Starting phenix.real_space_refine on Sun Jul 5 09:07:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vj9_65107/07_2026/9vj9_65107.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vj9_65107/07_2026/9vj9_65107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vj9_65107/07_2026/9vj9_65107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vj9_65107/07_2026/9vj9_65107.map" model { file = "/net/cci-nas-00/data/ceres_data/9vj9_65107/07_2026/9vj9_65107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vj9_65107/07_2026/9vj9_65107.cif" } resolution = 2.96 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= 0.001 sd= 0.021 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 P 178 5.49 5 S 65 5.16 5 C 16321 2.51 5 N 4422 2.21 5 O 5429 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26415 Number of models: 1 Model: "" Number of chains: 11 Chain: "B" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1790 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 3, 'TRANS': 215} Chain: "C" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1790 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 3, 'TRANS': 215} Chain: "D" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1790 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 3, 'TRANS': 215} Chain: "A" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1790 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 3, 'TRANS': 215} Chain: "K" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2347 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 278} Chain: "L" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2351 Classifications: {'peptide': 287} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain: "N" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 928 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain: "T" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 917 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain: "g" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 566 Classifications: {'RNA': 27} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 4, 'rna3p_pur': 9, 'rna3p_pyr': 13} Link IDs: {'rna2p': 5, 'rna3p': 21} Chain: "t" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1300 Classifications: {'RNA': 61} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 10, 'rna3p_pur': 30, 'rna3p_pyr': 18} Link IDs: {'rna2p': 13, 'rna3p': 47} Chain: "S" Number of atoms: 10846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1322, 10846 Classifications: {'peptide': 1322} Link IDs: {'PTRANS': 40, 'TRANS': 1281} Chain breaks: 1 Time building chain proxies: 4.79, per 1000 atoms: 0.18 Number of scatterers: 26415 At special positions: 0 Unit cell: (106.248, 165.896, 172.42, 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) S 65 16.00 P 178 15.00 O 5429 8.00 N 4422 7.00 C 16321 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: 2.10 Conformation dependent library (CDL) restraints added in 1.0 seconds 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5302 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 26 sheets defined 51.7% alpha, 10.3% beta 65 base pairs and 111 stacking pairs defined. Time for finding SS restraints: 3.06 Creating SS restraints... Processing helix chain 'B' and resid 24 through 37 Processing helix chain 'B' and resid 64 through 68 removed outlier: 3.789A pdb=" N GLY B 67 " --> pdb=" O ASP B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 90 removed outlier: 3.558A pdb=" N LYS B 90 " --> pdb=" O GLN B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 115 removed outlier: 3.521A pdb=" N LYS B 94 " --> pdb=" O LYS B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 134 Processing helix chain 'B' and resid 143 through 158 Processing helix chain 'B' and resid 169 through 172 removed outlier: 3.640A pdb=" N TYR B 172 " --> pdb=" O ALA B 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 169 through 172' Processing helix chain 'B' and resid 174 through 189 Processing helix chain 'C' and resid 24 through 37 Processing helix chain 'C' and resid 55 through 57 No H-bonds generated for 'chain 'C' and resid 55 through 57' Processing helix chain 'C' and resid 64 through 68 removed outlier: 3.506A pdb=" N GLY C 67 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR C 68 " --> pdb=" O ILE C 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 64 through 68' Processing helix chain 'C' and resid 72 through 89 Processing helix chain 'C' and resid 90 through 115 removed outlier: 4.190A pdb=" N MET C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 134 Processing helix chain 'C' and resid 143 through 158 Processing helix chain 'C' and resid 174 through 189 Processing helix chain 'D' and resid 24 through 36 Processing helix chain 'D' and resid 64 through 68 removed outlier: 3.604A pdb=" N GLY D 67 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR D 68 " --> pdb=" O ILE D 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 64 through 68' Processing helix chain 'D' and resid 72 through 90 removed outlier: 3.761A pdb=" N LYS D 90 " --> pdb=" O GLN D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 114 removed outlier: 3.540A pdb=" N LYS D 94 " --> pdb=" O LYS D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 134 Processing helix chain 'D' and resid 143 through 158 Processing helix chain 'D' and resid 174 through 189 Processing helix chain 'A' and resid 24 through 37 Processing helix chain 'A' and resid 55 through 59 removed outlier: 3.595A pdb=" N LEU A 59 " --> pdb=" O PRO A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 90 Processing helix chain 'A' and resid 90 through 115 Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 143 through 158 Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'K' and resid 51 through 59 Processing helix chain 'K' and resid 88 through 95 Processing helix chain 'K' and resid 97 through 123 removed outlier: 4.201A pdb=" N ARG K 123 " --> pdb=" O HIS K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 146 through 161 removed outlier: 3.590A pdb=" N LEU K 159 " --> pdb=" O TYR K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 170 through 195 Processing helix chain 'K' and resid 211 through 218 Processing helix chain 'K' and resid 219 through 221 No H-bonds generated for 'chain 'K' and resid 219 through 221' Processing helix chain 'K' and resid 222 through 232 removed outlier: 3.715A pdb=" N ASN K 232 " --> pdb=" O ILE K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 236 through 248 removed outlier: 3.964A pdb=" N PHE K 245 " --> pdb=" O LYS K 241 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA K 246 " --> pdb=" O ARG K 242 " (cutoff:3.500A) Processing helix chain 'K' and resid 261 through 277 removed outlier: 3.782A pdb=" N THR K 266 " --> pdb=" O THR K 262 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 60 Processing helix chain 'L' and resid 88 through 95 Processing helix chain 'L' and resid 97 through 122 Processing helix chain 'L' and resid 125 through 139 Processing helix chain 'L' and resid 146 through 160 removed outlier: 3.849A pdb=" N HIS L 150 " --> pdb=" O ASN L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 170 through 195 removed outlier: 3.506A pdb=" N ALA L 174 " --> pdb=" O ASN L 170 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 218 Processing helix chain 'L' and resid 221 through 231 removed outlier: 4.175A pdb=" N VAL L 225 " --> pdb=" O PHE L 221 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU L 231 " --> pdb=" O GLN L 227 " (cutoff:3.500A) Processing helix chain 'L' and resid 236 through 246 Processing helix chain 'L' and resid 262 through 278 removed outlier: 4.562A pdb=" N GLN L 278 " --> pdb=" O LYS L 274 " (cutoff:3.500A) Processing helix chain 'S' and resid 59 through 94 removed outlier: 4.947A pdb=" N GLU S 88 " --> pdb=" O ALA S 84 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ALA S 89 " --> pdb=" O PHE S 85 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP S 92 " --> pdb=" O GLU S 88 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU S 93 " --> pdb=" O ALA S 89 " (cutoff:3.500A) Processing helix chain 'S' and resid 96 through 103 Processing helix chain 'S' and resid 121 through 132 Processing helix chain 'S' and resid 134 through 145 removed outlier: 3.577A pdb=" N LEU S 138 " --> pdb=" O THR S 134 " (cutoff:3.500A) Processing helix chain 'S' and resid 150 through 164 Processing helix chain 'S' and resid 180 through 197 Processing helix chain 'S' and resid 223 through 235 removed outlier: 3.844A pdb=" N GLN S 234 " --> pdb=" O LYS S 230 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE S 235 " --> pdb=" O VAL S 231 " (cutoff:3.500A) Processing helix chain 'S' and resid 242 through 253 Processing helix chain 'S' and resid 258 through 263 Processing helix chain 'S' and resid 276 through 289 Processing helix chain 'S' and resid 292 through 310 Processing helix chain 'S' and resid 321 through 349 Processing helix chain 'S' and resid 349 through 358 Processing helix chain 'S' and resid 364 through 371 Processing helix chain 'S' and resid 376 through 388 Processing helix chain 'S' and resid 394 through 403 removed outlier: 3.862A pdb=" N LEU S 398 " --> pdb=" O ALA S 394 " (cutoff:3.500A) Processing helix chain 'S' and resid 412 through 418 removed outlier: 3.902A pdb=" N GLY S 416 " --> pdb=" O PHE S 413 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL S 417 " --> pdb=" O ASP S 414 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE S 418 " --> pdb=" O ASN S 415 " (cutoff:3.500A) Processing helix chain 'S' and resid 419 through 435 removed outlier: 4.015A pdb=" N HIS S 423 " --> pdb=" O PRO S 419 " (cutoff:3.500A) Processing helix chain 'S' and resid 438 through 444 removed outlier: 3.762A pdb=" N LYS S 442 " --> pdb=" O TYR S 438 " (cutoff:3.500A) Processing helix chain 'S' and resid 444 through 454 Processing helix chain 'S' and resid 492 through 504 Processing helix chain 'S' and resid 521 through 534 Processing helix chain 'S' and resid 549 through 561 Processing helix chain 'S' and resid 568 through 581 Processing helix chain 'S' and resid 599 through 608 removed outlier: 3.996A pdb=" N GLN S 603 " --> pdb=" O PHE S 599 " (cutoff:3.500A) Processing helix chain 'S' and resid 611 through 617 Processing helix chain 'S' and resid 620 through 634 Processing helix chain 'S' and resid 636 through 644 Processing helix chain 'S' and resid 645 through 647 No H-bonds generated for 'chain 'S' and resid 645 through 647' Processing helix chain 'S' and resid 652 through 660 removed outlier: 3.531A pdb=" N GLU S 660 " --> pdb=" O LEU S 656 " (cutoff:3.500A) Processing helix chain 'S' and resid 672 through 677 Processing helix chain 'S' and resid 686 through 693 Processing helix chain 'S' and resid 704 through 710 Processing helix chain 'S' and resid 715 through 725 Processing helix chain 'S' and resid 731 through 738 Processing helix chain 'S' and resid 742 through 764 Processing helix chain 'S' and resid 792 through 800 removed outlier: 4.261A pdb=" N ALA S 800 " --> pdb=" O GLU S 796 " (cutoff:3.500A) Processing helix chain 'S' and resid 801 through 803 No H-bonds generated for 'chain 'S' and resid 801 through 803' Processing helix chain 'S' and resid 806 through 810 Processing helix chain 'S' and resid 813 through 818 Processing helix chain 'S' and resid 819 through 828 removed outlier: 3.530A pdb=" N TYR S 826 " --> pdb=" O LEU S 822 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN S 828 " --> pdb=" O LEU S 824 " (cutoff:3.500A) Processing helix chain 'S' and resid 843 through 847 Processing helix chain 'S' and resid 862 through 864 No H-bonds generated for 'chain 'S' and resid 862 through 864' Processing helix chain 'S' and resid 883 through 890 Processing helix chain 'S' and resid 891 through 901 Processing helix chain 'S' and resid 904 through 916 Processing helix chain 'S' and resid 920 through 933 Processing helix chain 'S' and resid 936 through 951 Processing helix chain 'S' and resid 965 through 977 removed outlier: 3.988A pdb=" N THR S 969 " --> pdb=" O LYS S 965 " (cutoff:3.500A) Processing helix chain 'S' and resid 986 through 1007 removed outlier: 4.512A pdb=" N GLY S 990 " --> pdb=" O ASP S 986 " (cutoff:3.500A) Processing helix chain 'S' and resid 1010 through 1015 removed outlier: 3.896A pdb=" N PHE S1014 " --> pdb=" O LEU S1010 " (cutoff:3.500A) Processing helix chain 'S' and resid 1023 through 1035 Processing helix chain 'S' and resid 1061 through 1072 removed outlier: 3.666A pdb=" N LYS S1065 " --> pdb=" O ASN S1061 " (cutoff:3.500A) Processing helix chain 'S' and resid 1150 through 1157 Processing helix chain 'S' and resid 1157 through 1165 removed outlier: 3.694A pdb=" N LYS S1165 " --> pdb=" O PHE S1161 " (cutoff:3.500A) Processing helix chain 'S' and resid 1207 through 1221 removed outlier: 3.815A pdb=" N LEU S1221 " --> pdb=" O ALA S1217 " (cutoff:3.500A) Processing helix chain 'S' and resid 1227 through 1233 removed outlier: 3.641A pdb=" N GLU S1233 " --> pdb=" O LEU S1229 " (cutoff:3.500A) Processing helix chain 'S' and resid 1236 through 1251 removed outlier: 3.986A pdb=" N GLN S1240 " --> pdb=" O GLN S1236 " (cutoff:3.500A) Processing helix chain 'S' and resid 1256 through 1270 Processing helix chain 'S' and resid 1274 through 1285 Processing helix chain 'S' and resid 1286 through 1288 No H-bonds generated for 'chain 'S' and resid 1286 through 1288' Processing helix chain 'S' and resid 1312 through 1317 removed outlier: 3.854A pdb=" N PHE S1316 " --> pdb=" O LYS S1313 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 12 through 13 Processing sheet with id=AA2, first