Starting phenix.real_space_refine on Sun Jul 5 04:43:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vhn_32000/07_2026/7vhn_32000.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vhn_32000/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7vhn_32000/07_2026/7vhn_32000.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vhn_32000/07_2026/7vhn_32000.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7vhn_32000/07_2026/7vhn_32000.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vhn_32000/07_2026/7vhn_32000.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vhn_32000/07_2026/7vhn_32000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vhn_32000/07_2026/7vhn_32000.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 chiralities: 10 Time building chain proxies: 4.47, per 1000 atoms: 0.18 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: 2.18 Conformation dependent library (CDL) restraints added in 845.9 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: 0.91 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: 5.19 Time building geometry restraints manager: 2.90 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: 13759 17.83 - 35.66: 1224 35.66 - 53.49: 207 53.49 - 71.32: 29 71.32 - 89.15: 18 Dihedral angle restraints: 15237 sinusoidal: 5952 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 15234 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: 2.080 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: 0.290 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 21.900 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 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 : 13.640 89.150 9135 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/Z covalent geometry : bond 0.00607 / 0.36 (25973) covalent geometry : angle 0.84573 / 0.52 (35323) SS BOND : bond 0.00426 / 0.27 ( 42) SS BOND : angle 1.44841 / 1.05 ( 84) hydrogen bonds : bond 0.21830 / 14.03 ( 837) hydrogen bonds : angle 8.83993 / 6.05 ( 2283) link_NAG-ASN : bond 0.01499 / 0.93 ( 31) link_NAG-ASN : angle 5.23912 / 3.52 ( 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 : 0.998 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: 0.1613 time to fit residues: 54.1218 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 : 0.787 ------------------------------------------------------------------------------- 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... 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 = 0.108547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.078957 restraints weight = 66422.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.078052 restraints weight = 42553.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.078486 restraints weight = 51982.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.078969 restraints weight = 34951.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.079683 restraints weight = 30209.252| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26046 Z= 0.131 Angle : 0.661 11.286 35500 Z= 0.334 Chirality : 0.046 0.340 4088 Planarity : 0.004 0.051 4537 Dihedral : 5.522 57.519 3427 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.93 % Allowed : 6.96 % Favored : 92.11 % 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: -2.35 (0.14), residues: 3150 helix: -0.46 (0.20), residues: 651 sheet: -0.88 (0.19), residues: 642 loop : -2.33 (0.13), residues: 1857 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/Z covalent geometry : bond 0.00280 / 0.13 (25973) covalent geometry : angle 0.64675 / 0.33 (35323) SS BOND : bond 0.00339 / 0.24 ( 42) SS BOND : angle 1.39951 / 1.04 ( 84) hydrogen bonds : bond 0.05334 / 3.42 ( 837) hydrogen bonds : angle 6.19712 / 4.25 ( 2283) link_NAG-ASN : bond 0.00498 / 0.27 ( 31) link_NAG-ASN : angle 2.52544 / 1.72 ( 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 185 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 1.054 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: 0.7311 (m-10) cc_final: 0.6128 (m-10) REVERT: A 135 PHE cc_start: 0.7976 (m-80) cc_final: 0.7258 (m-80) REVERT: A 529 LYS cc_start: 0.7906 (tppt) cc_final: 0.7572 (tppt) REVERT: A 570 ASP cc_start: 0.8013 (p0) cc_final: 0.7622 (p0) REVERT: B 118 LEU cc_start: 0.8873 (tt) cc_final: 0.8232 (mp) REVERT: B 129 LYS cc_start: 0.7207 (mttt) cc_final: 0.6851 (mttt) REVERT: B 177 MET cc_start: -0.0460 (tpp) cc_final: -0.2147 (mtm) REVERT: B 1029 MET cc_start: 0.9345 (tpp) cc_final: 0.8999 (tpp) REVERT: C 238 PHE cc_start: 