Starting phenix.real_space_refine on Sun Aug 24 18:13:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ga8_29892/08_2025/8ga8_29892.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ga8_29892/08_2025/8ga8_29892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ga8_29892/08_2025/8ga8_29892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ga8_29892/08_2025/8ga8_29892.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ga8_29892/08_2025/8ga8_29892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ga8_29892/08_2025/8ga8_29892.map" } resolution = 3.5 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= 0.001 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 95 5.16 5 C 14023 2.51 5 N 3795 2.21 5 O 4096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22011 Number of models: 1 Model: "" Number of chains: 12 Chain: "H" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1206 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "A" Number of atoms: 4417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4417 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 10, 'TRANS': 514} Chain breaks: 5 Chain: "J" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 767 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "L" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1052 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain breaks: 1 Chain: "M" Number of atoms: 1832 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 223, 1824 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 223, 1824 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain breaks: 4 bond proxies already assigned to first conformer: 1839 Chain: "G" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 838 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain breaks: 1 Chain: "B" Number of atoms: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3039 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 18, 'TRANS': 364} Chain: "E" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3031 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 18, 'TRANS': 363} Chain: "K" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1587 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 14, 'TRANS': 184} Chain breaks: 1 Chain: "D" Number of atoms: 4240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4240 Classifications: {'peptide': 503} Link IDs: {'PTRANS': 12, 'TRANS': 490} Chain breaks: 5 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AILE M 169 " occ=0.51 ... (14 atoms not shown) pdb=" CD1BILE M 169 " occ=0.49 Time building chain proxies: 5.48, per 1000 atoms: 0.25 Number of scatterers: 22011 At special positions: 0 Unit cell: (104.076, 156.94, 199.892, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 95 16.00 O 4096 8.00 N 3795 7.00 C 14023 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 961.5 milliseconds Enol-peptide restraints added in 1.7 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 188 " pdb=" ZN E 501 " pdb="ZN ZN E 501 " - pdb=" ND1 HIS E 188 " 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5104 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 11 sheets defined 61.8% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'H' and resid 11 through 35 removed outlier: 4.057A pdb=" N ARG H 17 " --> pdb=" O ARG H 13 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG H 18 " --> pdb=" O LYS H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 56 removed outlier: 3.855A pdb=" N GLN H 56 " --> pdb=" O THR H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 117 Processing helix chain 'H' and resid 300 through 316 removed outlier: 3.873A pdb=" N GLU H 306 " --> pdb=" O ASP H 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 677 removed outlier: 3.647A pdb=" N GLU A 664 " --> pdb=" O ILE A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 694 Processing helix chain 'A' and resid 698 through 707 Processing helix chain 'A' and resid 713 through 724 Processing helix chain 'A' and resid 759 through 764 removed outlier: 4.285A pdb=" N PHE A 764 " --> pdb=" O LYS A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 777 removed outlier: 3.920A pdb=" N GLU A 776 " --> pdb=" O ASP A 772 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 777 " --> pdb=" O MET A 773 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 772 through 777' Processing helix chain 'A' and resid 803 through 839 removed outlier: 3.677A pdb=" N THR A 833 " --> pdb=" O GLN A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 841 No H-bonds generated for 'chain 'A' and resid 840 through 841' Processing helix chain 'A' and resid 842 through 846 Processing helix chain 'A' and resid 861 through 871 removed outlier: 3.587A pdb=" N VAL A 866 " --> pdb=" O ILE A 862 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 867 " --> pdb=" O TYR A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 886 removed outlier: 3.778A pdb=" N ILE A 879 " --> pdb=" O ARG A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 922 Proline residue: A 892 - end of helix removed outlier: 3.990A pdb=" N LYS A 914 " --> pdb=" O ARG A 910 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL A 915 " --> pdb=" O GLU A 911 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 929 removed outlier: 3.636A pdb=" N LEU A 928 " --> pdb=" O PHE A 924 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP A 929 " --> pdb=" O PHE A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 943 removed outlier: 3.524A pdb=" N LEU A 943 " --> pdb=" O ASP A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 961 removed outlier: 3.689A pdb=" N ILE A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 955 " --> pdb=" O GLU A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 999 removed outlier: 4.374A pdb=" N ASP A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 988 " --> pdb=" O ILE A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1023 Processing helix chain 'A' and resid 1066 through 1070 removed outlier: 3.795A pdb=" N HIS A1070 " --> pdb=" O LEU A1066 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1066 through 1070' Processing helix chain 'A' and resid 1070 through 1082 Processing helix chain 'A' and resid 1141 through 1163 removed outlier: 4.265A pdb=" N PHE A1147 " --> pdb=" O ASN A1143 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE A1161 " --> pdb=" O ARG A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1175 removed outlier: 3.811A pdb=" N LYS A1170 " --> pdb=" O GLU A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1194 Processing helix chain 'A' and resid 1202 through 1216 removed outlier: 3.869A pdb=" N ARG A1209 " --> pdb=" O LYS A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1233 removed outlier: 3.715A pdb=" N PHE A1224 " --> pdb=" O GLU A1220 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLU A1225 " --> pdb=" O HIS A1221 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU A1226 " --> pdb=" O GLN A1222 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA A1231 " --> pdb=" O SER A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1259 Processing helix chain 'A' and resid 1259 through 1274 removed outlier: 3.590A pdb=" N ASN A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1294 removed outlier: 3.744A pdb=" N HIS A1293 " --> pdb=" O GLN A1289 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 120 removed outlier: 3.538A pdb=" N LEU J 112 " --> pdb=" O THR J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 135 removed outlier: 3.971A pdb=" N GLY J 135 " --> pdb=" O GLY J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 141 Processing helix chain 'J' and resid 142 through 148 Processing helix chain 'J' and resid 158 through 173 removed outlier: 3.732A pdb=" N LEU J 162 " --> pdb=" O HIS J 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 191 Proline residue: J 182 - end of helix Processing helix chain 'L' and resid 13 through 39 Proline residue: L 22 - end of helix removed outlier: 3.648A pdb=" N CYS L 39 " --> pdb=" O ILE L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 54 Processing helix chain 'L' and resid 61 through 114 Proline residue: L 81 - end of helix removed outlier: 4.174A pdb=" N ASN L 114 " --> pdb=" O VAL L 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 152 removed outlier: 3.554A pdb=" N GLU L 136 " --> pdb=" O HIS L 132 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER L 150 " --> pdb=" O ASN L 146 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN L 151 " --> pdb=" O SER L 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 37 removed outlier: 4.240A pdb=" N GLU M 36 " --> pdb=" O ARG M 32 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS M 37 " --> pdb=" O ILE M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'M' and resid 156 through 160 Processing helix chain 'M' and resid 162 through 166 Processing helix chain 'M' and resid 180 through 186 Processing helix chain 'M' and resid 188 through 217 removed outlier: 3.773A pdb=" N SER M 207 " --> pdb=" O LYS M 203 " (cutoff:3.500A) Processing helix chain 'M' and resid 227 through 232 removed outlier: 3.624A pdb=" N ASN M 232 " --> pdb=" O GLU M 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 329 through 384 removed outlier: 3.518A pdb=" N LEU M 384 " --> pdb=" O SER M 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 298 removed outlier: 3.620A pdb=" N ASP G 297 " --> pdb=" O ARG G 293 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE G 298 " --> pdb=" O ARG