strand: chain 'B' and resid 60 through 62 removed outlier: 6.591A pdb=" N PHE B 60 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE B 167 " --> pdb=" O PHE B 60 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL B 62 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU B 164 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU B 195 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE B 166 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR B 18 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N GLU B 196 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU B 20 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N PHE B 204 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N PHE B 19 " --> pdb=" O PHE B 204 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG B 203 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 219 " --> pdb=" O ARG B 203 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 119 through 120 Processing sheet with id=AA4, first strand: chain 'C' and resid 12 through 13 Processing sheet with id=AA5, first strand: chain 'C' and resid 59 through 62 removed outlier: 6.975A pdb=" N LEU C 164 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU C 195 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N PHE C 166 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N ALA C 17 " --> pdb=" O PHE C 204 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N TYR C 206 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE C 19 " --> pdb=" O TYR C 206 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LEU C 208 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR C 21 " --> pdb=" O LEU C 208 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 12 through 13 Processing sheet with id=AA7, first strand: chain 'D' and resid 60 through 62 removed outlier: 6.536A pdb=" N PHE D 60 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ILE D 167 " --> pdb=" O PHE D 60 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL D 62 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU D 164 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU D 195 " --> pdb=" O LEU D 164 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N PHE D 166 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR D 18 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N GLU D 196 " --> pdb=" O THR D 18 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU D 20 " --> pdb=" O GLU D 196 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N PHE D 204 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N PHE D 19 " --> pdb=" O PHE D 204 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'D' and resid 136 through 137 removed outlier: 3.554A pdb=" N LYS D 136 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 12 through 13 Processing sheet with id=AB2, first strand: chain 'A' and resid 60 through 62 removed outlier: 6.721A pdb=" N PHE A 60 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ILE A 167 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL A 62 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU A 164 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N LEU A 195 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N PHE A 166 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N PHE A 204 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N PHE A 19 " --> pdb=" O PHE A 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 4 through 8 removed outlier: 6.985A pdb=" N ARG K 4 " --> pdb=" O ASP K 38 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU K 40 " --> pdb=" O ARG K 4 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL K 6 " --> pdb=" O LEU K 40 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LEU K 42 " --> pdb=" O VAL K 6 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL K 8 " --> pdb=" O LEU K 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'K' and resid 29 through 33 removed outlier: 3.515A pdb=" N SER K 15 " --> pdb=" O VAL K 22 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TYR K 16 " --> pdb=" O THR K 50 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR L 50 " --> pdb=" O LEU L 14 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TYR L 16 " --> pdb=" O THR L 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 66 through 67 removed outlier: 4.020A pdb=" N GLY K 75 " --> pdb=" O PHE K 66 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY L 75 " --> pdb=" O PHE L 66 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE L 77 " --> pdb=" O VAL L 64 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N VAL L 64 " --> pdb=" O ILE L 77 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ARG L 4 " --> pdb=" O ASP L 38 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU L 40 " --> pdb=" O ARG L 4 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL L 6 " --> pdb=" O LEU L 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 251 through 254 Processing sheet with id=AB7, first strand: chain 'L' and resid 252 through 254 removed outlier: 4.185A pdb=" N TYR L 252 " --> pdb=" O MET L 259 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N MET L 259 " --> pdb=" O TYR L 252 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 960 through 963 removed outlier: 6.773A pdb=" N TYR S 5 " --> pdb=" O ARG S 769 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N VAL S 771 " --> pdb=" O TYR S 5 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE S 7 " --> pdb=" O VAL S 771 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY S 17 " --> pdb=" O ASP S 10 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'S' and resid 29 through 33 Processing sheet with id=AC1, first strand: chain 'S' and resid 35 through 36 removed outlier: 6.372A pdb=" N TYR S 35 " --> pdb=" O ARG S1332 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N LYS S1334 " --> pdb=" O TYR S 35 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU S1181 " --> pdb=" O ILE S1321 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR S1180 " --> pdb=" O LEU S1192 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'S' and resid 256 through 257 Processing sheet with id=AC3, first strand: chain 'S' and resid 516 through 518 removed outlier: 5.295A pdb=" N LEU S 517 " --> pdb=" O GLY S 668 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'S' and resid 544 through 546 removed outlier: 3.743A pdb=" N ILE S 544 " --> pdb=" O ASP S 540 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR S 586 " --> pdb=" O THR S 539 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'S' and resid 850 through 851 Processing sheet with id=AC6, first strand: chain 'S' and resid 1104 through 1105 Processing sheet with id=AC7, first strand: chain 'S' and resid 1139 through 1147 removed outlier: 6.711A pdb=" N THR S1130 " --> pdb=" O VAL S1172 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N VAL S1172 " --> pdb=" O THR S1130 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'S' and resid 1297 through 1298 1111 hydrogen bonds defined for protein. 3216 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 156 hydrogen bonds 296 hydrogen bond angles 0 basepair planarities 65 basepair parallelities 111 stacking parallelities Total time for adding SS restraints: 6.87 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6050 1.33 - 1.45: 6270 1.45 - 1.57: 14487 1.57 - 1.69: 352 1.69 - 1.81: 118 Bond restraints: 27277 Sorted by residual: bond pdb=" C3' DT N -3 " pdb=" C2' DT N -3 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.43e+01 bond pdb=" C3' DA N -25 " pdb=" C2' DA N -25 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.23e+01 bond pdb=" C5' DT N -29 " pdb=" C4' DT N -29 " ideal model delta sigma weight residual 1.512 1.536 -0.024 7.00e-03 2.04e+04 1.16e+01 bond pdb=" C3' DA T 33 " pdb=" C2' DA T 33 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DT T -9 " pdb=" C2' DT T -9 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 ... (remaining 27272 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 36586 1.65 - 3.30: 877 3.30 - 4.96: 98 4.96 - 6.61: 38 6.61 - 8.26: 5 Bond angle restraints: 37604 Sorted by residual: angle pdb=" N VAL S 197 " pdb=" CA VAL S 197 " pdb=" C VAL S 197 " ideal model delta sigma weight residual 113.71 108.14 5.57 9.50e-01 1.11e+00 3.44e+01 angle pdb=" C1' U g 8 " pdb=" N1 U g 8 " pdb=" C2 U g 8 " ideal model delta sigma weight residual 117.70 123.09 -5.39 1.20e+00 6.94e-01 2.01e+01 angle pdb=" N3 DT T 12 " pdb=" C4 DT T 12 " pdb=" O4 DT T 12 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT N 3 " pdb=" C4 DT N 3 " pdb=" O4 DT N 3 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT T 15 " pdb=" C4 DT T 15 " pdb=" O4 DT T 15 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 ... (remaining 37599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 15612 35.75 - 71.51: 776 71.51 - 107.26: 35 107.26 - 143.02: 2 143.02 - 178.77: 5 Dihedral angle restraints: 16430 sinusoidal: 8239 harmonic: 8191 Sorted by residual: dihedral pdb=" O4' U g 8 " pdb=" C1' U g 8 " pdb=" N1 U g 8 " pdb=" C2 U g 8 " ideal model delta sinusoidal sigma weight residual 200.00 51.66 148.34 1 1.50e+01 4.44e-03 7.90e+01 dihedral pdb=" CA ASP B 142 " pdb=" C ASP B 142 " pdb=" N THR B 143 " pdb=" CA THR B 143 " ideal model delta harmonic sigma weight residual 180.00 158.49 21.51 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA ASP K 124 " pdb=" C ASP K 124 " pdb=" N TYR K 125 " pdb=" CA TYR K 125 " ideal model delta harmonic sigma weight residual -180.00 -158.59 -21.41 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 16427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3168 0.045 - 0.091: 947 0.091 - 0.136: 176 0.136 - 0.181: 11 0.181 - 0.227: 1 Chirality restraints: 4303 Sorted by residual: chirality pdb=" C3' C t 23 " pdb=" C4' C t 23 " pdb=" O3' C t 23 " pdb=" C2' C t 23 " both_signs ideal model delta sigma weight residual False -2.48 -2.25 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C1' G g 11 " pdb=" O4' G g 11 " pdb=" C2' G g 11 " pdb=" N9 G g 11 " both_signs ideal model delta sigma weight residual False 2.46 2.29 0.17 2.00e-01 2.50e+01 7.13e-01 chirality pdb=" P DA N 8 " pdb=" OP1 DA N 8 " pdb=" OP2 DA N 8 " pdb=" O5' DA N 8 " both_signs ideal model delta sigma weight residual True 2.34 -2.50 -0.16 2.00e-01 2.50e+01 6.48e-01 ... (remaining 4300 not shown) Planarity restraints: 4151 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G g 11 " 0.026 2.00e-02 2.50e+03 1.05e-02 3.30e+00 pdb=" N9 G g 11 " -0.022 2.00e-02 2.50e+03 pdb=" C8 G g 11 " -0.008 2.00e-02 2.50e+03 pdb=" N7 G g 11 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G g 11 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G g 11 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G g 11 " 0.008 2.00e-02 2.50e+03 pdb=" N1 G g 11 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G g 11 " -0.000 2.00e-02 2.50e+03 pdb=" N2 G g 11 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G g 11 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G g 11 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 10 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO B 11 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 11 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 11 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A t 30 " -0.023 2.00e-02 2.50e+03 1.03e-02 2.93e+00 pdb=" N9 A t 30 " 0.023 2.00e-02 2.50e+03 pdb=" C8 A t 30 " 0.004 2.00e-02 2.50e+03 pdb=" N7 A t 30 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A t 30 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A t 30 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A t 30 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A t 30 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A t 30 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A t 30 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A t 30 " 0.004 2.00e-02 2.50e+03 ... (remaining 4148 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3391 2.75 - 3.29: 25372 3.29 - 3.82: 46274 3.82 - 4.36: 55456 4.36 - 4.90: 89867 Nonbonded interactions: 220360 Sorted by model distance: nonbonded pdb=" OG SER S 537 " pdb=" OG SER S 588 " model vdw 2.212 3.040 nonbonded pdb=" O GLU S 307 " pdb=" OG1 THR S 310 " model vdw 2.244 3.040 nonbonded pdb=" NZ LYS A 16 " pdb=" OD1 ASN A 189 " model vdw 2.256 3.120 nonbonded pdb=" OP1 C t 28 " pdb=" NH1 ARG S 346 " model vdw 2.258 3.120 nonbonded pdb=" O ARG K 71 " pdb=" OG SER K 185 " model vdw 2.265 3.040 ... (remaining 220355 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'K' selection = (chain 'L' and resid 3 through 288) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 26.680 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 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 : 0.005 0.036 27277 Z= 0.293 Angle : 0.621 8.261 37604 Z= 0.417 Chirality : 0.043 0.227 4303 Planarity : 0.004 0.046 4151 Dihedral : 17.951 178.769 11128 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.81 % Favored : 93.97 % Rotamer: Outliers : 4.89 % Allowed : 10.30 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.16), residues: 2755 helix: 0.95 (0.14), residues: 1340 sheet: -0.49 (0.31), residues: 305 loop : -1.62 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 639 TYR 0.018 0.002 TYR S 368 PHE 0.017 0.002 PHE B 5 TRP 0.015 0.001 TRP K 105 HIS 0.006 0.001 HIS S 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.29 (27277) covalent geometry : angle 0.62106 / 0.42 (37604) hydrogen bonds : bond 0.14602 / 9.89 ( 1267) hydrogen bonds : angle 5.62221 / 3.85 ( 3512) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 592 