0.8449 (p90) cc_final: 0.7949 (p90) REVERT: C 327 VAL cc_start: 0.9277 (OUTLIER) cc_final: 0.9060 (t) REVERT: C 529 LYS cc_start: 0.6666 (mmmt) cc_final: 0.6378 (mmmt) REVERT: C 904 TYR cc_start: 0.7548 (m-10) cc_final: 0.7026 (m-10) outliers start: 26 outliers final: 18 residues processed: 179 average time/residue: 0.1554 time to fit residues: 46.6062 Evaluate side-chains 149 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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 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: 0.0050 chunk 37 optimal weight: 7.9990 chunk 312 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 176 optimal weight: 4.9990 chunk 69 optimal weight: 0.3980 chunk 166 optimal weight: 8.9990 chunk 170 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 135 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 overall best weight: 2.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3668 r_free = 0.3668 target = 0.105817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.076246 restraints weight = 66723.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.075031 restraints weight = 45905.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.075335 restraints weight = 59845.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.076089 restraints weight = 38821.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.076819 restraints weight = 32780.837| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 26046 Z= 0.247 Angle : 0.696 11.362 35500 Z= 0.353 Chirality : 0.047 0.275 4088 Planarity : 0.004 0.059 4537 Dihedral : 5.503 57.614 3424 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.43 % Favored : 92.54 % Rotamer: Outliers : 1.47 % Allowed : 10.58 % Favored : 87.94 % 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: -0.42 (0.20), residues: 644 sheet: -1.00 (0.19), residues: 666 loop : -2.30 (0.13), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 509 TYR 0.018 0.002 TYR C 204 PHE 0.024 0.002 PHE C 429 TRP 0.035 0.002 TRP B 436 HIS 0.005 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.25 (25973) covalent geometry : angle 0.68371 / 0.35 (35323) SS BOND : bond 0.00535 / 0.46 ( 42) SS BOND : angle 1.51509 / 1.08 ( 84) hydrogen bonds : bond 0.05615 / 3.60 ( 837) hydrogen bonds : angle 6.02778 / 4.15 ( 2283) link_NAG-ASN : bond 0.00335 / 0.19 ( 31) link_NAG-ASN : angle 2.30681 / 1.59 ( 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 175 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.8166 (m-80) cc_final: 0.7534 (m-80) REVERT: A 570 ASP cc_start: 0.8134 (p0) cc_final: 0.7879 (p0) REVERT: B 129 LYS cc_start: 0.7072 (mttt) cc_final: 0.6866 (mttt) REVERT: B 177 MET cc_start: -0.0470 (tpp) cc_final: -0.1719 (mtm) REVERT: B 515 PHE cc_start: 0.8651 (OUTLIER) cc_final: 0.7907 (p90) REVERT: B 1029 MET cc_start: 0.9296 (tpp) cc_final: 0.8939 (tpp) REVERT: C 238 PHE cc_start: 0.8589 (p90) cc_final: 0.8385 (p90) REVERT: C 342 PHE cc_start: 0.6195 (OUTLIER) cc_final: 0.5368 (t80) REVERT: C 378 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7619 (ttmt) REVERT: C 519 HIS cc_start: 0.6144 (OUTLIER) cc_final: 0.5885 (m90) REVERT: C 904 TYR cc_start: 0.7585 (m-10) cc_final: 0.7064 (m-10) outliers start: 41 outliers final: 23 residues processed: 165 average time/residue: 0.1620 time to fit residues: 44.5505 Evaluate side-chains 153 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 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 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 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: 5.9990 chunk 301 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 166 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 238 optimal weight: 4.9990 chunk 148 optimal weight: 10.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.106662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.076922 restraints weight = 65997.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.075976 restraints weight = 43432.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.076498 restraints weight = 52050.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.076955 restraints weight = 36031.