 974 SER cc_start: 0.8709 (m) cc_final: 0.8416 (m) outliers start: 49 outliers final: 43 residues processed: 170 average time/residue: 0.1607 time to fit residues: 45.5492 Evaluate side-chains 174 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 126 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 305 optimal weight: 3.9990 chunk 226 optimal weight: 8.9990 chunk 142 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 197 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 38 optimal weight: 0.0020 chunk 75 optimal weight: 0.7980 chunk 238 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 overall best weight: 1.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1106 GLN C 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.107085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.070775 restraints weight = 66546.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.072801 restraints weight = 38035.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.074156 restraints weight = 26537.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.074981 restraints weight = 21092.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.075527 restraints weight = 18270.975| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26046 Z= 0.134 Angle : 0.596 10.912 35500 Z= 0.299 Chirality : 0.044 0.275 4088 Planarity : 0.004 0.064 4537 Dihedral : 5.390 58.213 4071 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.97 % Allowed : 16.29 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.14), residues: 3150 helix: 0.49 (0.21), residues: 656 sheet: -0.51 (0.19), residues: 672 loop : -1.97 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 983 TYR 0.026 0.001 TYR A 421 PHE 0.024 0.001 PHE A 456 TRP 0.026 0.001 TRP B 436 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00313 (25973) covalent geometry : angle 0.58380 (35323) SS BOND : bond 0.00356 ( 42) SS BOND : angle 1.50517 ( 84) hydrogen bonds : bond 0.04076 ( 837) hydrogen bonds : angle 5.24860 ( 2283) link_NAG-ASN : bond 0.00308 ( 31) link_NAG-ASN : angle 2.00085 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3824.96 seconds wall clock time: 67 minutes 8.90 seconds (4028.90 seconds total)