G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 394 through 404 removed outlier: 3.577A pdb=" N PHE G 400 " --> pdb=" O ILE G 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.893A pdb=" N ASN B 31 " --> pdb=" O ASP B 28 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR B 32 " --> pdb=" O VAL B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 32' Processing helix chain 'B' and resid 42 through 55 removed outlier: 4.358A pdb=" N ARG B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.554A pdb=" N LYS B 59 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET B 61 " --> pdb=" O TYR B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 79 through 89 Processing helix chain 'B' and resid 97 through 105 Processing helix chain 'B' and resid 115 through 136 Processing helix chain 'B' and resid 164 through 175 removed outlier: 3.930A pdb=" N LEU B 168 " --> pdb=" O ASN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 243 through 262 Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 287 through 300 removed outlier: 3.909A pdb=" N CYS B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL B 295 " --> pdb=" O HIS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 Processing helix chain 'B' and resid 343 through 347 Processing helix chain 'B' and resid 365 through 381 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 42 through 56 removed outlier: 3.731A pdb=" N ARG E 46 " --> pdb=" O PRO E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 75 Processing helix chain 'E' and resid 79 through 89 Processing helix chain 'E' and resid 97 through 105 Processing helix chain 'E' and resid 115 through 136 Processing helix chain 'E' and resid 164 through 175 removed outlier: 3.673A pdb=" N LEU E 168 " --> pdb=" O ASN E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 196 Processing helix chain 'E' and resid 226 through 230 Processing helix chain 'E' and resid 243 through 262 Proline residue: E 253 - end of helix Processing helix chain 'E' and resid 287 through 300 removed outlier: 3.911A pdb=" N CYS E 294 " --> pdb=" O GLY E 290 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL E 295 " --> pdb=" O HIS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 330 removed outlier: 3.642A pdb=" N ASN E 330 " --> pdb=" O THR E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 347 Processing helix chain 'E' and resid 365 through 381 Processing helix chain 'K' and resid 70 through 80 Processing helix chain 'K' and resid 131 through 135 Processing helix chain 'K' and resid 144 through 153 removed outlier: 3.624A pdb=" N ASN K 153 " --> pdb=" O GLN K 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 163 Processing helix chain 'K' and resid 176 through 184 Processing helix chain 'D' and resid 662 through 677 Processing helix chain 'D' and resid 678 through 694 Processing helix chain 'D' and resid 698 through 710 removed outlier: 3.869A pdb=" N PHE D 708 " --> pdb=" O GLU D 704 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR D 709 " --> pdb=" O LYS D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 724 Processing helix chain 'D' and resid 760 through 764 removed outlier: 3.539A pdb=" N THR D 763 " --> pdb=" O LYS D 760 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE D 764 " --> pdb=" O SER D 761 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 760 through 764' Processing helix chain 'D' and resid 771 through 778 Processing helix chain 'D' and resid 801 through 841 removed outlier: 4.002A pdb=" N ASN D 840 " --> pdb=" O ASN D 836 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET D 841 " --> pdb=" O LYS D 837 " (cutoff:3.500A) Processing helix chain 'D' and resid 842 through 848 removed outlier: 3.523A pdb=" N ASN D 848 " --> pdb=" O ASN D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 861 through 871 removed outlier: 3.775A pdb=" N LYS D 865 " --> pdb=" O THR D 861 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL D 866 " --> pdb=" O ILE D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 872 through 886 removed outlier: 4.444A pdb=" N PHE D 877 " --> pdb=" O LYS D 873 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU D 878 " --> pdb=" O GLU D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 886 through 924 Proline residue: D 892 - end of helix removed outlier: 3.515A pdb=" N GLU D 903 " --> pdb=" O LYS D 899 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS D 914 " --> pdb=" O ARG D 910 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL D 915 " --> pdb=" O GLU D 911 " (cutoff:3.500A) Processing helix chain 'D' and resid 929 through 943 removed outlier: 3.940A pdb=" N LYS D 936 " --> pdb=" O GLY D 932 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU D 943 " --> pdb=" O ASP D 939 " (cutoff:3.500A) Processing helix chain 'D' and resid 944 through 960 removed outlier: 3.602A pdb=" N LEU D 948 " --> pdb=" O THR D 944 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE D 949 " --> pdb=" O THR D 945 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE D 952 " --> pdb=" O LEU D 948 " (cutoff:3.500A) Processing helix chain 'D' and resid 982 through 999 removed outlier: 4.379A pdb=" N TYR D 986 " --> pdb=" O LYS D 982 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP D 987 " --> pdb=" O ASN D 983 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE D 988 " --> pdb=" O ILE D 984 " (cutoff:3.500A) Processing helix chain 'D' and resid 1003 through 1023 removed outlier: 3.504A pdb=" N ARG D1009 " --> pdb=" O PRO D1005 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP D1012 " --> pdb=" O GLU D1008 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU D1014 " --> pdb=" O LEU D1010 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LYS D1015 " --> pdb=" O LYS D1011 " (cutoff:3.500A) Processing helix chain 'D' and resid 1066 through 1070 Processing helix chain 'D' and resid 1141 through 1160 removed outlier: 3.718A pdb=" N ARG D1157 " --> pdb=" O THR D1153 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU D1158 " --> pdb=" O ILE D1154 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D1160 " --> pdb=" O GLU D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1161 through 1163 No H-bonds generated for 'chain 'D' and resid 1161 through 1163' Processing helix chain 'D' and resid 1164 through 1173 removed outlier: 4.000A pdb=" N ASN D1173 " --> pdb=" O THR D1169 " (cutoff:3.500A) Processing helix chain 'D' and resid 1204 through 1216 removed outlier: 3.682A pdb=" N ARG D1213 " --> pdb=" O ARG D1209 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU D1214 " --> pdb=" O LEU D1210 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE D1215 " --> pdb=" O SER D1211 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN D1216 " --> pdb=" O ARG D1212 " (cutoff:3.500A) Processing helix chain 'D' and resid 1220 through 1232 removed outlier: 4.271A pdb=" N PHE D1224 " --> pdb=" O GLU D1220 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU D1225 " --> pdb=" O HIS D1221 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU D1226 " --> pdb=" O GLN D1222 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D1228 " --> pdb=" O PHE D1224 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG D1229 " --> pdb=" O GLU D1225 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN D1230 " --> pdb=" O GLU D1226 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA D1231 " --> pdb=" O SER D1227 " (cutoff:3.500A) Processing helix chain 'D' and resid 1241 through 1259 removed outlier: 3.568A pdb=" N ASP D1259 " --> pdb=" O THR D1255 " (cutoff:3.500A) Processing helix chain 'D' and resid 1259 through 1274 Processing helix chain 'D' and resid 1279 through 1293 removed outlier: 3.718A pdb=" N ILE D1284 " --> pdb=" O ALA D1280 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N HIS D1293 " --> pdb=" O GLN D1289 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 750 through 751 removed outlier: 4.268A pdb=" N TYR A 755 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 976 through 978 Processing sheet with id=AA3, first strand: chain 'M' and resid 89 through 90 removed outlier: 4.001A pdb=" N GLN M 89 " --> pdb=" O LEU M 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 22 through 24 Processing sheet with id=AA5, first strand: chain 'B' and resid 203 through 206 removed outlier: 6.758A pdb=" N LEU B 181 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLN B 270 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE B 183 " --> pdb=" O GLN B 270 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL B 267 " --> pdb=" O MET B 306 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N VAL B 308 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU B 269 " --> pdb=" O VAL B 308 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 62 through 64 removed outlier: 6.732A pdb=" N VAL E 21 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N TYR E 64 " --> pdb=" O VAL E 21 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYR E 23 " --> pdb=" O TYR E 64 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA E 142 " --> pdb=" O MET E 305 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU E 181 " --> pdb=" O VAL E 268 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N GLN E 270 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE E 183 " --> pdb=" O GLN E 270 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 90 through 91 removed outlier: 6.267A pdb=" N LEU K 90 " --> pdb=" O LYS K 142 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ASP