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.077424 restraints weight = 31574.879| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26046 Z= 0.180 Angle : 0.639 12.706 35500 Z= 0.322 Chirality : 0.045 0.282 4088 Planarity : 0.004 0.063 4537 Dihedral : 5.272 57.420 3422 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.22 % Allowed : 12.20 % Favored : 85.58 % 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: -2.17 (0.14), residues: 3150 helix: -0.17 (0.20), residues: 655 sheet: -0.87 (0.19), residues: 653 loop : -2.23 (0.13), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 983 TYR 0.016 0.001 TYR C 204 PHE 0.020 0.002 PHE A 456 TRP 0.011 0.001 TRP B 436 HIS 0.004 0.001 HIS C1118 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (25973) covalent geometry : angle 0.62770 / 0.32 (35323) SS BOND : bond 0.00342 / 0.22 ( 42) SS BOND : angle 1.43306 / 1.06 ( 84) hydrogen bonds : bond 0.04861 / 3.12 ( 837) hydrogen bonds : angle 5.69599 / 3.92 ( 2283) link_NAG-ASN : bond 0.00285 / 0.15 ( 31) link_NAG-ASN : angle 2.13377 / 1.47 ( 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 197 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 135 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.8099 (m-80) cc_final: 0.7463 (m-80) REVERT: A 570 ASP cc_start: 0.8170 (p0) cc_final: 0.7729 (p0) REVERT: A 878 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9055 (mp) REVERT: B 177 MET cc_start: -0.0684 (tpp) cc_final: -0.1909 (mtm) REVERT: B 515 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.7884 (p90) REVERT: B 1029 MET cc_start: 0.9333 (tpp) cc_final: 0.8994 (tpp) REVERT: C 21 ARG cc_start: 0.3948 (OUTLIER) cc_final: 0.3593 (mtt180) REVERT: C 238 PHE cc_start: 0.8586 (p90) cc_final: 0.8295 (p90) REVERT: C 327 VAL cc_start: 0.9157 (OUTLIER) cc_final: 0.8945 (t) REVERT: C 342 PHE cc_start: 0.6204 (OUTLIER) cc_final: 0.5377 (t80) REVERT: C 519 HIS cc_start: 0.6173 (OUTLIER) cc_final: 0.5960 (m90) REVERT: C 858 LEU cc_start: 0.9254 (mp) cc_final: 0.8707 (pp) REVERT: C 904 TYR cc_start: 0.7604 (m-10) cc_final: 0.7174 (m-10) outliers start: 62 outliers final: 40 residues processed: 189 average time/residue: 0.1633 time to fit residues: 51.4698 Evaluate side-chains 170 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 124 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 716 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1104 VAL 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 350 VAL 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 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 131 CYS 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 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 362 VAL 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 519 HIS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 719 THR 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 241 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 chunk 99 optimal weight: 3.9990 chunk 273 optimal weight: 5.9990 chunk 311 optimal weight: 2.9990 chunk 250 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 422 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 = 0.3665 r_free = 0.3665 target = 0.105508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.075645 restraints weight = 66205.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.074684 restraints weight = 44651.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.075195 restraints weight = 53882.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.075653 restraints weight = 36933.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.076154 restraints weight = 32271.638| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 26046 Z= 0.229 Angle : 0.667 13.097 35500 Z= 0.336 Chirality : 0.046 0.270 4088 Planarity : 0.004 0.065 4537 Dihedral : 5.327 57.449 3422 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.59 % Favored : 92.38 % Rotamer: Outliers : 2.40 % Allowed : 13.56 % Favored : 84.03 % 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: -2.20 (0.14), residues: 3150 helix: -0.16 (0.20), residues: 649 sheet: -0.89 (0.19), residues: 648 loop : -2.26 (0.13), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 983 TYR 0.035 0.001 TYR A 473 PHE 0.025 0.002 PHE A 456 TRP 0.031 0.002 TRP B 436 HIS 0.004 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.23 (25973) covalent geometry : angle 0.65524 / 0.33 (35323) SS BOND : bond 0.00351 / 0.23 ( 42) SS BOND : angle 1.36594 / 1.00 ( 84) hydrogen bonds : bond 0.05126 / 3.30 ( 837) hydrogen bonds : angle 5.72817 / 3.95 ( 2283) link_NAG-ASN : bond 0.00294 / 0.17 ( 31) link_NAG-ASN : angle 2.20908 / 1.52 ( 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 200 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 133 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.8161 (m-80) cc_final: 0.7530 (m-80) REVERT: A 570 ASP cc_start: 0.8171 (p0) cc_final: 0.7675 (p0) REVERT: A 878 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9067 (mp) REVERT: B 118 LEU cc_start: 0.9048 (tt) cc_final: 0.8308 (mp) REVERT: B 324 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8049 (pm20) REVERT: B 515 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8076 (p90) REVERT: B 1029 MET cc_start: 0.9285 (tpp) cc_final: 0.8980 (tpp) REVERT: C 21 ARG cc_start: 0.4027 (OUTLIER) cc_final: 0.3620 (mtt180) REVERT: C 238 PHE cc_start: 0.8637 (p90) cc_final: 0.8290 (p90) REVERT: C 327 VAL cc_start: 0.9161 (OUTLIER) cc_final: 0.8946 (t) REVERT: C 378 LYS cc_start: 0.8701 (tppt) cc_final: 0.8342 (ttmt) REVERT: C 455 LEU cc_start: 0.8091 (tp) cc_final: 0.7566 (mp) REVERT: C 519 HIS cc_start: 0.6227 (OUTLIER) cc_final: 0.6003 (m90) REVERT: C 904 TYR cc_start: 0.7680 (m-10) cc_final: 0.7192 (m-10) outliers start: 67 outliers final: 43 residues processed: 191 average time/residue: 0.1609 time to fit residues: 51.2211 Evaluate side-chains 170 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 121 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 1104 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 95 THR 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 267 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 350 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 569 ILE Chi-restraints excluded: chain B residue 595 VAL 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 131 CYS 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 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 500 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 719 THR 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 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 52 optimal weight: 0.8980 chunk 252 optimal weight: 9.9990 chunk 291 optimal weight: 1.9990 chunk 300 optimal weight: 1.9990 chunk 271 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.106673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.076654 restraints weight = 66652.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.075736 restraints weight = 44775.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.076154 restraints weight = 54072.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.076668 restraints weight = 36899.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.077231 restraints weight = 32179.353| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26046 Z= 0.150 Angle : 0.614 11.068 35500 Z= 0.309 Chirality : 0.044 0.273 4088 Planarity : 0.004 0.064 4537 Dihedral : 5.067 57.205 3420 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.58 % Allowed : 14.28 % Favored : 83.14 % 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: -2.02 (0.14), residues: 3150 helix: 0.01 (0.20), residues: 663 sheet: -0.76 (0.19), residues: 647 loop : -2.17 (0.13), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 983 TYR 0.032 0.001 TYR A 473 PHE 0.027 0.001 PHE C 133 TRP 0.053 0.002 TRP B 436 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (25973) covalent geometry : angle 0.60289 / 0.31 (35323) SS BOND : bond 0.00347 / 0.23 ( 42) SS BOND : angle 1.33458 / 1.00 ( 84) hydrogen bonds : bond 0.04505 / 2.90 ( 837) hydrogen bonds : angle 5.47614 / 3.78 ( 2283) link_NAG-ASN : bond 0.00307 / 0.17 ( 31) link_NAG-ASN : angle 2.09186 / 1.44 ( 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 211 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 139 time to evaluate : 0.970 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: 0.7386 (m-80) cc_final: 0.6191 (m-10) REVERT: A 135 PHE cc_start: 0.8109 (m-80) cc_final: 0.7465 (m-80) REVERT: A 570 ASP cc_start: 0.8174 (p0) cc_final: 0.7641 (p0) REVERT: A 878 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9020 (mp) REVERT: A 1031 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: B 118 LEU cc_start: 0.9055 (tt) cc_final: 0.8366 (mp) REVERT: B 324 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8048 (pm20) REVERT: B 396 TYR cc_start: 0.7915 (m-80) cc_final: 0.7410 (m-80) REVERT: B 515 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.7980 (p90) REVERT: B 1029 MET cc_start: 0.9257 (tpp) cc_final: 0.8970 (tpp) REVERT: C 238 PHE cc_start: 0.8643 (p90) cc_final: 0.8090 (p90) REVERT: C 327 VAL cc_start: 0.9137 (OUTLIER) cc_final: 0.8919 (t) REVERT: C 378 LYS cc_start: 0.8735 (tppt) cc_final: 0.8256 (ttmt) REVERT: C 455 LEU cc_start: 0.8159 (tp) cc_final: 0.7706 (mp) REVERT: C 519 HIS cc_start: 0.6271 (OUTLIER) cc_final: 0.6056 (m90) REVERT: C 773 GLU cc_start: 0.7539 (tp30) cc_final: 0.7295 (tp30) REVERT: C 904 TYR cc_start: 0.7572 (m-10) cc_final: 0.7173 (m-10) outliers start: 72 outliers final: 45 residues processed: 201 average time/residue: 0.1478 time to fit residues: 49.4475 Evaluate side-chains 181 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 130 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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 724 THR Chi-restraints excluded: chain A residue 878 LEU 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 125 ASN 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 389 ASP 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 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 377 PHE 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 519 HIS 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 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 249 optimal weight: 6.9990 chunk 239 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 230 optimal weight: 9.9990 chunk 305 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 139 optimal weight: 10.0000 chunk 140 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 105 optimal weight: 0.0050 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 859 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.105434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.075446 restraints weight = 66680.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.074601 restraints weight = 44844.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.074965 restraints weight = 54566.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.075502 restraints weight = 37461.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.075936 restraints weight = 32547.174| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 26046 Z= 0.209 Angle : 0.651 10.963 35500 Z= 0.328 Chirality : 0.045 0.264 4088 Planarity : 0.004 0.064 4537 Dihedral : 5.158 56.953 3420 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.51 % Allowed : 15.50 % Favored : 81.99 % 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: -2.04 (0.14), residues: 3150 helix: 0.05 (0.20), residues: 643 sheet: -0.81 (0.19), residues: 651 loop : -2.17 (0.13), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 983 TYR 0.034 0.001 TYR A 473 PHE 0.041 0.002 PHE C 429 TRP 0.068 0.002 TRP B 436 HIS 0.004 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 (25973) covalent geometry : angle 0.63795 / 0.32 (35323) SS BOND : bond 0.00327 / 0.22 ( 42) SS BOND : angle 1.68488 / 1.31 ( 84) hydrogen bonds : bond 0.04898 / 3.15 ( 837) hydrogen bonds : angle 5.56084 / 3.84 ( 2283) link_NAG-ASN : bond 0.00296 / 0.18 ( 31) link_NAG-ASN : angle 2.17585 / 1.49 ( 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 200 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 130 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7421 (m-80) cc_final: 0.6203 (m-10) REVERT: A 135 PHE cc_start: 0.8135 (m-80) cc_final: 0.7524 (m-80) REVERT: A 158 ARG cc_start: 0.7074 (ttm110) cc_final: 0.6757 (mmm-85) REVERT: A 392 PHE cc_start: 0.6740 (m-10) cc_final: 0.6291 (m-10) REVERT: A 570 ASP cc_start: 0.8175 (p0) cc_final: 0.7650 (p0) REVERT: A 878 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9056 (mp) REVERT: A 1031 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: B 118 LEU cc_start: 0.9081 (tt) cc_final: 0.8409 (mp) REVERT: B 177 MET cc_start: -0.2841 (mtm) cc_final: -0.3226 (tpp) REVERT: B 324 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7965 (pm20) REVERT: B 389 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7621 (t0) REVERT: B 396 TYR cc_start: 0.7934 (m-80) cc_final: 0.7443 (m-80) REVERT: B 515 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.8003 (p90) REVERT: B 1029 MET cc_start: 0.9272 (tpp) cc_final: 0.9001 (tpp) REVERT: C 238 PHE cc_start: 0.8677 (p90) cc_final: 0.8244 (p90) REVERT: C 327 VAL cc_start: 0.9162 (OUTLIER) cc_final: 0.8956 (t) REVERT: C 378 LYS cc_start: 0.8794 (tppt) cc_final: 0.8255 (ttmt) REVERT: C 455 LEU cc_start: 0.8113 (tp) cc_final: 0.7638 (mp) REVERT: C 519 HIS cc_start: 0.6197 (OUTLIER) cc_final: 0.5985 (m90) REVERT: C 904 TYR cc_start: 0.7664 (m-10) cc_final: 0.7202 (m-10) outliers start: 70 outliers final: 50 residues processed: 188 average time/residue: 0.1618 time to fit residues: 50.6176 Evaluate