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 GLU cc_start: 0.7601 (tp30) cc_final: 0.7168 (tp30) REVERT: B 16 LYS cc_start: 0.8354 (mmtp) cc_final: 0.7648 (mmtm) REVERT: B 39 ASP cc_start: 0.8170 (p0) cc_final: 0.7797 (p0) REVERT: B 42 ASN cc_start: 0.8309 (m-40) cc_final: 0.8106 (m-40) REVERT: B 204 PHE cc_start: 0.7514 (OUTLIER) cc_final: 0.7185 (m-10) REVERT: B 217 GLU cc_start: 0.7458 (pm20) cc_final: 0.7252 (pm20) REVERT: C 93 VAL cc_start: 0.5061 (p) cc_final: 0.4315 (p) REVERT: A 55 LYS cc_start: 0.8285 (ptpp) cc_final: 0.8083 (ptpp) REVERT: A 122 ASP cc_start: 0.4659 (OUTLIER) cc_final: 0.4441 (p0) REVERT: A 191 ASP cc_start: 0.5492 (m-30) cc_final: 0.5280 (m-30) REVERT: K 29 GLN cc_start: 0.7472 (tm-30) cc_final: 0.6944 (tm-30) REVERT: K 43 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: K 92 ARG cc_start: 0.8190 (ttm-80) cc_final: 0.7616 (ttm-80) REVERT: K 98 GLU cc_start: 0.8246 (tp30) cc_final: 0.7315 (mp0) REVERT: K 176 LEU cc_start: 0.6788 (OUTLIER) cc_final: 0.6541 (mp) REVERT: K 210 ASP cc_start: 0.7497 (t0) cc_final: 0.7152 (t0) REVERT: K 235 GLU cc_start: 0.7500 (mp0) cc_final: 0.6663 (mp0) REVERT: K 250 ASN cc_start: 0.7114 (t0) cc_final: 0.6776 (t0) REVERT: K 280 GLU cc_start: 0.6270 (tm-30) cc_final: 0.5759 (tm-30) REVERT: L 4 ARG cc_start: 0.7363 (mmm-85) cc_final: 0.6700 (mtm-85) REVERT: L 36 GLU cc_start: 0.7949 (pt0) cc_final: 0.7667 (pt0) REVERT: L 71 ARG cc_start: 0.7895 (mtt-85) cc_final: 0.7676 (mtt90) REVERT: L 76 LYS cc_start: 0.7127 (ptmm) cc_final: 0.6915 (pttp) REVERT: L 83 ARG cc_start: 0.4520 (OUTLIER) cc_final: 0.4266 (mmp-170) REVERT: L 92 ARG cc_start: 0.6804 (mtm180) cc_final: 0.6602 (mtm180) REVERT: L 189 ARG cc_start: 0.7398 (tmm160) cc_final: 0.6803 (ttt180) REVERT: L 254 TYR cc_start: 0.6043 (t80) cc_final: 0.5752 (t80) REVERT: S 76 ARG cc_start: 0.7893 (tpt90) cc_final: 0.7641 (tpt170) REVERT: S 87 GLU cc_start: 0.7337 (tt0) cc_final: 0.7122 (tt0) REVERT: S 102 GLN cc_start: 0.8184 (tp40) cc_final: 0.7924 (tp40) REVERT: S 183 GLU cc_start: 0.7372 (tp30) cc_final: 0.6878 (tp30) REVERT: S 189 MET cc_start: 0.6914 (pp-130) cc_final: 0.6665 (pp-130) REVERT: S 214 ILE cc_start: 0.7567 (OUTLIER) cc_final: 0.6992 (pp) REVERT: S 217 GLU cc_start: 0.8351 (mp0) cc_final: 0.7762 (mp0) REVERT: S 230 LYS cc_start: 0.8208 (mtpt) cc_final: 0.7739 (mtpt) REVERT: S 270 ILE cc_start: 0.8043 (tp) cc_final: 0.7636 (tp) REVERT: S 340 LYS cc_start: 0.8092 (mttt) cc_final: 0.7731 (mtmt) REVERT: S 352 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6859 (mm-30) REVERT: S 395 GLU cc_start: 0.6914 (tp30) cc_final: 0.6590 (tp30) REVERT: S 454 PHE cc_start: 0.8499 (t80) cc_final: 0.7839 (t80) REVERT: S 482 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8113 (mp) REVERT: S 506 ASN cc_start: 0.7824 (OUTLIER) cc_final: 0.7484 (m110) REVERT: S 619 ASP cc_start: 0.8040 (t0) cc_final: 0.7532 (t0) REVERT: S 657 LYS cc_start: 0.8409 (tttp) cc_final: 0.8043 (ttpp) REVERT: S 718 ASN cc_start: 0.8289 (m-40) cc_final: 0.8067 (m-40) REVERT: S 763 MET cc_start: 0.8395 (mmt) cc_final: 0.7988 (tpt) REVERT: S 816 GLN cc_start: 0.7748 (mp10) cc_final: 0.7547 (mp10) REVERT: S 890 MET cc_start: 0.7693 (tpp) cc_final: 0.7246 (tpp) REVERT: S 891 LYS cc_start: 0.7568 (tttt) cc_final: 0.7253 (tppp) REVERT: S 904 SER cc_start: 0.8338 (t) cc_final: 0.7938 (p) REVERT: S 923 ASP cc_start: 0.5758 (OUTLIER) cc_final: 0.5524 (t0) REVERT: S 1065 LYS cc_start: 0.8506 (ttmm) cc_final: 0.8222 (mmmm) REVERT: S 1107 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8440 (mmtt) REVERT: S 1268 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: S 1298 LYS cc_start: 0.8057 (mtpt) cc_final: 0.7497 (ttmm) REVERT: S 1302 LYS cc_start: 0.7171 (tppp) cc_final: 0.6895 (tppp) REVERT: S 1303 ASP cc_start: 0.7968 (m-30) cc_final: 0.7448 (m-30) outliers start: 122 outliers final: 38 residues processed: 675 average time/residue: 0.6747 time to fit residues: 524.2018 Evaluate side-chains 595 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 545 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 176 LEU Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 248 PHE Chi-restraints excluded: chain K residue 253 MET Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 83 ARG Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 240 MET Chi-restraints excluded: chain S residue 197 VAL Chi-restraints excluded: chain S residue 198 ASN Chi-restraints excluded: chain S residue 214 ILE Chi-restraints excluded: chain S residue 318 LYS Chi-restraints excluded: chain S residue 349 CYS Chi-restraints excluded: chain S residue 352 GLU Chi-restraints excluded: chain S residue 451 LEU Chi-restraints excluded: chain S residue 482 ILE Chi-restraints excluded: chain S residue 506 ASN Chi-restraints excluded: chain S residue 509 THR Chi-restraints excluded: chain S residue 516 VAL Chi-restraints excluded: chain S residue 539 THR Chi-restraints excluded: chain S residue 665 THR Chi-restraints excluded: chain S residue 799 MET Chi-restraints excluded: chain S residue 812 THR Chi-restraints excluded: chain S residue 923 ASP Chi-restraints excluded: chain S residue 1042 ARG Chi-restraints excluded: chain S residue 1064 LEU Chi-restraints excluded: chain S residue 1076 MET Chi-restraints excluded: chain S residue 1107 LYS Chi-restraints excluded: chain S residue 1204 MET Chi-restraints excluded: chain S residue 1268 GLU Chi-restraints excluded: chain S residue 1283 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 0.4980 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.0010 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 180 GLN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN D 37 GLN D 180 GLN A 26 GLN A 180 GLN A 197 GLN K 28 HIS K 89 GLN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 ASN K 157 ASN K 232 ASN L 33 HIS L 177 ASN L 232 ASN L 250 ASN L 271 HIS S 186 GLN S 193 ASN S 405 ASN S 617 HIS S 650 GLN S 710 ASN S 713 GLN S 865 ASN S1202 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.195341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.148766 restraints weight = 39026.121| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.11 r_work: 0.3504 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 27277 Z= 0.161 Angle : 0.614 11.379 37604 Z= 0.328 Chirality : 0.041 0.202 4303 Planarity : 0.004 0.047 4151 Dihedral : 19.749 176.991 5477 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.66 % Favored : 94.12 % Rotamer: Outliers : 5.21 % Allowed : 16.40 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.16), residues: 2755 helix: 1.36 (0.14), residues: 1354 sheet: -0.38 (0.33), residues: 264 loop : -1.55 (0.17), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 71 TYR 0.019 0.002 TYR D 36 PHE 0.023 0.001 PHE B 145 TRP 0.020 0.001 TRP K 3 HIS 0.005 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (27277) covalent geometry : angle 0.61423 / 0.33 (37604) hydrogen bonds : bond 0.04897 / 3.22 ( 1267) hydrogen bonds : angle 4.57956 / 3.14 ( 3512) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 549 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 GLU cc_start: 0.7941 (mp0) cc_final: 0.7722 (mp0) REVERT: B 39 ASP cc_start: 0.8195 (p0) cc_final: 0.7802 (p0) REVERT: B 197 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7924 (tm130) REVERT: C 55 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.7044 (ttmm) REVERT: C 60 PHE cc_start: 0.6926 (t80) cc_final: 0.6396 (t80) REVERT: C 98 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7784 (pp20) REVERT: D 98 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7225 (mm-30) REVERT: D 120 GLU cc_start: 0.7037 (mp0) cc_final: 0.6803 (mp0) REVERT: D 137 ILE cc_start: 0.6761 (mt) cc_final: 0.6397 (tt) REVERT: A 55 LYS cc_start: 0.8259 (ptpp) cc_final: 0.7942 (ptpp) REVERT: A 107 LEU cc_start: 0.7315 (pp) cc_final: 0.6745 (pp) REVERT: A 111 GLU cc_start: 0.6402 (mp0) cc_final: 0.5833 (mm-30) REVERT: A 115 HIS cc_start: 0.6538 (t70) cc_final: 0.5875 (t70) REVERT: A 196 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6968 (mt-10) REVERT: A 200 VAL cc_start: 0.7907 (t) cc_final: 0.7230 (m) REVERT: K 43 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: K 89 GLN cc_start: 0.7078 (tp40) cc_final: 0.6777 (tp-100) REVERT: K 98 GLU cc_start: 0.8199 (tp30) cc_final: 0.7579 (mp0) REVERT: K 112 LYS cc_start: 0.8204 (tttp) cc_final: 0.7978 (tttm) REVERT: K 176 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6800 (mp) REVERT: K 235 GLU cc_start: 0.7649 (mp0) cc_final: 0.6929 (mp0) REVERT: K 250 ASN cc_start: 0.7191 (t0) cc_final: 0.6730 (t0) REVERT: K 280 GLU cc_start: 0.6223 (tm-30) cc_final: 0.5807 (tm-30) REVERT: L 4 ARG cc_start: 0.7522 (mmm-85) cc_final: 0.6919 (mtm-85) REVERT: L 13 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8232 (ttpp) REVERT: L 36 GLU cc_start: 0.7931 (pt0) cc_final: 0.7639 (pt0) REVERT: L 92 ARG cc_start: 0.7012 (mtm180) cc_final: 0.6779 (mtm180) REVERT: L 254 TYR cc_start: 0.6473 (t80) cc_final: 0.5965 (t80) REVERT: S 76 ARG cc_start: 0.7840 (tpt90) cc_final: 0.7595 (tpt170) REVERT: S 183 GLU cc_start: 0.7565 (tp30) cc_final: 0.7109 (tp30) REVERT: S 187 GLN cc_start: 0.7802 (tp40) cc_final: 0.7477 (tp40) REVERT: S 189 MET cc_start: 0.6904 (pp-130) cc_final: 0.6673 (pp-130) REVERT: S 214 ILE cc_start: 0.7637 (OUTLIER) cc_final: 0.7147 (pp) REVERT: S 217 GLU cc_start: 0.8506 (mp0) cc_final: 0.7988 (mp0) REVERT: S 230 LYS cc_start: 0.8268 (mtpt) cc_final: 0.7750 (mtpt) REVERT: S 294 ASP cc_start: 0.7138 (p0) cc_final: 0.6917 (p0) REVERT: S 337 ASP cc_start: 0.8111 (m-30) cc_final: 0.7893 (m-30) REVERT: S 340 LYS cc_start: 0.8323 (mttt) cc_final: 0.8014 (mtmt) REVERT: S 395 GLU cc_start: 0.7194 (tp30) cc_final: 0.6785 (tp30) REVERT: S 405 ASN cc_start: 0.8024 (t0) cc_final: 0.7777 (t0) REVERT: S 454 PHE cc_start: 0.8642 (t80) cc_final: 0.8144 (t80) REVERT: S 619 ASP cc_start: 0.8226 (t0) cc_final: 0.7715 (t0) REVERT: S 657 LYS cc_start: 0.8556 (tttp) cc_final: 0.8242 (ttpp) REVERT: S 718 ASN cc_start: 0.8259 (m-40) cc_final: 0.8043 (m-40) REVERT: S 763 MET cc_start: 0.8402 (mmt) cc_final: 0.8151 (mmm) REVERT: S 890 MET cc_start: 0.7783 (tpp) cc_final: 0.7406 (tpp) REVERT: S 891 LYS cc_start: 0.7853 (tttt) cc_final: 0.7537 (tppp) REVERT: S 982 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7704 (mtp85) REVERT: S 1042 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7405 (mmm160) REVERT: S 1065 LYS cc_start: 0.8529 (ttmm) cc_final: 0.8266 (mmmm) REVERT: S 1107 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8386 (tptt) REVERT: S 1265 LYS cc_start: 0.7643 (mmtm) cc_final: 0.7159 (mmtm) REVERT: S 1268 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: S 1298 LYS cc_start: 0.8033 (mtpt) cc_final: 0.7500 (ttmm) REVERT: S 1303 ASP cc_start: 0.8026 (m-30) cc_final: 0.7545 (m-30) outliers start: 130 outliers final: 58 residues processed: 627 average time/residue: 0.7148 time to fit residues: 513.4680 Evaluate side-chains 599 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 531 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 205 GLN Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain K residue 28 HIS Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 176 LEU Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 248 PHE Chi-restraints excluded: chain L residue 13 LYS Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 240 MET Chi-restraints excluded: chain S residue 39 GLU Chi-restraints excluded: chain S residue 182 LYS Chi-restraints excluded: chain S residue 197 VAL Chi-restraints excluded: chain S residue 214 ILE Chi-restraints excluded: chain S residue 318 LYS Chi-restraints excluded: chain S residue 349 CYS Chi-restraints excluded: chain S residue 356 LEU Chi-restraints excluded: chain S residue 451 LEU Chi-restraints excluded: chain S residue 474 LEU Chi-restraints excluded: chain S residue 509 THR Chi-restraints excluded: chain S residue 516 VAL Chi-restraints excluded: chain S residue 549 SER Chi-restraints excluded: chain S residue 582 THR Chi-restraints excluded: chain S residue 583 GLU Chi-restraints excluded: chain S residue 665 THR Chi-restraints excluded: chain S residue 697 VAL Chi-restraints excluded: chain S residue 792 LEU Chi-restraints excluded: chain S residue 812 THR Chi-restraints excluded: chain S residue 863 LEU Chi-restraints excluded: chain S residue 981 VAL Chi-restraints excluded: chain S residue 982 ARG Chi-restraints excluded: chain S residue 1042 ARG Chi-restraints excluded: chain S residue 1060 SER Chi-restraints excluded: chain S residue 1064 LEU Chi-restraints excluded: chain S residue 1076 MET Chi-restraints excluded: chain S residue 1107 LYS Chi-restraints excluded: chain S residue 1159 ILE Chi-restraints excluded: chain S residue 1168 LEU Chi-restraints excluded: chain S residue 1171 ARG Chi-restraints excluded: chain S residue 1202 ASN Chi-restraints excluded: chain S residue 1204 MET Chi-restraints excluded: chain S residue 1268 GLU Chi-restraints excluded: chain S residue 1283 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 182 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 84 optimal weight: 0.0970 chunk 240 optimal weight: 0.5980 chunk 149 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 155 HIS ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 GLN A 197 GLN K 28 HIS K 111 GLN K 115 ASN K 232 ASN L 18 ASN ** L 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 204 HIS L 271 HIS S 102 GLN S 186 GLN S 193 ASN S 547 ASN S 617 HIS S 650 GLN S 713 GLN ** S1202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.193047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.146038 restraints