K 225 " --> pdb=" O ILE K 272 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ILE K 272 " --> pdb=" O ASP K 225 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU K 227 " --> pdb=" O ILE K 270 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ILE K 270 " --> pdb=" O GLU K 227 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLU K 229 " --> pdb=" O TYR K 268 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 90 through 91 removed outlier: 6.267A pdb=" N LEU K 90 " --> pdb=" O LYS K 142 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ASP K 225 " --> pdb=" O ILE K 272 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ILE K 272 " --> pdb=" O ASP K 225 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU K 227 " --> pdb=" O ILE K 270 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ILE K 270 " --> pdb=" O GLU K 227 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLU K 229 " --> pdb=" O TYR K 268 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 243 through 244 Processing sheet with id=AB1, first strand: chain 'D' and resid 755 through 757 Processing sheet with id=AB2, first strand: chain 'D' and resid 975 through 978 removed outlier: 3.794A pdb=" N LEU D 975 " --> pdb=" O ILE D1314 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE D1314 " --> pdb=" O LEU D 975 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N PHE D1301 " --> pdb=" O ALA D1140 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA D1140 " --> pdb=" O PHE D1301 " (cutoff:3.500A) 1177 hydrogen bonds defined for protein. 3450 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: 3.85 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5886 1.33 - 1.45: 4045 1.45 - 1.57: 12394 1.57 - 1.69: 1 1.69 - 1.81: 155 Bond restraints: 22481 Sorted by residual: bond pdb=" CB PRO B 111 " pdb=" CG PRO B 111 " ideal model delta sigma weight residual 1.492 1.618 -0.126 5.00e-02 4.00e+02 6.33e+00 bond pdb=" CB GLU M 36 " pdb=" CG GLU M 36 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.20e+00 bond pdb=" CG PRO B 111 " pdb=" CD PRO B 111 " ideal model delta sigma weight residual 1.503 1.553 -0.050 3.40e-02 8.65e+02 2.17e+00 bond pdb=" CB GLN D1222 " pdb=" CG GLN D1222 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.59e+00 bond pdb=" CB GLU A 843 " pdb=" CG GLU A 843 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.55e+00 ... (remaining 22476 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 30012 2.20 - 4.40: 244 4.40 - 6.61: 44 6.61 - 8.81: 15 8.81 - 11.01: 2 Bond angle restraints: 30317 Sorted by residual: angle pdb=" CA PRO B 111 " pdb=" N PRO B 111 " pdb=" CD PRO B 111 " ideal model delta sigma weight residual 112.00 103.47 8.53 1.40e+00 5.10e-01 3.71e+01 angle pdb=" CA GLU M 36 " pdb=" CB GLU M 36 " pdb=" CG GLU M 36 " ideal model delta sigma weight residual 114.10 121.30 -7.20 2.00e+00 2.50e-01 1.30e+01 angle pdb=" CA PRO B 253 " pdb=" N PRO B 253 " pdb=" CD PRO B 253 " ideal model delta sigma weight residual 112.00 107.05 4.95 1.40e+00 5.10e-01 1.25e+01 angle pdb=" N PHE D1017 " pdb=" CA PHE D1017 " pdb=" CB PHE D1017 " ideal model delta sigma weight residual 110.16 115.18 -5.02 1.48e+00 4.57e-01 1.15e+01 angle pdb=" CB GLU M 36 " pdb=" CG GLU M 36 " pdb=" CD GLU M 36 " ideal model delta sigma weight residual 112.60 118.13 -5.53 1.70e+00 3.46e-01 1.06e+01 ... (remaining 30312 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 11394 17.97 - 35.94: 1702 35.94 - 53.91: 406 53.91 - 71.88: 62 71.88 - 89.85: 21 Dihedral angle restraints: 13585 sinusoidal: 5698 harmonic: 7887 Sorted by residual: dihedral pdb=" CA TYR B 346 " pdb=" C TYR B 346 " pdb=" N TYR B 347 " pdb=" CA TYR B 347 " ideal model delta harmonic sigma weight residual -180.00 -161.32 -18.68 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA TYR E 313 " pdb=" C TYR E 313 " pdb=" N THR E 314 " pdb=" CA THR E 314 " ideal model delta harmonic sigma weight residual 180.00 162.47 17.53 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ASP A 695 " pdb=" CB ASP A 695 " pdb=" CG ASP A 695 " pdb=" OD1 ASP A 695 " ideal model delta sinusoidal sigma weight residual -30.00 -89.77 59.77 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 13582 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2427 0.040 - 0.079: 685 0.079 - 0.119: 152 0.119 - 0.158: 15 0.158 - 0.198: 3 Chirality restraints: 3282 Sorted by residual: chirality pdb=" CA MET L 80 " pdb=" N MET L 80 " pdb=" C MET L 80 " pdb=" CB MET L 80 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.75e-01 chirality pdb=" CA PHE A1180 " pdb=" N PHE A1180 " pdb=" C PHE A1180 " pdb=" CB PHE A1180 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.36e-01 chirality pdb=" CA GLU L 105 " pdb=" N GLU L 105 " pdb=" C GLU L 105 " pdb=" CB GLU L 105 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.44e-01 ... (remaining 3279 not shown) Planarity restraints: 3894 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 252 " -0.073 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO B 253 " 0.188 5.00e-02 4.00e+02 pdb=" CA PRO B 253 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 253 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 110 " 0.049 5.00e-02 4.00e+02 7.03e-02 7.91e+00 pdb=" N PRO B 111 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 111 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 111 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 90 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO B 91 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 91 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 91 " 0.028 5.00e-02 4.00e+02 ... (remaining 3891 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 264 2.60 - 3.18: 19004 3.18 - 3.75: 36049 3.75 - 4.33: 45415 4.33 - 4.90: 75987 Nonbonded interactions: 176719 Sorted by model distance: nonbonded pdb=" OD1 ASP B 186 " pdb="ZN ZN B 501 " model vdw 2.028 2.230 nonbonded pdb=" OD1 ASP E 186 " pdb="ZN ZN E 501 " model vdw 2.031 2.230 nonbonded pdb=" OD2 ASP E 274 " pdb="ZN ZN E 501 " model vdw 2.035 2.230 nonbonded pdb=" OD2 ASP B 274 " pdb="ZN ZN B 501 " model vdw 2.041 2.230 nonbonded pdb=" OD2 ASP B 186 " pdb="ZN ZN B 501 " model vdw 2.074 2.230 ... (remaining 176714 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 659 through 724 or resid 749 through 787 or resid 799 thro \ ugh 1070 or resid 1075 or resid 1079 through 1080 or resid 1135 through 1174 or \ resid 1203 through 1317)) selection = (chain 'D' and (resid 659 through 724 or resid 749 through 787 or resid 799 thro \ ugh 961 or resid 975 through 1070 or resid 1131 or resid 1133 through 1317)) } ncs_group { reference = (chain 'B' and resid 2 through 501) selection = chain 'E' } 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=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 23.220 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 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 : 0.003 0.126 22483 Z= 0.116 Angle : 0.540 11.010 30317 Z= 0.281 Chirality : 0.038 0.198 3282 Planarity : 0.004 0.109 3894 Dihedral : 17.426 89.848 8481 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.33 % Allowed : 29.89 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.17), residues: 2622 helix: 1.76 (0.13), residues: 1496 sheet: -0.52 (0.39), residues: 204 loop : -0.90 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1229 TYR 0.021 0.001 TYR B 58 PHE 0.019 0.001 PHE H 19 TRP 0.012 0.001 TRP D1151 HIS 0.009 0.001 HIS H 106 Details of bonding type rmsd covalent geometry : bond 0.00262 (22481) covalent geometry : angle 0.54031 (30317) hydrogen bonds : bond 0.12475 ( 1166) hydrogen bonds : angle 5.02365 ( 3450) metal coordination : bond 0.00200 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 240 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 841 MET cc_start: 0.6086 (tmm) cc_final: 0.5029 (tmm) REVERT: D 1222 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8551 (tm-30) REVERT: D 1226 GLU cc_start: 0.8132 (pp20) cc_final: 0.7926 (pp20) outliers start: 8 outliers final: 5 residues processed: 243 average time/residue: 0.1626 time to fit residues: 62.0724 Evaluate side-chains 231 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 226 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 928 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 829 GLN L 88 HIS ** M 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS B 54 ASN ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.141594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.121302 restraints weight = 64879.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.122695 restraints weight = 33906.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.124426 restraints weight = 23431.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.124553 restraints weight = 17866.