side-chains 178 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 121 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 302 THR 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 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 389 ASP 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 595 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 951 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 131 CYS 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 315 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 377 PHE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 519 HIS 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 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: 0.0470 chunk 55 optimal weight: 0.0470 chunk 224 optimal weight: 20.0000 chunk 193 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 133 optimal weight: 0.9980 chunk 156 optimal weight: 0.0670 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 859 ASN B1106 GLN C 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.108176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.077601 restraints weight = 66645.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.076802 restraints weight = 44781.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.077450 restraints weight = 50843.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.077806 restraints weight = 35662.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.078320 restraints weight = 31493.770| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 26046 Z= 0.103 Angle : 0.587 11.174 35500 Z= 0.293 Chirality : 0.044 0.266 4088 Planarity : 0.004 0.065 4537 Dihedral : 4.743 55.642 3420 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.08 % Allowed : 16.15 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.14), residues: 3150 helix: 0.43 (0.21), residues: 649 sheet: -0.64 (0.19), residues: 664 loop : -2.00 (0.14), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 983 TYR 0.032 0.001 TYR A 473 PHE 0.032 0.001 PHE C 429 TRP 0.079 0.002 TRP B 436 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (25973) covalent geometry : angle 0.57527 / 0.29 (35323) SS BOND : bond 0.00308 / 0.21 ( 42) SS BOND : angle 1.45202 / 1.14 ( 84) hydrogen bonds : bond 0.03780 / 2.42 ( 837) hydrogen bonds : angle 5.15985 / 3.56 ( 2283) link_NAG-ASN : bond 0.00393 / 0.24 ( 31) link_NAG-ASN : angle 1.94141 / 1.33 ( 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 204 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 146 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7153 (m-80) cc_final: 0.5948 (m-10) REVERT: A 135 PHE cc_start: 0.8061 (m-80) cc_final: 0.7392 (m-80) REVERT: A 158 ARG cc_start: 0.6943 (ttm110) cc_final: 0.6635 (mmm-85) REVERT: A 392 PHE cc_start: 0.6685 (m-10) cc_final: 0.6245 (m-10) REVERT: A 570 ASP cc_start: 0.8198 (p0) cc_final: 0.7690 (p0) REVERT: A 1031 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7740 (mp0) REVERT: B 118 LEU cc_start: 0.9069 (tt) cc_final: 0.8460 (mp) REVERT: B 177 MET cc_start: -0.3215 (mtm) cc_final: -0.3618 (tpp) REVERT: B 324 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8015 (pm20) REVERT: B 389 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7498 (t0) REVERT: B 396 TYR cc_start: 0.7873 (m-80) cc_final: 0.7367 (m-80) REVERT: B 515 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.7755 (p90) REVERT: B 1029 MET cc_start: 0.9270 (tpp) cc_final: 0.9011 (tpp) REVERT: C 238 PHE cc_start: 0.8645 (p90) cc_final: 0.8146 (p90) REVERT: C 378 LYS cc_start: 0.8780 (tppt) cc_final: 0.8254 (ttmt) REVERT: C 529 LYS cc_start: 0.5556 (OUTLIER) cc_final: 0.5297 (tppt) REVERT: C 904 TYR cc_start: 0.7474 (m-10) cc_final: 0.7123 (m-10) REVERT: C 974 SER cc_start: 0.8661 (m) cc_final: 0.8382 (m) outliers start: 58 outliers final: 36 residues processed: 195 average time/residue: 0.1487 time to fit residues: 48.5459 Evaluate side-chains 166 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 456 PHE 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 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 389 ASP 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 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 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 329 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 547 THR 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: 5.9990 chunk 278 optimal weight: 2.9990 chunk 26 optimal weight: 0.0060 chunk 188 optimal weight: 4.9990 chunk 249 optimal weight: 8.9990 chunk 258 optimal weight: 10.0000 chunk 302 optimal weight: 0.8980 chunk 317 optimal weight: 7.9990 chunk 276 optimal weight: 0.9990 chunk 226 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 overall best weight: 1.