weight = 38933.782| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 1.80 r_work: 0.3468 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 27277 Z= 0.289 Angle : 0.668 12.345 37604 Z= 0.356 Chirality : 0.046 0.239 4303 Planarity : 0.005 0.085 4151 Dihedral : 19.703 175.953 5436 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.39 % Favored : 93.36 % Rotamer: Outliers : 5.65 % Allowed : 17.76 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.16), residues: 2755 helix: 1.17 (0.14), residues: 1354 sheet: -0.46 (0.33), residues: 264 loop : -1.66 (0.17), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 71 TYR 0.026 0.002 TYR B 184 PHE 0.027 0.002 PHE C 130 TRP 0.015 0.002 TRP K 105 HIS 0.008 0.001 HIS S1253 Details of bonding type rmsd/Z covalent geometry : bond 0.00663 / 0.29 (27277) covalent geometry : angle 0.66824 / 0.36 (37604) hydrogen bonds : bond 0.05175 / 3.40 ( 1267) hydrogen bonds : angle 4.59400 / 3.15 ( 3512) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 553 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 39 ASP cc_start: 0.8178 (p0) cc_final: 0.7839 (p0) REVERT: B 149 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8252 (tpp) REVERT: B 161 LYS cc_start: 0.8500 (mtpp) cc_final: 0.8255 (mptp) REVERT: B 197 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7841 (tm130) REVERT: C 60 PHE cc_start: 0.7013 (t80) cc_final: 0.6536 (t80) REVERT: C 180 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7492 (mm-40) REVERT: D 98 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7349 (mm-30) REVERT: D 117 MET cc_start: 0.6760 (mmm) cc_final: 0.6553 (tpp) REVERT: D 131 LYS cc_start: 0.7355 (mtmm) cc_final: 0.7126 (mtmm) REVERT: D 149 MET cc_start: 0.6915 (mmm) cc_final: 0.6657 (mmm) REVERT: A 21 THR cc_start: 0.8538 (m) cc_final: 0.8290 (p) REVERT: A 55 LYS cc_start: 0.8421 (ptpp) cc_final: 0.8150 (ptpp) REVERT: A 107 LEU cc_start: 0.7222 (pp) cc_final: 0.6526 (pp) REVERT: A 111 GLU cc_start: 0.6424 (mp0) cc_final: 0.5791 (mm-30) REVERT: A 196 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7073 (mt-10) REVERT: A 200 VAL cc_start: 0.7957 (t) cc_final: 0.7327 (m) REVERT: K 41 LEU cc_start: 0.8685 (tp) cc_final: 0.8484 (tp) REVERT: K 43 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7310 (mp0) REVERT: K 98 GLU cc_start: 0.8190 (tp30) cc_final: 0.7548 (mp0) REVERT: K 176 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6843 (mp) REVERT: K 210 ASP cc_start: 0.7504 (t0) cc_final: 0.7292 (t0) REVERT: K 235 GLU cc_start: 0.7683 (mp0) cc_final: 0.6961 (mp0) REVERT: K 280 GLU cc_start: 0.6289 (tm-30) cc_final: 0.5942 (tm-30) REVERT: L 4 ARG cc_start: 0.7482 (mmm-85) cc_final: 0.6882 (mtm-85) REVERT: L 13 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8365 (ttpp) REVERT: L 36 GLU cc_start: 0.7977 (pt0) cc_final: 0.7672 (pt0) REVERT: L 92 ARG cc_start: 0.7043 (mtm180) cc_final: 0.6786 (mtm180) REVERT: L 189 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.5159 (ttm170) REVERT: L 253 MET cc_start: 0.6412 (tpp) cc_final: 0.6118 (tpp) REVERT: S 183 GLU cc_start: 0.7580 (tp30) cc_final: 0.7129 (tp30) REVERT: S 189 MET cc_start: 0.6877 (pp-130) cc_final: 0.6647 (pp-130) REVERT: S 214 ILE cc_start: 0.7699 (OUTLIER) cc_final: 0.7294 (pp) REVERT: S 217 GLU cc_start: 0.8527 (mp0) cc_final: 0.8046 (mp0) REVERT: S 230 LYS cc_start: 0.8292 (mtpt) cc_final: 0.7791 (mtpt) REVERT: S 304 ASP cc_start: 0.7998 (m-30) cc_final: 0.7574 (m-30) REVERT: S 340 LYS cc_start: 0.8334 (mttt) cc_final: 0.8008 (mtmt) REVERT: S 395 GLU cc_start: 0.7165 (tp30) cc_final: 0.6693 (tp30) REVERT: S 405 ASN cc_start: 0.7989 (t0) cc_final: 0.7725 (t0) REVERT: S 442 LYS cc_start: 0.8057 (ttpp) cc_final: 0.7831 (ttpp) REVERT: S 454 PHE cc_start: 0.8590 (t80) cc_final: 0.7847 (t80) REVERT: S 488 GLN cc_start: 0.8040 (mm110) cc_final: 0.7718 (mm110) REVERT: S 564 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7813 (mtm-85) REVERT: S 594 GLN cc_start: 0.8008 (tt0) cc_final: 0.7630 (tt0) REVERT: S 619 ASP cc_start: 0.8148 (t0) cc_final: 0.7613 (t0) REVERT: S 657 LYS cc_start: 0.8594 (tttp) cc_final: 0.8293 (ttpp) REVERT: S 718 ASN cc_start: 0.8218 (m-40) cc_final: 0.8010 (m-40) REVERT: S 832 ASP cc_start: 0.7374 (t0) cc_final: 0.7068 (t0) REVERT: S 859 LYS cc_start: 0.8803 (tmtt) cc_final: 0.8600 (tmtp) REVERT: S 890 MET cc_start: 0.7658 (tpp) cc_final: 0.7284 (tpp) REVERT: S 891 LYS cc_start: 0.7915 (tttt) cc_final: 0.7652 (tppp) REVERT: S 982 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7460 (mtp85) REVERT: S 1065 LYS cc_start: 0.8594 (ttmm) cc_final: 0.8359 (mmmm) REVERT: S 1107 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8499 (mttm) REVERT: S 1180 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8193 (m) REVERT: S 1265 LYS cc_start: 0.7635 (mmtm) cc_final: 0.7155 (mmtm) REVERT: S 1268 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7539 (mp0) REVERT: S 1298 LYS cc_start: 0.8068 (mtpt) cc_final: 0.7579 (ttmm) REVERT: S 1303 ASP cc_start: 0.7996 (m-30) cc_final: 0.7528 (m-30) outliers start: 141 outliers final: 69 residues processed: 637 average time/residue: 0.7120 time to fit residues: 520.7611 Evaluate side-chains 618 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 537 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 205 GLN Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 176 LEU Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 248 PHE Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain L residue 13 LYS Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 189 ARG Chi-restraints excluded: chain L residue 206 ASN Chi-restraints excluded: chain L residue 209 ASN Chi-restraints excluded: chain L residue 240 MET Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain S residue 21 MET Chi-restraints excluded: chain S residue 39 GLU Chi-restraints excluded: chain S residue 182 LYS Chi-restraints excluded: chain S residue 197 VAL Chi-restraints excluded: chain S residue 214 ILE Chi-restraints excluded: chain S residue 297 LEU Chi-restraints excluded: chain S residue 318 LYS Chi-restraints excluded: chain S residue 349 CYS Chi-restraints excluded: chain S residue 356 LEU Chi-restraints excluded: chain S residue 451 LEU Chi-restraints excluded: chain S residue 470 THR Chi-restraints excluded: chain S residue 474 LEU Chi-restraints excluded: chain S residue 482 ILE Chi-restraints excluded: chain S residue 509 THR Chi-restraints excluded: chain S residue 516 VAL Chi-restraints excluded: chain S residue 534 THR Chi-restraints excluded: chain S residue 549 SER Chi-restraints excluded: chain S residue 564 ARG Chi-restraints excluded: chain S residue 665 THR Chi-restraints excluded: chain S residue 792 LEU Chi-restraints excluded: chain S residue 812 THR Chi-restraints excluded: chain S residue 824 LEU Chi-restraints excluded: chain S residue 863 LEU Chi-restraints excluded: chain S residue 904 SER Chi-restraints excluded: chain S residue 981 VAL Chi-restraints excluded: chain S residue 982 ARG Chi-restraints excluded: chain S residue 984 VAL Chi-restraints excluded: chain S residue 1035 ILE Chi-restraints excluded: chain S residue 1045 THR Chi-restraints excluded: chain S residue 1060 SER Chi-restraints excluded: chain S residue 1064 LEU Chi-restraints excluded: chain S residue 1076 MET Chi-restraints excluded: chain S residue 1107 LYS Chi-restraints excluded: chain S residue 1125 TYR Chi-restraints excluded: chain S residue 1159 ILE Chi-restraints excluded: chain S residue 1168 LEU Chi-restraints excluded: chain S residue 1180 THR Chi-restraints excluded: chain S residue 1202 ASN Chi-restraints excluded: chain S residue 1204 MET Chi-restraints excluded: chain S residue 1220 CYS Chi-restraints excluded: chain S residue 1268 GLU Chi-restraints excluded: chain S residue 1283 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 138 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 268 optimal weight: 0.7980 chunk 273 optimal weight: 0.3980 chunk 83 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 279 optimal weight: 0.9990 chunk 257 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN A 153 GLN A 197 GLN K 28 HIS K 111 GLN K 115 ASN L 28 HIS L 271 HIS S 102 GLN S 193 ASN S 617 HIS S 650 GLN S 713 GLN S1202 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.193759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.147016 restraints weight = 38772.583| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.72 r_work: 0.3494 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 27277 Z= 0.186 Angle : 0.629 11.351 37604 Z= 0.335 Chirality : 0.043 0.217 4303 Planarity : 0.004 0.059 4151 Dihedral : 19.709 175.608 5426 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.66 % Favored : 94.08 % Rotamer: Outliers : 5.41 % Allowed : 19.13 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.16), residues: 2755 helix: 1.24 (0.14), residues: 1359 sheet: -0.32 (0.35), residues: 238 loop : -1.57 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 71 TYR 0.025 0.002 TYR S1019 PHE 0.054 0.002 PHE C 130 TRP 0.014 0.002 TRP K 3 HIS 0.006 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 (27277) covalent geometry : angle 0.62941 / 0.33 (37604) hydrogen bonds : bond 0.04582 / 3.01 ( 1267) hydrogen bonds : angle 4.44309 / 3.04 ( 3512) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 551 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 39 ASP cc_start: 0.8189 (p0) cc_final: 0.7919 (p0) REVERT: B 65 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7388 (mt) REVERT: B 149 MET cc_start: 0.8649 (mmm) cc_final: 0.8362 (tpp) REVERT: B 197 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7875 (tm130) REVERT: C 55 LYS cc_start: 0.7398 (OUTLIER) cc_final: 0.7112 (ttmm) REVERT: D 76 LEU cc_start: 0.8557 (mm) cc_final: 0.8255 (tm) REVERT: D 98 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7425 (mm-30) REVERT: D 100 LEU cc_start: 0.5217 (tp) cc_final: 0.4690 (pp) REVERT: D 120 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6991 (mp0) REVERT: D 131 LYS cc_start: 0.7409 (mtmm) cc_final: 0.7199 (mtmm) REVERT: A 21 THR cc_start: 0.8509 (m) cc_final: 0.8262 (p) REVERT: A 55 LYS cc_start: 0.8440 (ptpp) cc_final: 0.8149 (ptpp) REVERT: A 94 LYS cc_start: 0.7873 (mtpp) cc_final: 0.7294 (ttmm) REVERT: A 107 LEU cc_start: 0.7114 (pp) cc_final: 0.6811 (tp) REVERT: A 111 GLU cc_start: 0.6529 (mp0) cc_final: 0.5699 (mm-30) REVERT: A 196 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7186 (mt-10) REVERT: A 200 VAL cc_start: 0.7955 (t) cc_final: 0.7401 (m) REVERT: K 41 LEU cc_start: 0.8657 (tp) cc_final: 0.8450 (tp) REVERT: K 43 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: K 98 GLU cc_start: 0.8164 (tp30) cc_final: 0.7604 (mp0) REVERT: K 112 LYS cc_start: 0.8266 (tttm) cc_final: 0.8049 (tttp) REVERT: K 176 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6782 (mp) REVERT: K 242 ARG cc_start: 0.7704 (mpp80) cc_final: 0.7314 (mpp80) REVERT: K 280 GLU cc_start: 0.6219 (tm-30) cc_final: 0.5876 (tm-30) REVERT: L 4 ARG cc_start: 0.7480 (mmm-85) cc_final: 0.6853 (mtm-85) REVERT: L 36 GLU cc_start: 0.7925 (pt0) cc_final: 0.7623 (pt0) REVERT: L 92 ARG cc_start: 0.7012 (mtm180) cc_final: 0.6782 (mtm180) REVERT: S 183 GLU cc_start: 0.7543 (tp30) cc_final: 0.7089 (tp30) REVERT: S 214 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7255 (pp) REVERT: S 217 GLU cc_start: 0.8493 (mp0) cc_final: 0.8002 (mp0) REVERT: S 230 LYS cc_start: 0.8281 (mtpt) cc_final: 0.7774 (mtpt) REVERT: S 304 ASP cc_start: 0.7967 (m-30) cc_final: 0.7543 (m-30) REVERT: S 337 ASP cc_start: 0.8134 (m-30) cc_final: 0.7909 (m-30) REVERT: S 340 LYS cc_start: 0.8277 (mttt) cc_final: 0.7949 (mtmt) REVERT: S 395 GLU cc_start: 0.7145 (tp30) cc_final: 0.6664 (tp30) REVERT: S 442 LYS cc_start: 0.8050 (ttpp) cc_final: 0.7837 (ttpp) REVERT: S 454 PHE cc_start: 0.8577 (t80) cc_final: 0.7891 (t80) REVERT: S 564 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7730 (mtm-85) REVERT: S 566 LYS cc_start: 0.8506 (mmmt) cc_final: 0.8243 (tptm) REVERT: S 619 ASP cc_start: 0.8143 (t0) cc_final: 0.7614 (t0) REVERT: S 657 LYS cc_start: 0.8579 (tttp) cc_final: 0.8285 (ttpp) REVERT: S 832 ASP cc_start: 0.7381 (t0) cc_final: 0.7081 (t0) REVERT: S 890 MET cc_start: 0.7652 (tpp) cc_final: 0.7303 (tpp) REVERT: S 891 LYS cc_start: 0.7882 (tttt) cc_final: 0.7515 (tppp) REVERT: S 982 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7496 (mtp85) REVERT: S 1065 LYS cc_start: 0.8591 (ttmm) cc_final: 0.8345 (mmmm) REVERT: S 1107 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8374 (mttt) REVERT: S 1169 ARG cc_start: 0.7659 (ttm110) cc_final: 0.7388 (ttm110) REVERT: S 1265 LYS cc_start: 0.7603 (mmtm) cc_final: 0.7092 (mmtm) REVERT: S 1268 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7600 (mp0) REVERT: S 1298 LYS cc_start: 0.8027 (mtpt) cc_final: 0.7545 (ttmm) REVERT: S 1303 ASP cc_start: 0.7932 (m-30) cc_final: 0.7473 (m-30) outliers start: 135 outliers final: 62 residues processed: 630 average time/residue: 0.7044 time to fit residues: 510.2831 Evaluate side-chains 611 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 539 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 159 LEU Chi-restraints excluded: chain K residue 176 LEU Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 227 GLN Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 283 VAL Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 206 ASN Chi-restraints excluded: chain L residue 209 ASN Chi-restraints excluded: chain L residue 210 ASP Chi-restraints excluded: chain L residue 240 MET Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain S residue 39 GLU Chi-restraints