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.124943 restraints weight = 15902.999| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4002 r_free = 0.4002 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4002 r_free = 0.4002 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.0675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 22483 Z= 0.132 Angle : 0.521 11.015 30317 Z= 0.270 Chirality : 0.039 0.147 3282 Planarity : 0.004 0.068 3894 Dihedral : 4.097 47.997 2954 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.00 % Allowed : 27.18 % Favored : 69.82 % 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 aren not related in a simple way. whole: 0.97 (0.17), residues: 2622 helix: 1.75 (0.13), residues: 1502 sheet: -0.66 (0.38), residues: 203 loop : -0.90 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 87 TYR 0.036 0.001 TYR M 211 PHE 0.041 0.001 PHE D1017 TRP 0.010 0.001 TRP D1151 HIS 0.009 0.001 HIS H 106 Details of bonding type rmsd covalent geometry : bond 0.00300 (22481) covalent geometry : angle 0.52133 (30317) hydrogen bonds : bond 0.04096 ( 1166) hydrogen bonds : angle 4.10977 ( 3450) metal coordination : bond 0.00086 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 256 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: A 762 ASP cc_start: 0.8588 (t70) cc_final: 0.8248 (t70) REVERT: A 841 MET cc_start: 0.6269 (tmm) cc_final: 0.5371 (ppp) REVERT: A 1169 THR cc_start: 0.8641 (t) cc_final: 0.8411 (m) REVERT: L 131 MET cc_start: 0.7439 (tpp) cc_final: 0.6976 (tmm) REVERT: L 134 HIS cc_start: 0.7909 (OUTLIER) cc_final: 0.6729 (t70) REVERT: B 330 ASN cc_start: 0.8881 (m110) cc_final: 0.8665 (m-40) REVERT: B 375 ASN cc_start: 0.8532 (OUTLIER) cc_final: 0.8130 (t0) REVERT: E 207 SER cc_start: 0.7838 (t) cc_final: 0.7371 (p) REVERT: D 818 ASP cc_start: 0.7414 (t0) cc_final: 0.7134 (t0) REVERT: D 956 LYS cc_start: 0.8231 (tptt) cc_final: 0.7915 (tptt) REVERT: D 1257 MET cc_start: 0.7848 (tmm) cc_final: 0.7548 (tmm) outliers start: 71 outliers final: 38 residues processed: 310 average time/residue: 0.1524 time to fit residues: 75.8928 Evaluate side-chains 273 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 233 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain L residue 36 ASP Chi-restraints excluded: chain L residue 134 HIS Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 222 HIS Chi-restraints excluded: chain M residue 337 GLU Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 TYR Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 306 MET Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain K residue 75 PHE Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain D residue 676 ILE Chi-restraints excluded: chain D residue 777 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 901 LYS Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 1297 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 118 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 206 optimal weight: 8.9990 chunk 156 optimal weight: 5.9990 chunk 179 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 258 optimal weight: 6.9990 chunk 260 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1206 GLN L 88 HIS ** M 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 ASN E 382 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.141109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.120394 restraints weight = 84418.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.122939 restraints weight = 45276.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.123523 restraints weight = 31867.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.124428 restraints weight = 21635.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.124696 restraints weight = 18933.447| |-----------------------------------------------------------------------------| r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3995 r_free = 0.3995 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3995 r_free = 0.3995 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22483 Z= 0.126 Angle : 0.514 9.480 30317 Z= 0.265 Chirality : 0.039 0.175 3282 Planarity : 0.003 0.055 3894 Dihedral : 4.061 49.294 2949 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.44 % Allowed : 26.15 % Favored : 69.41 % 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 aren not related in a simple way. whole: 0.95 (0.17), residues: 2622 helix: 1.73 (0.13), residues: 1504 sheet: -0.75 (0.38), residues: 203 loop : -0.87 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 49 TYR 0.030 0.001 TYR M 211 PHE 0.029 0.001 PHE H 19 TRP 0.010 0.001 TRP D1151 HIS 0.009 0.001 HIS H 106 Details of bonding type rmsd covalent geometry : bond 0.00284 (22481) covalent geometry : angle 0.51405 (30317) hydrogen bonds : bond 0.03948 ( 1166) hydrogen bonds : angle 3.97818 ( 3450) metal coordination : bond 0.00124 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 248 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 314 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.6371 (tt) REVERT: A 762 ASP cc_start: 0.8597 (t70) cc_final: 0.8252 (t70) REVERT: A 841 MET cc_start: 0.6287 (tmm) cc_final: 0.5548 (ppp) REVERT: L 131 MET cc_start: 0.7423 (tpp) cc_final: 0.7127 (tmm) REVERT: L 134 HIS cc_start: 0.7957 (OUTLIER) cc_final: 0.6731 (t70) REVERT: M 88 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7599 (mt-10) REVERT: B 270 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.6686 (tm-30) REVERT: B 375 ASN cc_start: 0.8347 (OUTLIER) cc_final: 0.7978 (t0) REVERT: K 102 GLU cc_start: 0.6176 (OUTLIER) cc_final: 0.5885 (tt0) REVERT: K 152 PHE cc_start: 0.6570 (OUTLIER) cc_final: 0.6309 (t80) REVERT: K 161 ARG cc_start: 0.5727 (OUTLIER) cc_final: 0.5393 (tpt170) REVERT: D 818 ASP cc_start: 0.7555 (t0) cc_final: 0.7192 (t0) REVERT: D 956 LYS cc_start: 0.8262 (tptt) cc_final: 0.7940 (tptt) REVERT: D 1159 LEU cc_start: 0.7731 (mp) cc_final: 0.7340 (mp) REVERT: D 1204 TYR cc_start: 0.7822 (OUTLIER) cc_final: 0.5900 (t80) REVERT: D 1257 MET cc_start: 0.7835 (tmm) cc_final: 0.7538 (tmm) outliers start: 106 outliers final: 69 residues processed: 329 average time/residue: 0.1534 time to fit residues: 80.8323 Evaluate side-chains 307 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 229 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 1004 ASN Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain L residue 14 ILE Chi-restraints excluded: chain L residue 36 ASP Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 134 HIS Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain M residue 32 ARG Chi-restraints excluded: chain M residue 88 GLU Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 222 HIS Chi-restraints excluded: chain M residue 337 GLU Chi-restraints excluded: chain M residue 343 GLN Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 270 LYS Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 270 GLN Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 TYR Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 306 MET Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain K residue 75 PHE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain K residue 161 ARG Chi-restraints excluded: chain D residue 676 ILE Chi-restraints excluded: chain D residue 686 LEU Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 777 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 812 GLU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 901 LYS Chi-restraints excluded: chain D residue 928 LEU Chi-restraints excluded: chain D residue 943 LEU Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 1204 TYR Chi-restraints excluded: chain D residue 1228 LEU Chi-restraints excluded: chain D residue 1239 LEU Chi-restraints excluded: chain D residue 1255 THR Chi-restraints excluded: chain D residue 1297 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 50 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 246 optimal weight: 6.9990 chunk 75 optimal weight: 0.5980 chunk 221 optimal weight: 2.9990 chunk 207 optimal weight: 9.9990 chunk 224 optimal weight: 2.9990 chunk 208 optimal weight: 6.9990 chunk 233 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 198 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 71 ASN L 88 HIS M 352 ASN ** M 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.141889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.121058 restraints weight = 63655.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.122551 restraints weight = 36766.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.123695 restraints weight = 23083.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.124472 restraints weight = 18852.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.124690 restraints weight = 16652.781| |-----------------------------------------------------------------------------| r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4000 r_free = 0.4000 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4000 r_free = 0.4000 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 22483 Z= 0.109 Angle : 0.493 10.025 30317 Z= 0.253 Chirality : 0.038 0.150 3282 Planarity : 0.003 0.047 3894 Dihedral : 3.974 50.274 2949 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.40 % Allowed : 26.23 % Favored : 69.37 % 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 aren not related in a simple way. whole: 1.06 (0.17), residues: 2622 helix: 1.80 (0.13), residues: 1505 sheet: -0.65 (0.38), residues: 203 loop : -0.83 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1229 TYR 0.027 0.001 TYR M 211 PHE 0.027 0.001 PHE D1224 TRP 0.010 0.001 TRP D1151 HIS 0.009 0.001 HIS H 106 Details of bonding type rmsd covalent geometry : bond 0.00241 (22481) covalent geometry : angle 0.49329 (30317) hydrogen bonds : bond 0.03756 ( 1166) hydrogen bonds : angle 3.84023 ( 3450) metal coordination : bond 0.00035 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 251 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 314 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6615 (tt) REVERT: A 762 ASP cc_start: 0.8633 (t70) cc_final: 0.8249 (t0) REVERT: A 838 ILE cc_start: 0.5971 (OUTLIER) cc_final: 0.5643 (mt) REVERT: A 841 MET cc_start: 0.6281 (tmm) cc_final: 0.5368 (ppp) REVERT: L 131 MET cc_start: 0.7454 (tpp) cc_final: 0.7172 (tmm) REVERT: L 134 HIS cc_start: 0.7733 (OUTLIER) cc_final: 0.6448 (t70) REVERT: L 137 LEU cc_start: 0.5325 (OUTLIER) cc_final: 0.5004 (mp) REVERT: M 88 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7655 (mt-10) REVERT: M 343 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7711 (pm20) REVERT: B 270 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.6729 (tm-30) REVERT: B 375 ASN cc_start: 0.8272 (OUTLIER) cc_final: 0.7956 (t0) REVERT: E 55 TYR cc_start: 0.6804 (OUTLIER) cc_final: 0.5878 (t80) REVERT: K 102 GLU cc_start: 0.6148 (OUTLIER) cc_final: 0.5842 (tt0) REVERT: K 152 PHE cc_start: 0.6558 (OUTLIER) cc_final: 0.6340 (t80) REVERT: D 818 ASP cc_start: 0.7649 (t0) cc_final: 0.7308 (t0) REVERT: D 956 LYS cc_start: 0.8271 (tptt) cc_final: 0.7936 (tptt) REVERT: D 993 ASP cc_start: 0.6638 (m-30) cc_final: 0.6403 (m-30) REVERT: D 1159 LEU cc_start: 0.7748 (mp) cc_final: 0.7254 (mp) REVERT: D 1204 TYR cc_start: 0.7809 (OUTLIER) cc_final: 0.6020 (t80) outliers start: 105 outliers final: 67 residues processed: 332 average time/residue: 0.1524 time to fit residues: 80.9756 Evaluate side-chains 314 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 235 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain A residue 698 ASP Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1230 GLN Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain L residue 36 ASP Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 134 HIS Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain M residue 32 ARG Chi-restraints excluded: chain M residue 88 GLU Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain M residue 201 ILE Chi-restraints excluded: chain M residue 222 HIS Chi-restraints excluded: chain M residue 337 GLU Chi-restraints excluded: chain M residue 343 GLN Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 270 LYS Chi-restraints excluded: chain G residue 283 THR Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 270 GLN Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 TYR Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 306 MET Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain K residue 75 PHE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain D residue 676 ILE Chi-restraints excluded: chain D residue 777 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 901 LYS Chi-restraints excluded: chain D residue 943 LEU Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 991 LEU Chi-restraints excluded: chain D residue 1021 PHE Chi-restraints excluded: chain D residue 1204 TYR Chi-restraints excluded: chain D residue 1228 LEU Chi-restraints excluded: chain D residue 1239 LEU Chi-restraints excluded: chain D residue 1255 THR Chi-restraints excluded: chain D residue 1270 VAL Chi-restraints excluded: chain D residue 1297 THR Chi-restraints excluded: chain D residue 1316 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 57 optimal weight: 0.9980 chunk 209 optimal weight: 0.0980 chunk 123 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 237 optimal weight: 0.9980 chunk 252 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 71 ASN L 88 HIS ** M 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 HIS ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.142004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.121436 restraints weight = 78991.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.123720 restraints weight = 40317.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.124209 restraints weight = 30619.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.125116 restraints weight = 21188.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.125418 restraints weight = 18348.647| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4005 r_free = 0.4005 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4005 r_free = 0.4005 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 22483 Z= 0.110 Angle : 0.505 10.115 30317 Z= 0.256 Chirality : 0.038 0.151 3282 Planarity : 0.003 0.042 3894 Dihedral : 3.964 51.037 2949 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 5.06 % Allowed : 25.66 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.17), residues: 2622 helix: 1.81 (0.13), residues: 1505 sheet: -0.69 (0.38), residues: 203 loop : -0.80 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1229 TYR 0.025 0.001 TYR M 211 PHE 0.050 0.001 PHE D1017 TRP 0.011 0.001 TRP D1151 HIS 0.009 0.001 HIS H 106 Details of bonding type rmsd covalent geometry : bond 0.00245 (22481) covalent geometry : angle 0.50465 (30317) hydrogen bonds : bond 0.03707 ( 1166) hydrogen bonds : angle 3.78724 ( 3450) metal coordination : bond 0.00111 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 246 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 314 LEU cc_start: 0.6815 (OUTLIER) cc_final: 0.6603 (tt) REVERT: A 762 ASP cc_start: 0.8414 (t70) cc_final: 0.7954 (t0) REVERT: A 838 ILE cc_start: 0.5805 (OUTLIER) cc_final: 0.5481 (mt) REVERT: A 841 MET cc_start: 0.6142 (tmm) cc_final: 0.5194 (ppp) REVERT: L 131 MET cc_start: 0.7505 (tpp) cc_final: 0.7191 (tmm) REVERT: L 134 HIS cc_start: 0.7755 (OUTLIER) cc_final: 0.6471 (t70) REVERT: L 137 LEU cc_start: 0.5430 (OUTLIER) cc_final: 0.5104 (mp) REVERT: M 88 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7582 (mt-10) REVERT: M 343 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7658 (pm20) REVERT: B 270 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.6664 (tm-30) REVERT: B 375 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.7960 (t0) REVERT: E 160 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.8690 (m-80) REVERT: E 230 LYS cc_start: 0.6987 (OUTLIER) cc_final: 0.6278 (ttmt) REVERT: K 102 GLU cc_start: 0.6093 (OUTLIER) cc_final: 0.5779 (tt0) REVERT: K 182 ARG cc_start: 0.7833 (ttt-90) cc_final: 0.7576 (tpt-90) REVERT: D 818 ASP cc_start: 0.7676 (t0) cc_final: 0.7308 (t0) REVERT: D 948 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6378 (mm) REVERT: D 956 LYS cc_start: 0.8228 (tptt) cc_final: 0.7937 (tptt) REVERT: D 993 ASP cc_start: 0.6659 (m-30) cc_final: 0.6412 (m-30) REVERT: D 1159 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7593 (mp) REVERT: D 1204 TYR cc_start: 0.7789 (OUTLIER) cc_final: 0.5909 (t80) REVERT: D 1257 MET cc_start: 0.8196 (tmm) cc_final: 0.7913 (tmm) outliers start: 121 outliers final: 81 residues processed: 342 average time/residue: 0.1567 time to fit residues: 84.7720 Evaluate side-chains 326 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 231 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 698 ASP Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1230 GLN Chi-restraints excluded: chain A residue 1295 SER Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain L residue 14 ILE Chi-restraints excluded: chain L residue 36 ASP Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 71 ASN Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 134 HIS Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain M residue 32 ARG Chi-restraints excluded: chain M residue 88 GLU Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain M residue 201 ILE Chi-restraints excluded: chain M residue 222 HIS Chi-restraints excluded: chain M residue 337 GLU Chi-restraints excluded: chain M residue 343 GLN Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 283 THR Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 270 GLN Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 TYR Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 306 MET Chi-restraints excluded: chain E residue 316 ARG Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain K residue 75 PHE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain D residue 676 ILE Chi-restraints excluded: chain D residue 686 LEU Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 777 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 833 THR Chi-restraints excluded: chain D residue 901 LYS Chi-restraints excluded: chain D residue 943 LEU Chi-restraints excluded: chain D residue 948 LEU Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 1159 LEU Chi-restraints excluded: chain D residue 1204 TYR Chi-restraints excluded: chain D residue 1215 ILE Chi-restraints excluded: chain D residue 1228 LEU Chi-restraints excluded: chain D residue 1239 LEU Chi-restraints excluded: chain D residue 1255 THR Chi-restraints excluded: chain D residue 1270 VAL Chi-restraints excluded: chain D residue 1290 VAL Chi-restraints excluded: chain D residue 1297 THR Chi-restraints excluded: chain D residue 1316 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 44 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 212 optimal weight: 0.8980 chunk 230 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 chunk 220 optimal weight: 6.9990 chunk 167 optimal weight: 1.9990 chunk 209 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 71 ASN L 88 HIS M 296 GLN ** M 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.141551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.120733 restraints weight = 92341.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.123051 restraints weight = 50364.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.123862 restraints weight = 34676.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.125239 restraints weight = 23335.