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.106272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.069841 restraints weight = 67121.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.071864 restraints weight = 38590.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.073193 restraints weight = 26998.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.073996 restraints weight = 21521.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.074439 restraints weight = 18687.284| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 26046 Z= 0.177 Angle : 0.622 11.429 35500 Z= 0.313 Chirality : 0.045 0.264 4088 Planarity : 0.004 0.063 4537 Dihedral : 4.884 55.614 3420 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.94 % Allowed : 16.51 % Favored : 81.56 % 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: -1.71 (0.14), residues: 3150 helix: 0.37 (0.20), residues: 642 sheet: -0.57 (0.19), residues: 682 loop : -2.00 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 983 TYR 0.024 0.001 TYR B 265 PHE 0.022 0.002 PHE A 377 TRP 0.065 0.002 TRP B 436 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (25973) covalent geometry : angle 0.60811 / 0.31 (35323) SS BOND : bond 0.00324 / 0.22 ( 42) SS BOND : angle 1.81142 / 1.30 ( 84) hydrogen bonds : bond 0.04445 / 2.86 ( 837) hydrogen bonds : angle 5.33755 / 3.67 ( 2283) link_NAG-ASN : bond 0.00276 / 0.16 ( 31) link_NAG-ASN : angle 2.02536 / 1.38 ( 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 183 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 129 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7243 (m-80) cc_final: 0.6032 (m-10) REVERT: A 135 PHE cc_start: 0.8138 (m-80) cc_final: 0.7489 (m-80) REVERT: A 392 PHE cc_start: 0.6865 (m-10) cc_final: 0.6391 (m-10) REVERT: A 570 ASP cc_start: 0.8152 (p0) cc_final: 0.7611 (p0) REVERT: A 1031 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: B 118 LEU cc_start: 0.9068 (tt) cc_final: 0.8429 (mp) REVERT: B 177 MET cc_start: -0.2800 (mtm) cc_final: -0.3302 (tpp) REVERT: B 324 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7942 (pm20) REVERT: B 396 TYR cc_start: 0.7891 (m-80) cc_final: 0.7293 (m-80) REVERT: B 515 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.7748 (p90) REVERT: B 1029 MET cc_start: 0.9367 (tpp) cc_final: 0.9048 (tpp) REVERT: C 238 PHE cc_start: 0.8722 (p90) cc_final: 0.8126 (p90) REVERT: C 378 LYS cc_start: 0.8817 (tppt) cc_final: 0.8163 (ttmt) REVERT: C 455 LEU cc_start: 0.8093 (tp) cc_final: 0.7432 (mp) REVERT: C 529 LYS cc_start: 0.5944 (OUTLIER) cc_final: 0.5622 (mmmt) REVERT: C 904 TYR cc_start: 0.7679 (m-10) cc_final: 0.7267 (m-10) REVERT: C 974 SER cc_start: 0.8717 (m) cc_final: 0.8427 (m) outliers start: 54 outliers final: 40 residues processed: 176 average time/residue: 0.1603 time to fit residues: 46.6098 Evaluate side-chains 168 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 124 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 302 THR 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 980 ILE 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 402 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 595 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 131 CYS 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 515 PHE Chi-restraints excluded: chain C residue 529 LYS 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: 0.9980 chunk 35 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 292 optimal weight: 3.9990 chunk 287 optimal weight: 0.9980 chunk 281 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 250 optimal weight: 2.9990 chunk 243 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 37 optimal weight: 20.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.106680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.070185 restraints weight = 66718.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.072206 restraints weight = 38602.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.073538 restraints weight = 27107.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.074405 restraints weight = 21568.