excluded: chain S residue 140 LYS Chi-restraints excluded: chain S residue 182 LYS Chi-restraints excluded: chain S residue 197 VAL Chi-restraints excluded: chain S residue 214 ILE Chi-restraints excluded: chain S residue 318 LYS Chi-restraints excluded: chain S residue 349 CYS Chi-restraints excluded: chain S residue 356 LEU Chi-restraints excluded: chain S residue 451 LEU Chi-restraints excluded: chain S residue 470 THR Chi-restraints excluded: chain S residue 474 LEU Chi-restraints excluded: chain S residue 509 THR Chi-restraints excluded: chain S residue 516 VAL Chi-restraints excluded: chain S residue 564 ARG Chi-restraints excluded: chain S residue 582 THR Chi-restraints excluded: chain S residue 662 LYS Chi-restraints excluded: chain S residue 665 THR Chi-restraints excluded: chain S residue 792 LEU Chi-restraints excluded: chain S residue 812 THR Chi-restraints excluded: chain S residue 824 LEU Chi-restraints excluded: chain S residue 827 MET Chi-restraints excluded: chain S residue 863 LEU Chi-restraints excluded: chain S residue 930 ARG Chi-restraints excluded: chain S residue 981 VAL Chi-restraints excluded: chain S residue 982 ARG Chi-restraints excluded: chain S residue 1045 THR Chi-restraints excluded: chain S residue 1060 SER Chi-restraints excluded: chain S residue 1064 LEU Chi-restraints excluded: chain S residue 1076 MET Chi-restraints excluded: chain S residue 1107 LYS Chi-restraints excluded: chain S residue 1159 ILE Chi-restraints excluded: chain S residue 1168 LEU Chi-restraints excluded: chain S residue 1202 ASN Chi-restraints excluded: chain S residue 1204 MET Chi-restraints excluded: chain S residue 1220 CYS Chi-restraints excluded: chain S residue 1268 GLU Chi-restraints excluded: chain S residue 1283 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 182 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 254 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 199 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 224 optimal weight: 0.3980 chunk 181 optimal weight: 3.9990 chunk 230 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN A 197 GLN K 28 HIS K 111 GLN K 115 ASN K 232 ASN L 28 HIS L 29 GLN L 271 HIS S 102 GLN S 405 ASN S 617 HIS S 650 GLN S 713 GLN S 926 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.194077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.147965 restraints weight = 38800.085| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.00 r_work: 0.3488 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 27277 Z= 0.173 Angle : 0.642 11.961 37604 Z= 0.341 Chirality : 0.043 0.264 4303 Planarity : 0.004 0.062 4151 Dihedral : 19.672 175.330 5418 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.81 % Favored : 93.90 % Rotamer: Outliers : 5.25 % Allowed : 20.61 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.16), residues: 2755 helix: 1.25 (0.14), residues: 1359 sheet: -0.47 (0.34), residues: 250 loop : -1.54 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 71 TYR 0.030 0.002 TYR B 184 PHE 0.064 0.002 PHE C 130 TRP 0.014 0.001 TRP K 3 HIS 0.005 0.001 HIS S 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (27277) covalent geometry : angle 0.64185 / 0.34 (37604) hydrogen bonds : bond 0.04487 / 2.93 ( 1267) hydrogen bonds : angle 4.41860 / 3.04 ( 3512) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 541 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7413 (mt) REVERT: B 149 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8448 (tpp) REVERT: B 161 LYS cc_start: 0.8538 (mtpp) cc_final: 0.8295 (mptp) REVERT: B 197 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7942 (tm130) REVERT: C 55 LYS cc_start: 0.7424 (OUTLIER) cc_final: 0.7133 (ttmm) REVERT: C 96 MET cc_start: 0.7065 (OUTLIER) cc_final: 0.6583 (pp-130) REVERT: D 76 LEU cc_start: 0.8560 (mm) cc_final: 0.8263 (tm) REVERT: D 98 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7552 (mm-30) REVERT: D 100 LEU cc_start: 0.5345 (tp) cc_final: 0.4817 (pp) REVERT: D 120 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6997 (mp0) REVERT: D 131 LYS cc_start: 0.7396 (mtmm) cc_final: 0.7173 (mtmm) REVERT: A 21 THR cc_start: 0.8528 (m) cc_final: 0.8283 (p) REVERT: A 55 LYS cc_start: 0.8466 (ptpp) cc_final: 0.8185 (ptpp) REVERT: A 94 LYS cc_start: 0.7889 (mtpp) cc_final: 0.7490 (ttmm) REVERT: A 107 LEU cc_start: 0.7132 (pp) cc_final: 0.6493 (pp) REVERT: A 111 GLU cc_start: 0.6354 (mp0) cc_final: 0.5739 (mm-30) REVERT: A 196 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7145 (mt-10) REVERT: A 200 VAL cc_start: 0.7929 (t) cc_final: 0.7447 (m) REVERT: K 41 LEU cc_start: 0.8657 (tp) cc_final: 0.8452 (tp) REVERT: K 43 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7261 (mp0) REVERT: K 92 ARG cc_start: 0.8266 (ttm-80) cc_final: 0.7926 (ttm-80) REVERT: K 98 GLU cc_start: 0.8182 (tp30) cc_final: 0.7613 (mp0) REVERT: K 112 LYS cc_start: 0.8133 (tttm) cc_final: 0.7694 (tttp) REVERT: K 176 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6777 (mp) REVERT: K 186 ILE cc_start: 0.7404 (OUTLIER) cc_final: 0.6890 (mp) REVERT: K 235 GLU cc_start: 0.7687 (mp0) cc_final: 0.6980 (mp0) REVERT: K 242 ARG cc_start: 0.7708 (mpp80) cc_final: 0.7318 (mpp80) REVERT: K 280 GLU cc_start: 0.6242 (tm-30) cc_final: 0.5883 (tm-30) REVERT: L 4 ARG cc_start: 0.7532 (mmm-85) cc_final: 0.6907 (mtm-85) REVERT: L 18 ASN cc_start: 0.8237 (m-40) cc_final: 0.7974 (t0) REVERT: L 36 GLU cc_start: 0.7989 (pt0) cc_final: 0.7696 (pt0) REVERT: L 189 ARG cc_start: 0.7545 (ttm170) cc_final: 0.7225 (ttt180) REVERT: S 183 GLU cc_start: 0.7552 (tp30) cc_final: 0.7093 (tp30) REVERT: S 214 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7273 (pp) REVERT: S 217 GLU cc_start: 0.8486 (mp0) cc_final: 0.8000 (mp0) REVERT: S 230 LYS cc_start: 0.8274 (mtpt) cc_final: 0.7763 (mtpt) REVERT: S 304 ASP cc_start: 0.7996 (m-30) cc_final: 0.7570 (m-30) REVERT: S 337 ASP cc_start: 0.8147 (m-30) cc_final: 0.7915 (m-30) REVERT: S 340 LYS cc_start: 0.8285 (mttt) cc_final: 0.7960 (mtmt) REVERT: S 395 GLU cc_start: 0.7140 (tp30) cc_final: 0.6600 (tp30) REVERT: S 442 LYS cc_start: 0.8062 (ttpp) cc_final: 0.7858 (ttpp) REVERT: S 454 PHE cc_start: 0.8594 (t80) cc_final: 0.7896 (t80) REVERT: S 488 GLN cc_start: 0.8058 (mm110) cc_final: 0.7700 (mm110) REVERT: S 492 ASP cc_start: 0.7793 (t0) cc_final: 0.7587 (t0) REVERT: S 564 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7754 (mtm-85) REVERT: S 619 ASP cc_start: 0.8183 (t0) cc_final: 0.7645 (t0) REVERT: S 657 LYS cc_start: 0.8605 (tttp) cc_final: 0.8320 (ttpp) REVERT: S 763 MET cc_start: 0.8680 (mmm) cc_final: 0.8443 (mmm) REVERT: S 832 ASP cc_start: 0.7447 (t0) cc_final: 0.7074 (t0) REVERT: S 890 MET cc_start: 0.7575 (tpp) cc_final: 0.7242 (tpp) REVERT: S 891 LYS cc_start: 0.7868 (tttt) cc_final: 0.7512 (tppp) REVERT: S 982 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7950 (mtt90) REVERT: S 1036 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7898 (pt) REVERT: S 1065 LYS cc_start: 0.8608 (ttmm) cc_final: 0.8343 (mmmm) REVERT: S 1107 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8210 (mmtm) REVERT: S 1169 ARG cc_start: 0.7704 (ttm110) cc_final: 0.7430 (ttm110) REVERT: S 1268 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7603 (mp0) REVERT: S 1298 LYS cc_start: 0.8038 (mtpt) cc_final: 0.7551 (ttmm) REVERT: S 1303 ASP cc_start: 0.7952 (m-30) cc_final: 0.7499 (m-30) outliers start: 131 outliers final: 69 residues processed: 619 average time/residue: 0.7307 time to fit residues: 520.6156 Evaluate side-chains 621 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 538 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 159 LEU Chi-restraints excluded: chain K residue 176 LEU Chi-restraints excluded: chain K residue 186 ILE Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 227 GLN Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 283 VAL Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 206 ASN Chi-restraints excluded: chain L residue 209 ASN Chi-restraints excluded: chain L residue 210 ASP Chi-restraints excluded: chain L residue 240 MET Chi-restraints excluded: chain S residue 39 GLU Chi-restraints excluded: chain S residue 140 LYS Chi-restraints excluded: chain S residue 182 LYS Chi-restraints excluded: chain S residue 197 VAL Chi-restraints excluded: chain S residue 214 ILE Chi-restraints excluded: chain S residue 248 LEU Chi-restraints excluded: chain S residue 297 LEU Chi-restraints excluded: chain S residue 318 LYS Chi-restraints excluded: chain S residue 349 CYS Chi-restraints excluded: chain S residue 356 LEU Chi-restraints excluded: chain S residue 451 LEU Chi-restraints excluded: chain S residue 470 THR Chi-restraints excluded: chain S residue 474 LEU Chi-restraints excluded: chain S residue 509 THR Chi-restraints excluded: chain S residue 516 VAL Chi-restraints excluded: chain S residue 564 ARG Chi-restraints excluded: chain S residue 582 THR Chi-restraints excluded: chain S residue 583 GLU Chi-restraints excluded: chain S residue 662 LYS Chi-restraints excluded: chain S residue 665 THR Chi-restraints excluded: chain S residue 724 GLN Chi-restraints excluded: chain S residue 812 THR Chi-restraints excluded: chain S residue 824 LEU Chi-restraints excluded: chain S residue 863 LEU Chi-restraints excluded: chain S residue 904 SER Chi-restraints excluded: chain S residue 960 GLN Chi-restraints excluded: chain S residue 981 VAL Chi-restraints excluded: chain S residue 982 ARG Chi-restraints excluded: chain S residue 1036 ILE Chi-restraints excluded: chain S residue 1045 THR Chi-restraints excluded: chain S residue 1060 SER Chi-restraints excluded: chain S residue 1076 MET Chi-restraints excluded: chain S residue 1107 LYS Chi-restraints excluded: chain S residue 1125 TYR Chi-restraints excluded: chain S residue 1159 ILE Chi-restraints excluded: chain S residue 1168 LEU Chi-restraints excluded: chain S residue 1202 ASN Chi-restraints excluded: chain S residue 1204 MET Chi-restraints excluded: chain S residue 1220 CYS Chi-restraints excluded: chain S residue 1268 GLU Chi-restraints excluded: chain S residue 1283 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 233 optimal weight: 2.9990 chunk 271 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 255 optimal weight: 0.9990 chunk 237 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 GLN A 153 GLN A 197 GLN K 28 HIS K 93 GLN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 ASN L 28 HIS L 29 GLN L 89 GLN L 271 HIS L 277 ASN S 102 GLN S 617 HIS S 650 GLN S 713 GLN S 926 HIS S1202 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.193527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.147562 restraints weight = 38829.634| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.02 r_work: 0.3476 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27277 Z= 0.194 Angle : 0.649 12.515 37604 Z= 0.344 Chirality : 0.043 0.250 4303 Planarity : 0.004 0.064 4151 Dihedral : 19.673 174.970 5416 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.81 % Favored : 93.94 % Rotamer: Outliers : 5.57 % Allowed : 20.81 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.16), residues: 2755 helix: 1.21 (0.14), residues: 1358 sheet: -0.51 (0.33), residues: 260 loop : -1.52 (0.17), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG K 71 TYR 0.027 0.002 TYR L 254 PHE 0.051 0.002 PHE D 130 TRP 0.017 0.002 TRP K 3 HIS 0.006 0.001 HIS S 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (27277) covalent geometry : angle 0.64921 / 0.34 (37604) hydrogen bonds : bond 0.04515 / 2.94 ( 1267) hydrogen bonds : angle 4.42960 / 3.05 ( 3512) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 554 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 PHE cc_start: 0.8093 (t80) cc_final: 0.7874 (t80) REVERT: B 65 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7432 (mt) REVERT: B 197 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7949 (tm130) REVERT: C 55 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.7145 (ttmm) REVERT: D 98 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7667 (mm-30) REVERT: D 100 LEU cc_start: 0.5247 (tp) cc_final: 0.4795 (pp) REVERT: D 120 GLU cc_start: 0.7328 (mm-30) cc_final: 0.7037 (mp0) REVERT: D 122 ASP cc_start: 0.6181 (OUTLIER) cc_final: 0.5883 (p0) REVERT: D 131 LYS cc_start: 0.7397 (mtmm) cc_final: 0.7182 (mtmm) REVERT: A 21 THR cc_start: 0.8544 (m) cc_final: 0.8305 (p) REVERT: A 55 LYS cc_start: 0.8522 (ptpp) cc_final: 0.8290 (ptpp) REVERT: A 111 GLU cc_start: 0.6358 (mp0) cc_final: 0.5795 (mt-10) REVERT: A 167 ILE cc_start: 0.8274 (mp) cc_final: 0.8049 (mm) REVERT: A 196 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7151 (mt-10) REVERT: A 200 VAL cc_start: 0.7905 (t) cc_final: 0.7430 (m) REVERT: K 92 ARG cc_start: 0.8246 (ttm-80) cc_final: 0.7958 (ttm-80) REVERT: K 98 GLU cc_start: 0.8195 (tp30) cc_final: 0.7631 (mp0) REVERT: K 112 LYS cc_start: 0.8111 (tttm) cc_final: 0.7724 (tttp) REVERT: K 176 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6783 (mp) REVERT: K 235 GLU cc_start: 0.7741 (mp0) cc_final: 0.7026 (mp0) REVERT: K 280 GLU cc_start: 0.6298 (tm-30) cc_final: 0.5983 (tm-30) REVERT: L 4 ARG cc_start: 0.7537 (mmm-85) cc_final: 0.6914 (mtm-85) REVERT: L 18 ASN cc_start: 0.8257 (m-40) cc_final: 0.8040 (t0) REVERT: L 36 GLU cc_start: 0.8024 (pt0) cc_final: 0.7780 (pt0) REVERT: L 92 ARG cc_start: 0.6807 (mtm180) cc_final: 0.6539 (mtm180) REVERT: L 189 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7248 (ttt180) REVERT: S 88 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7444 (pm20) REVERT: S 173 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8185 (mtmm) REVERT: S 183 GLU