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.125444 restraints weight = 20096.944| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4003 r_free = 0.4003 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4003 r_free = 0.4003 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22483 Z= 0.116 Angle : 0.511 10.251 30317 Z= 0.259 Chirality : 0.038 0.162 3282 Planarity : 0.003 0.044 3894 Dihedral : 3.820 47.964 2947 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.89 % Allowed : 26.23 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.17), residues: 2622 helix: 1.80 (0.13), residues: 1505 sheet: -0.69 (0.38), residues: 203 loop : -0.79 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 757 TYR 0.024 0.001 TYR M 211 PHE 0.021 0.001 PHE A1180 TRP 0.010 0.001 TRP D1151 HIS 0.009 0.001 HIS H 106 Details of bonding type rmsd covalent geometry : bond 0.00262 (22481) covalent geometry : angle 0.51149 (30317) hydrogen bonds : bond 0.03722 ( 1166) hydrogen bonds : angle 3.79546 ( 3450) metal coordination : bond 0.00133 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 241 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 ASP cc_start: 0.8529 (t70) cc_final: 0.8045 (t0) REVERT: A 838 ILE cc_start: 0.5818 (OUTLIER) cc_final: 0.5476 (mt) REVERT: A 841 MET cc_start: 0.5888 (tmm) cc_final: 0.5174 (ppp) REVERT: L 131 MET cc_start: 0.7496 (tpp) cc_final: 0.7177 (tmm) REVERT: L 134 HIS cc_start: 0.7758 (OUTLIER) cc_final: 0.6481 (t70) REVERT: L 137 LEU cc_start: 0.5450 (OUTLIER) cc_final: 0.5124 (mp) REVERT: M 88 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7612 (mt-10) REVERT: M 343 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7655 (pm20) REVERT: B 270 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.6666 (tm-30) REVERT: E 55 TYR cc_start: 0.6766 (OUTLIER) cc_final: 0.5776 (t80) REVERT: E 160 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8694 (m-80) REVERT: E 230 LYS cc_start: 0.7103 (OUTLIER) cc_final: 0.6461 (ttmt) REVERT: K 102 GLU cc_start: 0.6106 (OUTLIER) cc_final: 0.5793 (tt0) REVERT: D 818 ASP cc_start: 0.7676 (t0) cc_final: 0.7380 (t0) REVERT: D 956 LYS cc_start: 0.8247 (tptt) cc_final: 0.7940 (tptt) REVERT: D 993 ASP cc_start: 0.6672 (m-30) cc_final: 0.6415 (m-30) REVERT: D 1159 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7631 (mp) REVERT: D 1204 TYR cc_start: 0.7771 (OUTLIER) cc_final: 0.5849 (t80) REVERT: D 1257 MET cc_start: 0.8276 (tmm) cc_final: 0.7954 (tmm) REVERT: D 1261 LYS cc_start: 0.3779 (tptt) cc_final: 0.3506 (tptt) outliers start: 117 outliers final: 87 residues processed: 333 average time/residue: 0.1541 time to fit residues: 81.7276 Evaluate side-chains 330 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 231 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 698 ASP Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 1004 ASN Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1230 GLN Chi-restraints excluded: chain A residue 1237 PHE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 172 GLU Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain L residue 36 ASP Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 134 HIS Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain M residue 32 ARG Chi-restraints excluded: chain M residue 88 GLU Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain M residue 201 ILE Chi-restraints excluded: chain M residue 222 HIS Chi-restraints excluded: chain M residue 337 GLU Chi-restraints excluded: chain M residue 343 GLN Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 283 THR Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 270 GLN Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 TYR Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 306 MET Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain K residue 75 PHE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain D residue 676 ILE Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 777 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 833 THR Chi-restraints excluded: chain D residue 901 LYS Chi-restraints excluded: chain D residue 943 LEU Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 991 LEU Chi-restraints excluded: chain D residue 1159 LEU Chi-restraints excluded: chain D residue 1204 TYR Chi-restraints excluded: chain D residue 1205 LYS Chi-restraints excluded: chain D residue 1215 ILE Chi-restraints excluded: chain D residue 1228 LEU Chi-restraints excluded: chain D residue 1255 THR Chi-restraints excluded: chain D residue 1270 VAL Chi-restraints excluded: chain D residue 1290 VAL Chi-restraints excluded: chain D residue 1297 THR Chi-restraints excluded: chain D residue 1316 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 168 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 260 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 226 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 167 optimal weight: 0.8980 chunk 145 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 71 ASN L 88 HIS ** M 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.141206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.120501 restraints weight = 60683.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.122913 restraints weight = 32896.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.123660 restraints weight = 20396.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.124397 restraints weight = 16219.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.124590 restraints weight = 14978.907| |-----------------------------------------------------------------------------| r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3994 r_free = 0.3994 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3994 r_free = 0.3994 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22483 Z= 0.124 Angle : 0.524 10.620 30317 Z= 0.266 Chirality : 0.038 0.162 3282 Planarity : 0.003 0.047 3894 Dihedral : 3.871 48.676 2947 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 5.10 % Allowed : 26.15 % Favored : 68.75 % 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 aren not related in a simple way. whole: 1.02 (0.17), residues: 2622 helix: 1.75 (0.13), residues: 1506 sheet: -0.72 (0.38), residues: 203 loop : -0.79 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 294 TYR 0.022 0.001 TYR M 211 PHE 0.017 0.001 PHE B 77 TRP 0.013 0.001 TRP D1151 HIS 0.007 0.001 HIS A1311 Details of bonding type rmsd covalent geometry : bond 0.00281 (22481) covalent geometry : angle 0.52403 (30317) hydrogen bonds : bond 0.03794 ( 1166) hydrogen bonds : angle 3.81481 ( 3450) metal coordination : bond 0.00206 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 241 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 ASP cc_start: 0.8541 (t70) cc_final: 0.8049 (t0) REVERT: A 838 ILE cc_start: 0.5935 (OUTLIER) cc_final: 0.5693 (mt) REVERT: A 841 MET cc_start: 0.5886 (tmm) cc_final: 0.5186 (ppp) REVERT: L 131 MET cc_start: 0.7545 (tpp) cc_final: 0.7237 (tmm) REVERT: L 134 HIS cc_start: 0.7680 (OUTLIER) cc_final: 0.6345 (t70) REVERT: L 137 LEU cc_start: 0.5343 (OUTLIER) cc_final: 0.5031 (mp) REVERT: M 343 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7667 (pm20) REVERT: B 270 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.6887 (tm-30) REVERT: B 375 ASN cc_start: 0.8239 (OUTLIER) cc_final: 0.7091 (m-40) REVERT: E 160 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8723 (m-80) REVERT: E 230 LYS cc_start: 0.6950 (OUTLIER) cc_final: 0.6342 (ttmt) REVERT: K 102 GLU cc_start: 0.6193 (OUTLIER) cc_final: 0.5925 (tt0) REVERT: D 818 ASP cc_start: 0.7646 (t0) cc_final: 0.7371 (t0) REVERT: D 993 ASP cc_start: 0.6662 (m-30) cc_final: 0.6418 (m-30) REVERT: D 1159 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7516 (mp) REVERT: D 1204 TYR cc_start: 0.7663 (OUTLIER) cc_final: 0.5779 (t80) REVERT: D 1261 LYS cc_start: 0.3328 (tptt) cc_final: 0.3020 (tptt) REVERT: D 1313 SER cc_start: 0.7396 (OUTLIER) cc_final: 0.7027 (t) outliers start: 122 outliers final: 96 residues processed: 337 average time/residue: 0.1492 time to fit residues: 81.2097 Evaluate side-chains 338 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 230 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 698 ASP Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1004 ASN Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1230 GLN Chi-restraints excluded: chain A residue 1237 PHE Chi-restraints excluded: chain A residue 1295 SER Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 172 GLU Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain L residue 14 ILE Chi-restraints excluded: chain L residue 36 ASP Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 134 HIS Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain M residue 32 ARG Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain M residue 201 ILE Chi-restraints excluded: chain M residue 222 HIS Chi-restraints excluded: chain M residue 337 GLU Chi-restraints excluded: chain M residue 343 GLN Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 283 THR Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 270 GLN Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 TYR Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 306 MET Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain K residue 75 PHE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain D residue 676 ILE Chi-restraints excluded: chain D residue 686 LEU Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 833 THR Chi-restraints excluded: chain D residue 901 LYS Chi-restraints excluded: chain D residue 943 LEU Chi-restraints excluded: chain D residue 944 THR Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 991 LEU Chi-restraints excluded: chain D residue 1159 LEU Chi-restraints excluded: chain D residue 1204 TYR Chi-restraints excluded: chain D residue 1205 LYS Chi-restraints excluded: chain D residue 1215 ILE Chi-restraints excluded: chain D residue 1228 LEU Chi-restraints excluded: chain D residue 1255 THR Chi-restraints excluded: chain D residue 1270 VAL Chi-restraints excluded: chain D residue 1290 VAL Chi-restraints excluded: chain D residue 1297 THR Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain D residue 1316 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 4 optimal weight: 0.8980 chunk 199 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 255 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 139 optimal weight: 0.0570 chunk 231 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 71 ASN L 88 HIS ** M 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.142348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.121501 restraints weight = 83967.