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.074934 restraints weight = 18687.213| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 26046 Z= 0.153 Angle : 0.618 11.399 35500 Z= 0.310 Chirality : 0.044 0.261 4088 Planarity : 0.004 0.064 4537 Dihedral : 4.850 55.170 3420 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.79 % Allowed : 16.65 % Favored : 81.56 % 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: -1.69 (0.14), residues: 3150 helix: 0.38 (0.20), residues: 649 sheet: -0.53 (0.19), residues: 680 loop : -2.00 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 983 TYR 0.025 0.001 TYR A 473 PHE 0.022 0.001 PHE C 133 TRP 0.057 0.002 TRP B 436 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (25973) covalent geometry : angle 0.60433 / 0.31 (35323) SS BOND : bond 0.00366 / 0.26 ( 42) SS BOND : angle 1.88298 / 1.34 ( 84) hydrogen bonds : bond 0.04297 / 2.77 ( 837) hydrogen bonds : angle 5.28899 / 3.64 ( 2283) link_NAG-ASN : bond 0.00290 / 0.17 ( 31) link_NAG-ASN : angle 1.98712 / 1.35 ( 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 180 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 130 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7236 (m-80) cc_final: 0.5998 (m-10) REVERT: A 135 PHE cc_start: 0.8133 (m-80) cc_final: 0.7458 (m-80) REVERT: A 570 ASP cc_start: 0.8143 (p0) cc_final: 0.7600 (p0) REVERT: A 1031 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: B 118 LEU cc_start: 0.9058 (tt) cc_final: 0.8428 (mp) REVERT: B 177 MET cc_start: -0.2789 (mtm) cc_final: -0.3153 (tpp) REVERT: B 324 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7918 (pm20) REVERT: B 396 TYR cc_start: 0.7882 (m-80) cc_final: 0.7285 (m-80) REVERT: B 515 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.7732 (p90) REVERT: B 1029 MET cc_start: 0.9351 (tpp) cc_final: 0.9006 (tpp) REVERT: C 238 PHE cc_start: 0.8710 (p90) cc_final: 0.8151 (p90) REVERT: C 378 LYS cc_start: 0.8785 (tppt) cc_final: 0.8144 (ttmt) REVERT: C 455 LEU cc_start: 0.8142 (tp) cc_final: 0.7506 (mp) REVERT: C 529 LYS cc_start: 0.5964 (OUTLIER) cc_final: 0.5602 (mmmt) REVERT: C 904 TYR cc_start: 0.7641 (m-10) cc_final: 0.7252 (m-10) REVERT: C 974 SER cc_start: 0.8685 (m) cc_final: 0.8398 (m) outliers start: 50 outliers final: 43 residues processed: 173 average time/residue: 0.1497 time to fit residues: 43.4000 Evaluate side-chains 176 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 129 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 302 THR 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 980 ILE 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 582 LEU Chi-restraints excluded: chain B residue 595 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 131 CYS 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 515 PHE Chi-restraints excluded: chain C residue 529 LYS 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: 1.9990 chunk 226 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 197 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 75 optimal weight: 0.0980 chunk 238 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.107674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.071511 restraints weight = 66347.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.073551 restraints weight = 37621.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.074927 restraints weight = 26037.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.075817 restraints weight = 20542.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.076354 restraints weight = 17672.700| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26046 Z= 0.117 Angle : 0.591 10.997 35500 Z= 0.295 Chirality : 0.044 0.258 4088 Planarity : 0.004 0.065 4537 Dihedral : 4.664 53.640 3420 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.79 % Allowed : 16.90 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.54 (0.14), residues: 3150 helix: 0.59 (0.21), residues: 650 sheet: -0.43 (0.19), residues: 693 loop : -1.96 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 983 TYR 0.041 0.001 TYR A 473 PHE 0.042 0.001 PHE C 429 TRP 0.049 0.001 TRP B 436 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (25973) covalent geometry : angle 0.57894 / 0.29 (35323) SS BOND : bond 0.00365 / 0.27 ( 42) SS BOND : angle 1.63873 / 1.18 ( 84) hydrogen bonds : bond 0.03863 / 2.48 ( 837) hydrogen bonds : angle 5.13385 / 3.53 ( 2283) link_NAG-ASN : bond 0.00310 / 0.18 ( 31) link_NAG-ASN : angle 1.89282 / 1.28 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3758.20 seconds wall clock time: 66 minutes 20.53 seconds (3980.53 seconds total)