cc_start: 0.7587 (tp30) cc_final: 0.7119 (tp30) REVERT: S 214 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7220 (pp) REVERT: S 217 GLU cc_start: 0.8476 (mp0) cc_final: 0.7950 (mp0) REVERT: S 230 LYS cc_start: 0.8299 (mtpt) cc_final: 0.7784 (mtpt) REVERT: S 304 ASP cc_start: 0.8017 (m-30) cc_final: 0.7591 (m-30) REVERT: S 337 ASP cc_start: 0.8175 (m-30) cc_final: 0.7944 (m-30) REVERT: S 340 LYS cc_start: 0.8300 (mttt) cc_final: 0.7967 (mtmt) REVERT: S 395 GLU cc_start: 0.7182 (tp30) cc_final: 0.6697 (tp30) REVERT: S 442 LYS cc_start: 0.8085 (ttpp) cc_final: 0.7880 (ttpp) REVERT: S 454 PHE cc_start: 0.8580 (t80) cc_final: 0.7881 (t80) REVERT: S 488 GLN cc_start: 0.8059 (mm110) cc_final: 0.7697 (mm110) REVERT: S 564 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7728 (mtm-85) REVERT: S 619 ASP cc_start: 0.8163 (t0) cc_final: 0.7637 (t0) REVERT: S 657 LYS cc_start: 0.8613 (tttp) cc_final: 0.8336 (ttpp) REVERT: S 763 MET cc_start: 0.8693 (mmm) cc_final: 0.8490 (mmm) REVERT: S 832 ASP cc_start: 0.7509 (t0) cc_final: 0.7167 (t0) REVERT: S 890 MET cc_start: 0.7565 (tpp) cc_final: 0.7248 (tpp) REVERT: S 891 LYS cc_start: 0.7896 (tttt) cc_final: 0.7541 (tppp) REVERT: S 970 SER cc_start: 0.8397 (t) cc_final: 0.8126 (m) REVERT: S 982 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7966 (mtt90) REVERT: S 1036 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7904 (pt) REVERT: S 1065 LYS cc_start: 0.8587 (ttmm) cc_final: 0.8333 (mmmm) REVERT: S 1107 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8564 (mttm) REVERT: S 1169 ARG cc_start: 0.7719 (ttm110) cc_final: 0.7444 (ttm110) REVERT: S 1268 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7636 (mp0) REVERT: S 1298 LYS cc_start: 0.8059 (mtpt) cc_final: 0.7591 (ttmm) REVERT: S 1303 ASP cc_start: 0.7954 (m-30) cc_final: 0.7494 (m-30) outliers start: 139 outliers final: 74 residues processed: 624 average time/residue: 0.6724 time to fit residues: 484.5865 Evaluate side-chains 641 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 552 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 159 LEU Chi-restraints excluded: chain K residue 176 LEU Chi-restraints excluded: chain K residue 186 ILE Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 227 GLN Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 283 VAL Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 189 ARG Chi-restraints excluded: chain L residue 206 ASN Chi-restraints excluded: chain L residue 209 ASN Chi-restraints excluded: chain L residue 240 MET Chi-restraints excluded: chain L residue 254 TYR Chi-restraints excluded: chain S residue 39 GLU Chi-restraints excluded: chain S residue 88 GLU Chi-restraints excluded: chain S residue 140 LYS Chi-restraints excluded: chain S residue 173 LYS Chi-restraints excluded: chain S residue 182 LYS Chi-restraints excluded: chain S residue 197 VAL Chi-restraints excluded: chain S residue 214 ILE Chi-restraints excluded: chain S residue 297 LEU Chi-restraints excluded: chain S residue 318 LYS Chi-restraints excluded: chain S residue 349 CYS Chi-restraints excluded: chain S residue 356 LEU Chi-restraints excluded: chain S residue 451 LEU Chi-restraints excluded: chain S residue 470 THR Chi-restraints excluded: chain S residue 474 LEU Chi-restraints excluded: chain S residue 509 THR Chi-restraints excluded: chain S residue 516 VAL Chi-restraints excluded: chain S residue 549 SER Chi-restraints excluded: chain S residue 564 ARG Chi-restraints excluded: chain S residue 582 THR Chi-restraints excluded: chain S residue 583 GLU Chi-restraints excluded: chain S residue 662 LYS Chi-restraints excluded: chain S residue 665 THR Chi-restraints excluded: chain S residue 724 GLN Chi-restraints excluded: chain S residue 812 THR Chi-restraints excluded: chain S residue 824 LEU Chi-restraints excluded: chain S residue 863 LEU Chi-restraints excluded: chain S residue 904 SER Chi-restraints excluded: chain S residue 939 THR Chi-restraints excluded: chain S residue 981 VAL Chi-restraints excluded: chain S residue 982 ARG Chi-restraints excluded: chain S residue 1036 ILE Chi-restraints excluded: chain S residue 1045 THR Chi-restraints excluded: chain S residue 1060 SER Chi-restraints excluded: chain S residue 1076 MET Chi-restraints excluded: chain S residue 1107 LYS Chi-restraints excluded: chain S residue 1125 TYR Chi-restraints excluded: chain S residue 1159 ILE Chi-restraints excluded: chain S residue 1168 LEU Chi-restraints excluded: chain S residue 1202 ASN Chi-restraints excluded: chain S residue 1204 MET Chi-restraints excluded: chain S residue 1220 CYS Chi-restraints excluded: chain S residue 1268 GLU Chi-restraints excluded: chain S residue 1283 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 135 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 69 optimal weight: 0.3980 chunk 4 optimal weight: 0.6980 chunk 199 optimal weight: 0.8980 chunk 281 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 4 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN A 197 GLN K 28 HIS K 115 ASN L 28 HIS L 29 GLN L 271 HIS S 102 GLN S 617 HIS S 650 GLN S 713 GLN S 926 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.194513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.148104 restraints weight = 38365.937| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.86 r_work: 0.3499 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 27277 Z= 0.164 Angle : 0.647 12.804 37604 Z= 0.342 Chirality : 0.043 0.272 4303 Planarity : 0.004 0.051 4151 Dihedral : 19.638 174.721 5413 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.81 % Favored : 93.94 % Rotamer: Outliers : 4.93 % Allowed : 21.81 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.16), residues: 2755 helix: 1.28 (0.14), residues: 1356 sheet: -0.42 (0.34), residues: 248 loop : -1.52 (0.17), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K 71 TYR 0.028 0.001 TYR L 254 PHE 0.052 0.002 PHE D 130 TRP 0.018 0.001 TRP K 3 HIS 0.005 0.001 HIS S 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (27277) covalent geometry : angle 0.64676 / 0.34 (37604) hydrogen bonds : bond 0.04361 / 2.84 ( 1267) hydrogen bonds : angle 4.40848 / 3.03 ( 3512) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 555 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 LYS cc_start: 0.8632 (mttm) cc_final: 0.8415 (mtmm) REVERT: B 60 PHE cc_start: 0.8029 (t80) cc_final: 0.7820 (t80) REVERT: B 65 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7428 (mt) REVERT: B 149 MET cc_start: 0.8810 (tpp) cc_final: 0.8429 (tpp) REVERT: B 197 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7954 (tm130) REVERT: C 55 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.7187 (ttmm) REVERT: C 147 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7787 (mmtm) REVERT: D 76 LEU cc_start: 0.8625 (mm) cc_final: 0.8381 (tm) REVERT: D 98 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7667 (mm-30) REVERT: D 100 LEU cc_start: 0.5207 (tp) cc_final: 0.4800 (pp) REVERT: D 120 GLU cc_start: 0.7323 (mm-30) cc_final: 0.7086 (mp0) REVERT: D 122 ASP cc_start: 0.6169 (OUTLIER) cc_final: 0.5870 (p0) REVERT: D 127 GLN cc_start: 0.8246 (mm110) cc_final: 0.7851 (mm-40) REVERT: D 131 LYS cc_start: 0.7294 (mtmm) cc_final: 0.7066 (mtmm) REVERT: D 149 MET cc_start: 0.7125 (mmm) cc_final: 0.6702 (mmm) REVERT: A 21 THR cc_start: 0.8520 (m) cc_final: 0.8296 (p) REVERT: A 94 LYS cc_start: 0.7993 (mtpp) cc_final: 0.7528 (mtmm) REVERT: A 111 GLU cc_start: 0.6389 (OUTLIER) cc_final: 0.5561 (mt-10) REVERT: A 161 LYS cc_start: 0.8290 (mmpt) cc_final: 0.7861 (mmmt) REVERT: A 167 ILE cc_start: 0.8286 (mp) cc_final: 0.8077 (mm) REVERT: A 196 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7177 (mt-10) REVERT: A 200 VAL cc_start: 0.7881 (t) cc_final: 0.7350 (m) REVERT: K 92 ARG cc_start: 0.8225 (ttm-80) cc_final: 0.7947 (ttm-80) REVERT: K 98 GLU cc_start: 0.8119 (tp30) cc_final: 0.7639 (mp0) REVERT: K 112 LYS cc_start: 0.8104 (tttm) cc_final: 0.7726 (ttpp) REVERT: K 176 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6773 (mp) REVERT: K 235 GLU cc_start: 0.7777 (mp0) cc_final: 0.7053 (mp0) REVERT: K 280 GLU cc_start: 0.6297 (tm-30) cc_final: 0.5971 (tm-30) REVERT: L 4 ARG cc_start: 0.7549 (mmm-85) cc_final: 0.6920 (mtm-85) REVERT: L 36 GLU cc_start: 0.7943 (pt0) cc_final: 0.7691 (pt0) REVERT: L 92 ARG cc_start: 0.6812 (mtm180) cc_final: 0.6515 (mtm180) REVERT: L 189 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.7214 (ttt180) REVERT: S 87 GLU cc_start: 0.7849 (tt0) cc_final: 0.7418 (tm-30) REVERT: S 88 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7336 (pm20) REVERT: S 173 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8154 (mtmm) REVERT: S 183 GLU cc_start: 0.7515 (tp30) cc_final: 0.7063 (tp30) REVERT: S 214 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7189 (pp) REVERT: S 217 GLU cc_start: 0.8452 (mp0) cc_final: 0.7956 (mp0) REVERT: S 230 LYS cc_start: 0.8277 (mtpt) cc_final: 0.7758 (mtpt) REVERT: S 304 ASP cc_start: 0.7968 (m-30) cc_final: 0.7555 (m-30) REVERT: S 337 ASP cc_start: 0.8171 (m-30) cc_final: 0.7933 (m-30) REVERT: S 340 LYS cc_start: 0.8293 (mttt) cc_final: 0.7976 (mtmt) REVERT: S 395 GLU cc_start: 0.7129 (tp30) cc_final: 0.6614 (tp30) REVERT: S 454 PHE cc_start: 0.8574 (t80) cc_final: 0.7916 (t80) REVERT: S 488 GLN cc_start: 0.8023 (mm110) cc_final: 0.7669 (mm-40) REVERT: S 492 ASP cc_start: 0.7825 (t0) cc_final: 0.7624 (t0) REVERT: S 564 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7699 (mtm-85) REVERT: S 566 LYS cc_start: 0.8446 (mtpp) cc_final: 0.8218 (ttmm) REVERT: S 619 ASP cc_start: 0.8179 (t0) cc_final: 0.7661 (t0) REVERT: S 657 LYS cc_start: 0.8592 (tttp) cc_final: 0.8326 (ttpp) REVERT: S 826 TYR cc_start: 0.7050 (m-10) cc_final: 0.6845 (m-10) REVERT: S 832 ASP cc_start: 0.7451 (t0) cc_final: 0.7111 (t0) REVERT: S 890 MET cc_start: 0.7596 (tpp) cc_final: 0.7327 (tpp) REVERT: S 891 LYS cc_start: 0.7953 (tttt) cc_final: 0.7621 (tppp) REVERT: S 970 SER cc_start: 0.8414 (t) cc_final: 0.8146 (m) REVERT: S 982 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7990 (mtt90) REVERT: S 1036 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7903 (pt) REVERT: S 1065 LYS cc_start: 0.8611 (ttmm) cc_final: 0.8353 (mmmm) REVERT: S 1107 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8541 (mmtt) REVERT: S 1169 ARG cc_start: 0.7684 (ttm110) cc_final: 0.7415 (ttm110) REVERT: S 1268 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: S 1298 LYS cc_start: 0.7996 (mtpt) cc_final: 0.7534 (ttmm) REVERT: S 1303 ASP cc_start: 0.7951 (m-30) cc_final: 0.7493 (m-30) outliers start: 123 outliers final: 73 residues processed: 624 average time/residue: 0.6887 time to fit residues: 493.8046 Evaluate side-chains 636 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 546 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 159 LEU Chi-restraints excluded: chain K residue 176 LEU Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 227 GLN Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 283 VAL Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 189 ARG Chi-restraints excluded: chain L residue 206 ASN Chi-restraints excluded: chain L residue 210 ASP Chi-restraints excluded: chain L residue 240 MET Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain S residue 39 GLU Chi-restraints excluded: chain S residue 88 GLU Chi-restraints excluded: chain S residue 140 LYS Chi-restraints excluded: chain S residue 173 LYS Chi-restraints excluded: chain S residue 182 LYS Chi-restraints excluded: chain S residue 197 VAL Chi-restraints excluded: chain S residue 214 ILE Chi-restraints excluded: chain S residue 248 LEU Chi-restraints excluded: chain S residue 297 LEU Chi-restraints excluded: chain S residue 318 LYS Chi-restraints excluded: chain S residue 349 CYS Chi-restraints excluded: chain S residue 356 LEU Chi-restraints excluded: chain S residue 451 LEU Chi-restraints excluded: chain S residue 470 THR Chi-restraints excluded: chain S residue 474 LEU Chi-restraints excluded: chain S residue 516 VAL Chi-restraints excluded: chain S residue 549 SER Chi-restraints excluded: chain S residue 564 ARG Chi-restraints excluded: chain S residue 582 THR Chi-restraints excluded: chain S residue 583 GLU Chi-restraints excluded: chain S residue 637 ARG Chi-restraints excluded: chain S residue 665 THR Chi-restraints excluded: chain S residue 724 GLN Chi-restraints excluded: chain S residue 812 THR Chi-restraints excluded: chain S residue 863 LEU Chi-restraints excluded: chain S residue 904 SER Chi-restraints excluded: chain S residue 939 THR Chi-restraints excluded: chain S residue 960 GLN Chi-restraints excluded: chain S residue 981 VAL Chi-restraints excluded: chain S residue 982 ARG Chi-restraints excluded: chain S residue 1036 ILE Chi-restraints excluded: chain S residue 1045 THR Chi-restraints excluded: chain S residue 1060 SER Chi-restraints excluded: chain S residue 1076 MET Chi-restraints excluded: chain S residue 1107 LYS Chi-restraints excluded: chain S residue 1125 TYR Chi-restraints excluded: chain S residue 1159 ILE Chi-restraints excluded: chain S residue 1168 LEU Chi-restraints excluded: chain S residue 1202 ASN Chi-restraints excluded: chain S residue 1204 MET Chi-restraints excluded: chain S residue 1220 CYS Chi-restraints excluded: chain S residue 1268 GLU Chi-restraints excluded: chain S residue 1283 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 261 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 230 optimal weight: 0.6980 chunk 225 optimal weight: 0.6980 chunk 125 optimal weight: 0.8980 chunk 169 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 210 