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.124070 restraints weight = 44305.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.124633 restraints weight = 32250.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.125644 restraints weight = 22192.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.126014 restraints weight = 19070.437| |-----------------------------------------------------------------------------| r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4007 r_free = 0.4007 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4007 r_free = 0.4007 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 22483 Z= 0.109 Angle : 0.521 12.590 30317 Z= 0.263 Chirality : 0.038 0.152 3282 Planarity : 0.003 0.048 3894 Dihedral : 3.801 49.940 2947 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.52 % Allowed : 26.77 % Favored : 68.71 % 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 aren not related in a simple way. whole: 1.09 (0.17), residues: 2622 helix: 1.80 (0.13), residues: 1506 sheet: -0.67 (0.37), residues: 207 loop : -0.74 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 757 TYR 0.022 0.001 TYR M 211 PHE 0.015 0.001 PHE B 77 TRP 0.012 0.001 TRP D1151 HIS 0.007 0.001 HIS A1311 Details of bonding type rmsd covalent geometry : bond 0.00243 (22481) covalent geometry : angle 0.52090 (30317) hydrogen bonds : bond 0.03678 ( 1166) hydrogen bonds : angle 3.77585 ( 3450) metal coordination : bond 0.00107 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 244 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 ASP cc_start: 0.8777 (t70) cc_final: 0.8278 (t0) REVERT: A 841 MET cc_start: 0.5948 (tmm) cc_final: 0.5158 (ppp) REVERT: L 131 MET cc_start: 0.7731 (tpp) cc_final: 0.7351 (tmm) REVERT: L 134 HIS cc_start: 0.7711 (OUTLIER) cc_final: 0.6489 (t70) REVERT: L 137 LEU cc_start: 0.5410 (OUTLIER) cc_final: 0.5099 (mp) REVERT: M 166 LEU cc_start: 0.7593 (tt) cc_final: 0.7084 (pp) REVERT: M 343 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7660 (pm20) REVERT: B 270 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.6674 (tm-30) REVERT: E 55 TYR cc_start: 0.6732 (OUTLIER) cc_final: 0.5768 (t80) REVERT: E 160 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.8719 (m-80) REVERT: E 176 TYR cc_start: 0.6435 (m-80) cc_final: 0.5942 (m-80) REVERT: E 230 LYS cc_start: 0.6955 (OUTLIER) cc_final: 0.6299 (ttmt) REVERT: K 102 GLU cc_start: 0.6095 (OUTLIER) cc_final: 0.5777 (tt0) REVERT: D 818 ASP cc_start: 0.7678 (t0) cc_final: 0.7394 (t0) REVERT: D 956 LYS cc_start: 0.8225 (tptt) cc_final: 0.7921 (tptt) REVERT: D 993 ASP cc_start: 0.6675 (m-30) cc_final: 0.6452 (m-30) REVERT: D 1159 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7661 (mp) REVERT: D 1204 TYR cc_start: 0.7041 (OUTLIER) cc_final: 0.5347 (t80) REVERT: D 1313 SER cc_start: 0.7344 (OUTLIER) cc_final: 0.6983 (t) outliers start: 108 outliers final: 88 residues processed: 331 average time/residue: 0.1519 time to fit residues: 80.9068 Evaluate side-chains 334 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 235 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 698 ASP Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1004 ASN Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1230 GLN Chi-restraints excluded: chain A residue 1237 PHE Chi-restraints excluded: chain A residue 1295 SER Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 172 GLU Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain L residue 14 ILE Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 71 ASN Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 134 HIS Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain M residue 32 ARG Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain M residue 201 ILE Chi-restraints excluded: chain M residue 222 HIS Chi-restraints excluded: chain M residue 337 GLU Chi-restraints excluded: chain M residue 343 GLN Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 283 THR Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 270 GLN Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 TYR Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 306 MET Chi-restraints excluded: chain E residue 316 ARG Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 330 ASN Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain K residue 75 PHE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain D residue 676 ILE Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 833 THR Chi-restraints excluded: chain D residue 901 LYS Chi-restraints excluded: chain D residue 943 LEU Chi-restraints excluded: chain D residue 944 THR Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 991 LEU Chi-restraints excluded: chain D residue 1159 LEU Chi-restraints excluded: chain D residue 1204 TYR Chi-restraints excluded: chain D residue 1205 LYS Chi-restraints excluded: chain D residue 1215 ILE Chi-restraints excluded: chain D residue 1228 LEU Chi-restraints excluded: chain D residue 1255 THR Chi-restraints excluded: chain D residue 1290 VAL Chi-restraints excluded: chain D residue 1297 THR Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain D residue 1316 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 29 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 125 optimal weight: 0.0270 chunk 256 optimal weight: 0.8980 chunk 141 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 204 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 202 optimal weight: 0.8980 chunk 250 optimal weight: 1.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 HIS ** M 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.142073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.121178 restraints weight = 81831.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.124175 restraints weight = 41658.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.124889 restraints weight = 25858.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.125264 restraints weight = 20053.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.125949 restraints weight = 18056.169| |-----------------------------------------------------------------------------| r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4016 r_free = 0.4016 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4016 r_free = 0.4016 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 22483 Z= 0.107 Angle : 0.524 12.778 30317 Z= 0.264 Chirality : 0.038 0.170 3282 Planarity : 0.003 0.050 3894 Dihedral : 3.772 50.806 2945 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.28 % Allowed : 27.22 % Favored : 68.50 % 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 aren not related in a simple way. whole: 1.11 (0.17), residues: 2622 helix: 1.80 (0.13), residues: 1507 sheet: -0.69 (0.37), residues: 207 loop : -0.71 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 757 TYR 0.022 0.001 TYR M 211 PHE 0.017 0.001 PHE K 152 TRP 0.013 0.001 TRP D1151 HIS 0.006 0.001 HIS A1311 Details of bonding type rmsd covalent geometry : bond 0.00237 (22481) covalent geometry : angle 0.52419 (30317) hydrogen bonds : bond 0.03641 ( 1166) hydrogen bonds : angle 3.75657 ( 3450) metal coordination : bond 0.00068 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 239 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 ASP cc_start: 0.8775 (t70) cc_final: 0.8259 (t0) REVERT: A 841 MET cc_start: 0.5941 (tmm) cc_final: 0.5199 (ppp) REVERT: L 131 MET cc_start: 0.7675 (tpp) cc_final: 0.7254 (tmm) REVERT: L 134 HIS cc_start: 0.7690 (OUTLIER) cc_final: 0.6478 (t70) REVERT: L 137 LEU cc_start: 0.5385 (OUTLIER) cc_final: 0.5116 (mp) REVERT: M 166 LEU cc_start: 0.7569 (tt) cc_final: 0.7107 (pp) REVERT: M 343 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7480 (pm20) REVERT: E 55 TYR cc_start: 0.6788 (OUTLIER) cc_final: 0.5944 (t80) REVERT: E 160 PHE cc_start: 0.9080 (OUTLIER) cc_final: 0.8728 (m-80) REVERT: E 176 TYR cc_start: 0.6212 (m-80) cc_final: 0.5874 (m-80) REVERT: E 230 LYS cc_start: 0.6918 (OUTLIER) cc_final: 0.6305 (ttmt) REVERT: K 102 GLU cc_start: 0.6062 (OUTLIER) cc_final: 0.5731 (tt0) REVERT: D 818 ASP cc_start: 0.7632 (t0) cc_final: 0.7354 (t0) REVERT: D 956 LYS cc_start: 0.8180 (tptt) cc_final: 0.7901 (tptt) REVERT: D 1159 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7698 (mp) REVERT: D 1313 SER cc_start: 0.7333 (OUTLIER) cc_final: 0.6872 (t) outliers start: 102 outliers final: 86 residues processed: 322 average time/residue: 