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 GLN ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN A 197 GLN K 28 HIS K 115 ASN K 232 ASN L 28 HIS L 29 GLN L 271 HIS S 102 GLN S 405 ASN S 617 HIS S 650 GLN S 713 GLN S 926 HIS S1202 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.194280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.148197 restraints weight = 38588.120| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.89 r_work: 0.3495 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 27277 Z= 0.185 Angle : 0.671 12.721 37604 Z= 0.351 Chirality : 0.043 0.277 4303 Planarity : 0.004 0.049 4151 Dihedral : 19.636 174.502 5412 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.88 % Favored : 93.87 % Rotamer: Outliers : 4.89 % Allowed : 22.65 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.16), residues: 2755 helix: 1.24 (0.14), residues: 1357 sheet: -0.40 (0.34), residues: 252 loop : -1.53 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 71 TYR 0.023 0.002 TYR S1019 PHE 0.054 0.002 PHE C 130 TRP 0.024 0.002 TRP K 3 HIS 0.005 0.001 HIS S 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (27277) covalent geometry : angle 0.67088 / 0.35 (37604) hydrogen bonds : bond 0.04398 / 2.87 ( 1267) hydrogen bonds : angle 4.41589 / 3.04 ( 3512) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 549 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 PHE cc_start: 0.8044 (t80) cc_final: 0.7832 (t80) REVERT: B 65 ILE cc_start: 0.7657 (OUTLIER) cc_final: 0.7392 (mt) REVERT: B 184 TYR cc_start: 0.7475 (t80) cc_final: 0.7239 (t80) REVERT: B 197 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7949 (tm130) REVERT: C 55 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.7166 (ttmm) REVERT: D 66 LEU cc_start: 0.7693 (mt) cc_final: 0.7376 (mt) REVERT: D 94 LYS cc_start: 0.5929 (OUTLIER) cc_final: 0.5544 (mmtm) REVERT: D 100 LEU cc_start: 0.5175 (tp) cc_final: 0.4803 (pp) REVERT: D 120 GLU cc_start: 0.7306 (mm-30) cc_final: 0.7071 (mp0) REVERT: D 122 ASP cc_start: 0.6147 (OUTLIER) cc_final: 0.5848 (p0) REVERT: D 127 GLN cc_start: 0.8239 (mm110) cc_final: 0.7820 (mm-40) REVERT: D 131 LYS cc_start: 0.7271 (mtmm) cc_final: 0.7055 (mtmm) REVERT: A 21 THR cc_start: 0.8532 (m) cc_final: 0.8318 (p) REVERT: A 33 LYS cc_start: 0.8312 (tttp) cc_final: 0.7889 (tptp) REVERT: A 107 LEU cc_start: 0.7173 (pp) cc_final: 0.6870 (tp) REVERT: A 111 GLU cc_start: 0.6411 (OUTLIER) cc_final: 0.5695 (mm-30) REVERT: A 167 ILE cc_start: 0.8272 (mp) cc_final: 0.8065 (mm) REVERT: A 196 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7179 (mt-10) REVERT: A 200 VAL cc_start: 0.7862 (t) cc_final: 0.7368 (m) REVERT: K 92 ARG cc_start: 0.8218 (ttm-80) cc_final: 0.7949 (ttm-80) REVERT: K 98 GLU cc_start: 0.8126 (tp30) cc_final: 0.7626 (mp0) REVERT: K 112 LYS cc_start: 0.8123 (tttm) cc_final: 0.7752 (tttp) REVERT: K 176 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6788 (mp) REVERT: K 235 GLU cc_start: 0.7769 (mp0) cc_final: 0.7052 (mp0) REVERT: K 280 GLU cc_start: 0.6297 (tm-30) cc_final: 0.5977 (tm-30) REVERT: L 4 ARG cc_start: 0.7561 (mmm-85) cc_final: 0.6930 (mtm-85) REVERT: L 18 ASN cc_start: 0.8177 (m-40) cc_final: 0.7934 (t0) REVERT: L 36 GLU cc_start: 0.7956 (pt0) cc_final: 0.7693 (pt0) REVERT: L 92 ARG cc_start: 0.6845 (mtm180) cc_final: 0.6497 (mtm180) REVERT: L 189 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.7249 (ttt180) REVERT: S 87 GLU cc_start: 0.7883 (tt0) cc_final: 0.7428 (tm-30) REVERT: S 88 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7335 (pm20) REVERT: S 173 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8172 (mtmm) REVERT: S 183 GLU cc_start: 0.7521 (tp30) cc_final: 0.7065 (tp30) REVERT: S 214 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7181 (pp) REVERT: S 217 GLU cc_start: 0.8434 (mp0) cc_final: 0.7951 (mp0) REVERT: S 230 LYS cc_start: 0.8310 (mtpt) cc_final: 0.7794 (mtpt) REVERT: S 304 ASP cc_start: 0.7980 (m-30) cc_final: 0.7578 (m-30) REVERT: S 340 LYS cc_start: 0.8284 (mttt) cc_final: 0.7964 (mtmt) REVERT: S 395 GLU cc_start: 0.7104 (tp30) cc_final: 0.6596 (tp30) REVERT: S 454 PHE cc_start: 0.8565 (t80) cc_final: 0.7912 (t80) REVERT: S 488 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7668 (mm-40) REVERT: S 564 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7679 (mtm-85) REVERT: S 619 ASP cc_start: 0.8177 (t0) cc_final: 0.7688 (t0) REVERT: S 657 LYS cc_start: 0.8568 (tttp) cc_final: 0.8312 (ttpp) REVERT: S 832 ASP cc_start: 0.7475 (t0) cc_final: 0.7160 (t0) REVERT: S 890 MET cc_start: 0.7603 (tpp) cc_final: 0.7339 (tpp) REVERT: S 891 LYS cc_start: 0.7944 (tttt) cc_final: 0.7612 (tppp) REVERT: S 970 SER cc_start: 0.8408 (t) cc_final: 0.8140 (m) REVERT: S 982 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7993 (mtt90) REVERT: S 1036 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7940 (pt) REVERT: S 1065 LYS cc_start: 0.8596 (ttmm) cc_final: 0.8334 (mmmm) REVERT: S 1107 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8227 (mmtm) REVERT: S 1169 ARG cc_start: 0.7663 (ttm110) cc_final: 0.7398 (ttm110) REVERT: S 1268 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7568 (mp0) REVERT: S 1298 LYS cc_start: 0.7962 (mtpt) cc_final: 0.7527 (ttmm) REVERT: S 1303 ASP cc_start: 0.7946 (m-30) cc_final: 0.7492 (m-30) outliers start: 122 outliers final: 75 residues processed: 616 average time/residue: 0.6454 time to fit residues: 457.0502 Evaluate side-chains 635 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 542 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 159 LEU Chi-restraints excluded: chain K residue 176 LEU Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 227 GLN Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 283 VAL Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 189 ARG Chi-restraints excluded: chain L residue 206 ASN Chi-restraints excluded: chain L residue 210 ASP Chi-restraints excluded: chain L residue 240 MET Chi-restraints excluded: chain S residue 39 GLU Chi-restraints excluded: chain S residue 88 GLU Chi-restraints excluded: chain S residue 140 LYS Chi-restraints excluded: chain S residue 173 LYS Chi-restraints excluded: chain S residue 182 LYS Chi-restraints excluded: chain S residue 197 VAL Chi-restraints excluded: chain S residue 214 ILE Chi-restraints excluded: chain S residue 248 LEU Chi-restraints excluded: chain S residue 297 LEU Chi-restraints excluded: chain S residue 318 LYS Chi-restraints excluded: chain S residue 349 CYS Chi-restraints excluded: chain S residue 356 LEU Chi-restraints excluded: chain S residue 451 LEU Chi-restraints excluded: chain S residue 470 THR Chi-restraints excluded: chain S residue 474 LEU Chi-restraints excluded: chain S residue 488 GLN Chi-restraints excluded: chain S residue 509 THR Chi-restraints excluded: chain S residue 516 VAL Chi-restraints excluded: chain S residue 549 SER Chi-restraints excluded: chain S residue 564 ARG Chi-restraints excluded: chain S residue 582 THR Chi-restraints excluded: chain S residue 583 GLU Chi-restraints excluded: chain S residue 637 ARG Chi-restraints excluded: chain S residue 665 THR Chi-restraints excluded: chain S residue 724 GLN Chi-restraints excluded: chain S residue 812 THR Chi-restraints excluded: chain S residue 863 LEU Chi-restraints excluded: chain S residue 904 SER Chi-restraints excluded: chain S residue 939 THR Chi-restraints excluded: chain S residue 960 GLN Chi-restraints excluded: chain S residue 981 VAL Chi-restraints excluded: chain S residue 982 ARG Chi-restraints excluded: chain S residue 1001 THR Chi-restraints excluded: chain S residue 1036 ILE Chi-restraints excluded: chain S residue 1045 THR Chi-restraints excluded: chain S residue 1060 SER Chi-restraints excluded: chain S residue 1076 MET Chi-restraints excluded: chain S residue 1107 LYS Chi-restraints excluded: chain S residue 1125 TYR Chi-restraints excluded: chain S residue 1159 ILE Chi-restraints excluded: chain S residue 1168 LEU Chi-restraints excluded: chain S residue 1202 ASN Chi-restraints excluded: chain S residue 1204 MET Chi-restraints excluded: chain S residue 1220 CYS Chi-restraints excluded: chain S residue 1268 GLU Chi-restraints excluded: chain S residue 1283 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 273 optimal weight: 0.8980 chunk 123 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 143 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 HIS ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 GLN C 168 ASN ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN ** A 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 GLN K 28 HIS K 115 ASN K 232 ASN L 271 HIS S 102 GLN S 405 ASN S 617 HIS S 650 GLN S 713 GLN S 926 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.194281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.148229 restraints weight = 38652.958| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.85 r_work: 0.3502 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 27277 Z= 0.195 Angle : 0.690 12.653 37604 Z= 0.361 Chirality : 0.044 0.257 4303 Planarity : 0.004 0.056 4151 Dihedral : 19.644 174.245 5412 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.88 % Favored : 93.87 % Rotamer: Outliers : 4.77 % Allowed : 23.42 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.16), residues: 2755 helix: 1.18 (0.14), residues: 1357 sheet: -0.46 (0.33), residues: 257 loop : -1.49 (0.17), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 71 TYR 0.027 0.002 TYR D 80 PHE 0.052 0.002 PHE D 130 TRP 0.030 0.002 TRP K 3 HIS 0.007 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 (27277) covalent geometry : angle 0.69015 / 0.36 (37604) hydrogen bonds : bond 0.04463 / 2.90 ( 1267) hydrogen bonds : angle 4.45459 / 3.07 ( 3512) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 542 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 PHE cc_start: 0.8109 (t80) cc_final: 0.7908 (t80) REVERT: B 65 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7385 (mt) REVERT: B 197 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7915 (tm130) REVERT: C 55 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.7158 (ttmm) REVERT: C 90 LYS cc_start: 0.5617 (pmtt) cc_final: 0.5407 (pmtt) REVERT: C 147 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7758 (mmtm) REVERT: D 66 LEU cc_start: 0.7696 (mt) cc_final: 0.7495 (tp) REVERT: D 77 LYS cc_start: 0.8272 (mmtp) cc_final: 0.7956 (mmtp) REVERT: D 120 GLU cc_start: 0.7318 (mm-30) cc_final: 0.7064 (mp0) REVERT: D 122 ASP cc_start: 0.6149 (OUTLIER) cc_final: 0.5864 (p0) REVERT: D 127 GLN cc_start: 0.8269 (mm110) cc_final: 0.7852 (mm-40) REVERT: D 131 LYS cc_start: 0.7403 (mtmm) cc_final: 0.7170 (mtmm) REVERT: A 21 THR cc_start: 0.8545 (m) cc_final: 0.8306 (p) REVERT: A 107 LEU cc_start: 0.7202 (pp) cc_final: 0.6877 (tp) REVERT: A 111 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.5579 (mm-30) REVERT: A 167 ILE cc_start: 0.8283 (mp) cc_final: 0.8079 (mm) REVERT: A 196 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7156 (mt-10) REVERT: A 200 VAL cc_start: 0.7794 (t) cc_final: 0.7315 (m) REVERT: K 98 GLU cc_start: 0.8127 (tp30) cc_final: 0.7621 (mp0) REVERT: K 112 LYS cc_start: 0.8055 (tttm) cc_final: 0.7733 (tttp) REVERT: K 176 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6794 (mp) REVERT: K 235 GLU cc_start: 0.7748 (mp0) cc_final: 0.7017 (mp0) REVERT: K 280 GLU cc_start: 0.6279 (tm-30) cc_final: 0.5946 (tm-30) REVERT: L 4 ARG cc_start: 0.7554 (mmm-85) cc_final: 0.6896 (mtm-85) REVERT: L 18 ASN cc_start: 0.8161 (m-40) cc_final: 0.7916 (t0) REVERT: L 36 GLU cc_start: 0.7956 (pt0) cc_final: 0.7680 (pt0) REVERT: L 92 ARG cc_start: 0.6851 (mtm180) cc_final: 0.6486 (mtm180) REVERT: L 189 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.7202 (ttt180) REVERT: S 87 GLU cc_start: 0.7896 (tt0) cc_final: 0.7441 (tm-30) REVERT: S 88 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7272 (pm20) REVERT: S 173 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8134 (mtmm) REVERT: S 183 GLU cc_start: 0.7504 (tp30) cc_final: 0.7042 (tp30) REVERT: S 214 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7172 (pp) REVERT: S 217 GLU cc_start: 0.8404 (mp0) cc_final: 0.7908 (mp0) REVERT: S 230 LYS cc_start: 0.8294 (mtpt) cc_final: 0.7775 (mtpt) REVERT: S 304 ASP cc_start: 0.7960 (m-30) cc_final: 0.7559 (m-30) REVERT: S 340 LYS cc_start: 0.8256 (mttt) cc_final: 0.7928 (mtmt) REVERT: S 352 GLU cc_start: 0.6865 (mm-30) cc_final: 0.6639 (mm-30) REVERT: S 395 GLU cc_start: 0.7056 (tp30) cc_final: 0.6537 (tp30) REVERT: S 454 PHE cc_start: 0.8557 (t80) cc_final: 0.7906 (t80) REVERT: S 488 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7657 (mm-40) REVERT: S 564 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7666 (mtm-85) REVERT: S 619 ASP cc_start: 0.8127 (t0) cc_final: 0.7634 (t0) REVERT: S 657 LYS cc_start: 0.8572 (tttp) cc_final: 0.8289 (ttpp) REVERT: S 832 ASP cc_start: 0.7471 (t0) cc_final: 0.7152 (t0) REVERT: S 890 MET cc_start: 0.7508 (tpp) cc_final: 0.7252 (tpp) REVERT: S 891 LYS cc_start: 0.7933 (tttt) cc_final: 0.7609 (tppp) REVERT: S 970 SER cc_start: 0.8406 (t) cc_final: 0.8138 (m) REVERT: S 982 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7969 (mtt90) REVERT: S 1036 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7936 (pt) REVERT: S 1065 LYS cc_start: 0.8581 (ttmm) cc_final: 0.8320 (mmmm) REVERT: S 1107 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8229 (mmtm) REVERT: S 1169 ARG cc_start: 0.7690 (ttm110) cc_final: 0.7422 (ttm110) REVERT: S 1268 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: S 1298 LYS cc_start: 0.7956 (mtpt) cc_final: 0.7512 (ttmm) REVERT: S 1303 ASP cc_start: 0.7922 (m-30) cc_final: 0.7489 (m-30) outliers start: 119 outliers final: 74 residues processed: 604 average time/residue: 0.7060 time to fit residues: 490.2551 Evaluate side-chains 627 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 535 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 159 LEU Chi-restraints excluded: chain K residue 176 LEU Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 227 GLN Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 283 VAL Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 189 ARG Chi-restraints excluded: chain L residue 210 ASP Chi-restraints excluded: chain L residue 240 MET Chi-restraints excluded: chain S residue 39 GLU Chi-restraints excluded: chain S residue 88 GLU Chi-restraints excluded: chain S residue 140 LYS Chi-restraints excluded: chain S residue 173 LYS Chi-restraints excluded: chain S residue 182 LYS Chi-restraints excluded: chain S residue 197 VAL Chi-restraints excluded: chain S residue 214 ILE Chi-restraints excluded: chain S residue 248 LEU Chi-restraints excluded: chain S residue 297 LEU Chi-restraints excluded: chain S residue 318 LYS Chi-restraints excluded: chain S residue 349 CYS Chi-restraints excluded: chain S residue 356 LEU Chi-restraints excluded: chain S residue 451 LEU Chi-restraints excluded: chain S residue 470 THR Chi-restraints excluded: chain S residue 474 LEU Chi-restraints excluded: chain S residue 488 GLN Chi-restraints excluded: chain S residue 509 THR Chi-restraints excluded: chain S residue 516 VAL Chi-restraints excluded: chain S residue 549 SER Chi-restraints excluded: chain S residue 564 ARG Chi-restraints excluded: chain S residue 582 THR Chi-restraints excluded: chain S residue 583 GLU Chi-restraints excluded: chain S residue 637 ARG Chi-restraints excluded: chain S residue 665 THR Chi-restraints excluded: chain S residue 724 GLN Chi-restraints excluded: chain S residue 812 THR Chi-restraints excluded: chain S residue 863 LEU Chi-restraints excluded: chain S residue 904 SER Chi-restraints excluded: chain S residue 939 THR Chi-restraints excluded: chain S residue 960 GLN Chi-restraints excluded: chain S residue 981 VAL Chi-restraints excluded: chain S residue 982 ARG Chi-restraints excluded: chain S residue 1001 THR Chi-restraints excluded: chain S residue 1036 ILE Chi-restraints excluded: chain S residue 1045 THR Chi-restraints excluded: chain S residue 1060 SER Chi-restraints excluded: chain S residue 1076 MET Chi-restraints excluded: chain S residue 1107 LYS Chi-restraints excluded: chain S residue 1125 TYR Chi-restraints excluded: chain S residue 1159 ILE Chi-restraints excluded: chain S residue 1168 LEU Chi-restraints excluded: chain S residue 1204 MET Chi-restraints excluded: chain S residue 1218 LYS Chi-restraints excluded: chain S residue 1220 CYS Chi-restraints excluded: chain S residue 1268 GLU Chi-restraints excluded: chain S residue 1283 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 163 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 121 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 233 optimal weight: 1.9990 chunk 269 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 260 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 144 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 HIS ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN ** A 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 GLN K 28 HIS K 115 ASN K 232 ASN L 271 HIS S 102 GLN S 405 ASN S 617 HIS S 650 GLN S 713 GLN S 926 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.193049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.147054 restraints weight = 38471.708| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.99 r_work: 0.3482 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 27277 Z= 0.266 Angle : 0.738 12.540 37604 Z= 0.386 Chirality : 0.047 0.271 4303 Planarity : 0.004 0.073 4151 Dihedral : 19.664 174.056 5412 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.32 % Favored : 93.47 % Rotamer: Outliers : 4.21 % Allowed : 24.14 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.16), residues: 2755 helix: 1.02 (0.14), residues: 1357 sheet: -0.51 (0.33), residues: 258 loop : -1.50 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 71 TYR 0.031 0.002 TYR C 157 PHE 0.052 0.002 PHE D 130 TRP 0.035 0.002 TRP K 3 HIS 0.006 0.001 HIS S 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.27 (27277) covalent geometry : angle 0.73788 / 0.39 (37604) hydrogen bonds : bond 0.04801 / 3.13 ( 1267) hydrogen bonds : angle 4.57736 / 3.16 ( 3512) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 544 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7582 (mm-30) REVERT: B 60 PHE cc_start: 0.8159 (t80) cc_final: 0.7954 (t80) REVERT: B 65 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7388 (mt) REVERT: B 184 TYR cc_start: 0.7533 (t80) cc_final: 0.7107 (t80) REVERT: B 197 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7914 (tm130) REVERT: C 55 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7190 (ttmm) REVERT: C 147 LYS cc_start: 0.7980 (mttt) cc_final: 0.7712 (mmtm) REVERT: D 66 LEU cc_start: 0.7661 (mt) cc_final: 0.7326 (mt) REVERT: D 77 LYS cc_start: 0.8288 (mmtp) cc_final: 0.7945 (mmtp) REVERT: D 100 LEU cc_start: 0.4564 (tp) cc_final: 0.4170 (pp) REVERT: D 120 GLU cc_start: 0.7334 (mm-30) cc_final: 0.7069 (mp0) REVERT: D 122 ASP cc_start: 0.6213 (OUTLIER) cc_final: 0.5991 (p0) REVERT: D 127 GLN cc_start: 0.8279 (mm110) cc_final: 0.7890 (mm-40) REVERT: D 131 LYS cc_start: 0.7399 (mtmm) cc_final: 0.7156 (mtmm) REVERT: D 149 MET cc_start: 0.7137 (mmm) cc_final: 0.6720 (mmm) REVERT: A 1 MET cc_start: 0.6327 (OUTLIER) cc_final: 0.6102 (mtp) REVERT: A 21 THR cc_start: 0.8560 (m) cc_final: 0.8325 (p) REVERT: A 94 LYS cc_start: 0.8093 (mtpp) cc_final: 0.7616 (mttm) REVERT: A 107 LEU cc_start: 0.7242 (pp) cc_final: 0.6872 (tp) REVERT: A 111 GLU cc_start: 0.6426 (OUTLIER) cc_final: 0.5492 (tp30) REVERT: A 131 LYS cc_start: 0.8147 (tttp) cc_final: 0.7938 (tttp) REVERT: A 167 ILE cc_start: 0.8307 (mp) cc_final: 0.8102 (mm) REVERT: A 196 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7184 (mt-10) REVERT: A 200 VAL cc_start: 0.7803 (t) cc_final: 0.7325 (m) REVERT: K 98 GLU cc_start: 0.8181 (tp30) cc_final: 0.7622 (mp0) REVERT: K 112 LYS cc_start: 0.8097 (tttm) cc_final: 0.7778 (tttp) REVERT: K 176 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6702 (mp) REVERT: K 235 GLU cc_start: 0.7795 (mp0) cc_final: 0.7074 (mp0) REVERT: K 280 GLU cc_start: 0.6322 (tm-30) cc_final: 0.5995 (tm-30) REVERT: L 4 ARG cc_start: 0.7572 (mmm-85) cc_final: 0.6917 (mtm-85) REVERT: L 18 ASN cc_start: 0.8206 (m-40) cc_final: 0.7954 (t0) REVERT: L 24 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7963 (mttp) REVERT: L 36 GLU cc_start: 0.7955 (pt0) cc_final: 0.7684 (pt0) REVERT: L 92 ARG cc_start: 0.6842 (mtm180) cc_final: 0.6464 (mtm180) REVERT: L 189 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.7003 (ttt180) REVERT: S 87 GLU cc_start: 0.7914 (tt0) cc_final: 0.7437 (tm-30) REVERT: S 88 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7278 (pm20) REVERT: S 173 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8158 (mtmm) REVERT: S 183 GLU cc_start: 0.7566 (tp30) cc_final: 0.7088 (tp30) REVERT: S 214 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7190 (pp) REVERT: S 217 GLU cc_start: 0.8428 (mp0) cc_final: 0.7912 (mp0) REVERT: S 230 LYS cc_start: 0.8291 (mtpt) cc_final: 0.7772 (mtpt) REVERT: S 304 ASP cc_start: 0.7990 (m-30) cc_final: 0.7585 (m-30) REVERT: S 340 LYS cc_start: 0.8267 (mttt) cc_final: 0.7930 (mtmt) REVERT: S 352 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6699 (mm-30) REVERT: S 395 GLU cc_start: 0.7031 (tp30) cc_final: 0.6536 (tp30) REVERT: S 454 PHE cc_start: 0.8546 (t80) cc_final: 0.7882 (t80) REVERT: S 488 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7671 (mm-40) REVERT: S 564 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7706 (mtm-85) REVERT: S 619 ASP cc_start: 0.8177 (t0) cc_final: 0.7654 (t0) REVERT: S 657 LYS cc_start: 0.8577 (tttp) cc_final: 0.8290 (ttpp) REVERT: S 832 ASP cc_start: 0.7529 (t0) cc_final: 0.7235 (t0) REVERT: S 890 MET cc_start: 0.7549 (tpp) cc_final: 0.7289 (tpp) REVERT: S 891 LYS cc_start: 0.7936 (tttt) cc_final: 0.7598 (tppp) REVERT: S 970 SER cc_start: 0.8420 (t) cc_final: 0.8134 (m) REVERT: S 982 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7959 (mtt90) REVERT: S 1036 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7948 (pt) REVERT: S 1065 LYS cc_start: 0.8600 (ttmm) cc_final: 0.8346 (mmmm) REVERT: S 1107 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8386 (mttt) REVERT: S 1169 ARG cc_start: 0.7669 (ttm110) cc_final: 0.7394 (ttm110) REVERT: S 1268 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7561 (mp0) REVERT: S 1298 LYS cc_start: 0.7969 (mtpt) cc_final: 0.7524 (ttmm) REVERT: S 1303 ASP cc_start: 0.7936 (m-30) cc_final: 0.7476 (m-30) outliers start: 105 outliers final: 74 residues processed: 602 average time/residue: 0.7267 time to fit residues: 503.3544 Evaluate side-chains 632 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 539 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 159 LEU Chi-restraints excluded: chain K residue 176 LEU Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 227 GLN Chi-restraints excluded: chain K residue 232 ASN Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 283 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 24 LYS Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 189 ARG Chi-restraints excluded: chain L residue 209 ASN Chi-restraints excluded: chain L residue 240 MET Chi-restraints excluded: chain S residue 39 GLU Chi-restraints excluded: chain S residue 88 GLU Chi-restraints excluded: chain S residue 140 LYS Chi-restraints excluded: chain S residue 173 LYS Chi-restraints excluded: chain S residue 182 LYS Chi-restraints excluded: chain S residue 197 VAL Chi-restraints excluded: chain S residue 214 ILE Chi-restraints excluded: chain S residue 248 LEU Chi-restraints excluded: chain S residue 297 LEU Chi-restraints excluded: chain S residue 318 LYS Chi-restraints excluded: chain S residue 349 CYS Chi-restraints excluded: chain S residue 356 LEU Chi-restraints excluded: chain S residue 451 LEU Chi-restraints excluded: chain S residue 470 THR Chi-restraints excluded: chain S residue 474 LEU Chi-restraints excluded: chain S residue 488 GLN Chi-restraints excluded: chain S residue 509 THR Chi-restraints excluded: chain S residue 516 VAL Chi-restraints excluded: chain S residue 549 SER Chi-restraints excluded: chain S residue 564 ARG Chi-restraints excluded: chain S residue 582 THR Chi-restraints excluded: chain S residue 583 GLU Chi-restraints excluded: chain S residue 637 ARG Chi-restraints excluded: chain S residue 665 THR Chi-restraints excluded: chain S residue 681 LYS Chi-restraints excluded: chain S residue 724 GLN Chi-restraints excluded: chain S residue 812 THR Chi-restraints excluded: chain S residue 863 LEU Chi-restraints excluded: chain S residue 904 SER Chi-restraints excluded: chain S residue 960 GLN Chi-restraints excluded: chain S residue 981 VAL Chi-restraints excluded: chain S residue 982 ARG Chi-restraints excluded: chain S residue 1001 THR Chi-restraints excluded: chain S residue 1036 ILE Chi-restraints excluded: chain S residue 1045 THR Chi-restraints excluded: chain S residue 1060 SER Chi-restraints excluded: chain S residue 1076 MET Chi-restraints excluded: chain S residue 1107 LYS Chi-restraints excluded: chain S residue 1125 TYR Chi-restraints excluded: chain S residue 1159 ILE Chi-restraints excluded: chain S residue 1168 LEU Chi-restraints excluded: chain S residue 1204 MET Chi-restraints excluded: chain S residue 1220 CYS Chi-restraints excluded: chain S residue 1268 GLU Chi-restraints excluded: chain S residue 1283 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 138 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 147 optimal weight: 30.0000 chunk 55 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 167 optimal weight: 0.3980 chunk 120 optimal weight: 2.9990 chunk 269 optimal weight: 0.7980 chunk 11 optimal weight: 0.0870 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN ** A 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 GLN K 28 HIS K 115 ASN K 232 ASN L 28 HIS L 271 HIS S 102 GLN S 617 HIS S 650 GLN S 713 GLN S 926 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.193036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.146781 restraints weight = 38384.923| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.70 r_work: 0.3499 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.176 27277 Z= 0.275 Angle : 0.838 59.145 37604 Z= 0.464 Chirality : 0.046 0.674 4303 Planarity : 0.004 0.072 4151 Dihedral : 19.668 174.055 5412 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.28 % Favored : 93.50 % Rotamer: Outliers : 4.25 % Allowed : 24.42 % Favored : 71.33 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.16), residues: 2755 helix: 1.04 (0.14), residues: 1357 sheet: -0.49 (0.33), residues: 257 loop : -1.51 (0.17), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 71 TYR 0.038 0.002 TYR C 157 PHE 0.051 0.002 PHE D 130 TRP 0.032 0.002 TRP K 3 HIS 0.009 0.001 HIS K 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.27 (27277) covalent geometry : angle 0.83830 / 0.46 (37604) hydrogen bonds : bond 0.04779 / 3.12 ( 1267) hydrogen bonds : angle 4.58394 / 3.16 ( 3512) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13460.60 seconds wall clock time: 244 minutes 52.70 seconds (14692.70 seconds total)