0.1525 time to fit residues: 78.9434 Evaluate side-chains 327 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 232 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 698 ASP Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1004 ASN Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1230 GLN Chi-restraints excluded: chain A residue 1237 PHE Chi-restraints excluded: chain A residue 1295 SER Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 172 GLU Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 134 HIS Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain M residue 32 ARG Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain M residue 201 ILE Chi-restraints excluded: chain M residue 222 HIS Chi-restraints excluded: chain M residue 337 GLU Chi-restraints excluded: chain M residue 343 GLN Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 270 LYS Chi-restraints excluded: chain G residue 283 THR Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 TYR Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 306 MET Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 330 ASN Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain K residue 75 PHE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain D residue 676 ILE Chi-restraints excluded: chain D residue 686 LEU Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 833 THR Chi-restraints excluded: chain D residue 901 LYS Chi-restraints excluded: chain D residue 943 LEU Chi-restraints excluded: chain D residue 944 THR Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 991 LEU Chi-restraints excluded: chain D residue 1159 LEU Chi-restraints excluded: chain D residue 1205 LYS Chi-restraints excluded: chain D residue 1215 ILE Chi-restraints excluded: chain D residue 1228 LEU Chi-restraints excluded: chain D residue 1255 THR Chi-restraints excluded: chain D residue 1270 VAL Chi-restraints excluded: chain D residue 1290 VAL Chi-restraints excluded: chain D residue 1297 THR Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain D residue 1316 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 166 optimal weight: 5.9990 chunk 97 optimal weight: 0.1980 chunk 225 optimal weight: 0.6980 chunk 246 optimal weight: 0.3980 chunk 140 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 193 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 196 optimal weight: 4.9990 chunk 102 optimal weight: 0.0370 chunk 199 optimal weight: 0.6980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 71 ASN L 88 HIS M 230 ASN ** M 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.143279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.122837 restraints weight = 68811.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.124652 restraints weight = 37005.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.125982 restraints weight = 23254.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.126348 restraints weight = 18008.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.126637 restraints weight = 17335.386| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4027 r_free = 0.4027 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4027 r_free = 0.4027 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 22483 Z= 0.101 Angle : 0.528 13.403 30317 Z= 0.263 Chirality : 0.038 0.242 3282 Planarity : 0.003 0.051 3894 Dihedral : 3.697 52.114 2945 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.50 % Allowed : 27.84 % Favored : 68.67 % 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 aren not related in a simple way. whole: 1.20 (0.17), residues: 2622 helix: 1.88 (0.13), residues: 1506 sheet: -0.62 (0.38), residues: 207 loop : -0.67 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 757 TYR 0.021 0.001 TYR M 211 PHE 0.022 0.001 PHE A1180 TRP 0.018 0.001 TRP D1151 HIS 0.006 0.001 HIS A1311 Details of bonding type rmsd covalent geometry : bond 0.00220 (22481) covalent geometry : angle 0.52780 (30317) hydrogen bonds : bond 0.03520 ( 1166) hydrogen bonds : angle 3.70613 ( 3450) metal coordination : bond 0.00041 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 251 time to evaluate : 0.908 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 762 ASP cc_start: 0.8750 (t70) cc_final: 0.8266 (t70) REVERT: A 841 MET cc_start: 0.5688 (tmm) cc_final: 0.4817 (ppp) REVERT: L 106 LEU cc_start: 0.6764 (mt) cc_final: 0.6244 (mm) REVERT: L 131 MET cc_start: 0.7726 (tpp) cc_final: 0.7317 (tmm) REVERT: L 134 HIS cc_start: 0.7725 (OUTLIER) cc_final: 0.6576 (t70) REVERT: L 137 LEU cc_start: 0.5281 (OUTLIER) cc_final: 0.4931 (mp) REVERT: M 166 LEU cc_start: 0.7496 (tt) cc_final: 0.7117 (pp) REVERT: M 343 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7393 (pm20) REVERT: B 330 ASN cc_start: 0.8661 (m110) cc_final: 0.8300 (m110) REVERT: E 160 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8721 (m-80) REVERT: E 176 TYR cc_start: 0.6185 (m-80) cc_final: 0.5243 (m-80) REVERT: E 230 LYS cc_start: 0.6879 (OUTLIER) cc_final: 0.6277 (ttmt) REVERT: K 102 GLU cc_start: 0.5964 (OUTLIER) cc_final: 0.5615 (tt0) REVERT: D 818 ASP cc_start: 0.7527 (t0) cc_final: 0.7312 (t0) REVERT: D 956 LYS cc_start: 0.8180 (tptt) cc_final: 0.7876 (tptt) REVERT: D 1159 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7553 (mp) REVERT: D 1313 SER cc_start: 0.7299 (OUTLIER) cc_final: 0.6840 (t) outliers start: 83 outliers final: 70 residues processed: 318 average time/residue: 0.1509 time to fit residues: 76.9083 Evaluate side-chains 317 residues out of total 2430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 239 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 55 HIS Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1230 GLN Chi-restraints excluded: chain A residue 1237 PHE Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 172 GLU Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain L residue 71 ASN Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain L residue 134 HIS Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain M residue 32 ARG Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain M residue 222 HIS Chi-restraints excluded: chain M residue 337 GLU Chi-restraints excluded: chain M residue 343 GLN Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 270 LYS Chi-restraints excluded: chain G residue 283 THR Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 55 TYR Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 230 LYS Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 306 MET Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 330 ASN Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain K residue 75 PHE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain D residue 676 ILE Chi-restraints excluded: chain D residue 686 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 833 THR Chi-restraints excluded: chain D residue 901 LYS Chi-restraints excluded: chain D residue 943 LEU Chi-restraints excluded: chain D residue 944 THR Chi-restraints excluded: chain D residue 949 ILE Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 991 LEU Chi-restraints excluded: chain D residue 1159 LEU Chi-restraints excluded: chain D residue 1205 LYS Chi-restraints excluded: chain D residue 1215 ILE Chi-restraints excluded: chain D residue 1228 LEU Chi-restraints excluded: chain D residue 1255 THR Chi-restraints excluded: chain D residue 1270 VAL Chi-restraints excluded: chain D residue 1297 THR Chi-restraints excluded: chain D residue 1313 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 121 optimal weight: 0.0870 chunk 234 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 211 optimal weight: 5.9990 chunk 204 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 253 optimal weight: 0.0980 chunk 221 optimal weight: 0.9980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 71 ASN L 88 HIS M 230 ASN ** M 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.143316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.122426 restraints weight = 90753.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.125120 restraints weight = 47310.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.125800 restraints weight = 32115.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.126546 restraints weight = 22746.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.126967 restraints weight = 20139.004| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4028 r_free = 0.4028 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4028 r_free = 0.4028 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 22483 Z= 0.134 Angle : 0.691 59.188 30317 Z= 0.391 Chirality : 0.038 0.180 3282 Planarity : 0.003 0.050 3894 Dihedral : 3.713 52.098 2945 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.45 % Allowed : 27.96 % Favored : 68.59 % Cbeta Deviations : 0.04 % 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 aren not related in a simple way. whole: 1.19 (0.17), residues: 2622 helix: 1.87 (0.13), residues: 1506 sheet: -0.62 (0.38), residues: 207 loop : -0.67 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 757 TYR 0.024 0.001 TYR M 211 PHE 0.014 0.001 PHE J 170 TRP 0.016 0.001 TRP D1151 HIS 0.014 0.001 HIS E 78 Details of bonding type rmsd covalent geometry : bond 0.00262 (22481) covalent geometry : angle 0.69121 (30317) hydrogen bonds : bond 0.03569 ( 1166) hydrogen bonds : angle 3.71381 ( 3450) metal coordination : bond 0.00060 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3993.91 seconds wall clock time: 70 minutes 16.34 seconds (4216.34 seconds total)