Starting phenix.real_space_refine on Tue May 5 04:38:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vj9_65107/05_2026/9vj9_65107.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vj9_65107/05_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_65107/05_2026/9vj9_65107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vj9_65107/05_2026/9vj9_65107.map" model { file = "/net/cci-nas-00/data/ceres_data/9vj9_65107/05_2026/9vj9_65107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vj9_65107/05_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/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: 5.53, per 1000 atoms: 0.21 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: 2.27 Conformation dependent library (CDL) restraints added in 920.6 milliseconds 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: 3.25 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: 6.28 Time building geometry restraints manager: 2.97 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=" C GLU S1183 " pdb=" N PHE S1184 " ideal model delta sigma weight residual 1.327 1.301 0.025 1.71e-02 3.42e+03 2.21e+00 bond pdb=" CA LEU C 7 " pdb=" C LEU C 7 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.80e-02 3.09e+03 2.16e+00 bond pdb=" C3' DG N -1 " pdb=" O3' DG N -1 " ideal model delta sigma weight residual 1.422 1.465 -0.043 3.00e-02 1.11e+03 2.03e+00 bond pdb=" C GLY L 2 " pdb=" N TRP L 3 " ideal model delta sigma weight residual 1.333 1.311 0.021 1.52e-02 4.33e+03 1.94e+00 bond pdb=" N GLU S 809 " pdb=" CA GLU S 809 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.53e+00 ... (remaining 27272 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 36772 1.65 - 3.30: 695 3.30 - 4.96: 94 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=" C LYS B 16 " pdb=" CA LYS B 16 " pdb=" CB LYS B 16 " ideal model delta sigma weight residual 116.34 110.75 5.59 1.40e+00 5.10e-01 1.59e+01 angle pdb=" N VAL C 93 " pdb=" CA VAL C 93 " pdb=" C VAL C 93 " ideal model delta sigma weight residual 112.96 109.07 3.89 1.00e+00 1.00e+00 1.51e+01 angle pdb=" C LYS K 17 " pdb=" N ASN K 18 " pdb=" CA ASN K 18 " ideal model delta sigma weight residual 122.46 127.85 -5.39 1.41e+00 5.03e-01 1.46e+01 angle pdb=" N GLU S 87 " pdb=" CA GLU S 87 " pdb=" C GLU S 87 " ideal model delta sigma weight residual 111.02 115.60 -4.58 1.22e+00 6.72e-01 1.41e+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: 3267 0.045 - 0.091: 865 0.091 - 0.136: 160 0.136 - 0.181: 10 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 2.35 -2.50 -0.15 2.00e-01 2.50e+01 5.68e-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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 26.450 Find NCS groups from input model: 0.220 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: 0.010 Load rotamer database and sin/cos tables:7.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 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 0.043 27277 Z= 0.204 Angle : 0.592 8.261 37604 Z= 0.326 Chirality : 0.041 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 covalent geometry : bond 0.00469 (27277) covalent geometry : angle 0.59226 (37604) hydrogen bonds : bond 0.14602 ( 1267) hydrogen bonds : angle 5.62221 ( 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 : 0.731 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: 0.6692 time to fit residues: 517.4818 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 : 0.865 ------------------------------------------------------------------------------- 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: 1.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 153 GLN A 180 GLN A 197 GLN K 28 HIS K 89 GLN K 111 GLN K 115 ASN K 157 ASN K 232 ASN L 33 HIS L 116 GLN L 177 ASN L 232 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: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.195423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.149004 restraints weight = 39070.638| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.95 r_work: 0.3504 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27277 Z= 0.158 Angle : 0.595 13.703 37604 Z= 0.310 Chirality : 0.040 0.197 4303 Planarity : 0.004 0.043 4151 Dihedral : 19.593 179.284 5477 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.30 % Favored : 94.48 % Rotamer: Outliers : 5.17 % Allowed : 15.92 % Favored : 78.91 % 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: 0.07 (0.16), residues: 2755 helix: 1.41 (0.14), residues: 1357 sheet: -0.37 (0.32), residues: 277 loop : -1.59 (0.17), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 71 TYR 0.016 0.001 TYR S1182 PHE 0.020 0.001 PHE B 145 TRP 0.018 0.001 TRP K 3 HIS 0.004 0.001 HIS S 420 Details of bonding type rmsd covalent geometry : bond 0.00345 (27277) covalent geometry : angle 0.59530 (37604) hydrogen bonds : bond 0.04357 ( 1267) hydrogen bonds : angle 4.37567 ( 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 687 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 558 time to evaluate : 1.039 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: B 39 ASP cc_start: 0.8206 (p0) cc_final: 0.7797 (p0) REVERT: B 60 PHE cc_start: 0.8074 (t80) cc_final: 0.7826 (t80) REVERT: B 197 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7924 (tm130) REVERT: C 55 LYS cc_start: 0.7332 (OUTLIER) cc_final: 0.6995 (ttmm) REVERT: C 60 PHE cc_start: 0.7005 (t80) cc_final: 0.6601 (t80) REVERT: C 90 LYS cc_start: 0.6713 (tttt) cc_final: 0.6436 (ptpp) REVERT: C 98 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7757 (pp20) REVERT: D 146 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6610 (tt0) REVERT: A 21 THR cc_start: 0.8401 (m) cc_final: 0.8180 (p) REVERT: A 58 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.6104 (pp20) REVERT: A 107 LEU cc_start: 0.7345 (pp) cc_final: 0.6609 (pp) REVERT: A 111 GLU cc_start: 0.6410 (mp0) cc_final: 0.5726 (mm-30) REVERT: A 115 HIS cc_start: 0.6636 (t70) cc_final: 0.6331 (t70) REVERT: A 188 ASN cc_start: 0.7788 (m-40) cc_final: 0.7582 (t0) REVERT: A 196 GLU cc_start: 0.7337 (mt-10) cc_final: 0.6981 (mt-10) REVERT: A 200 VAL cc_start: 0.7935 (t) cc_final: 0.7353 (m) REVERT: K 43 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: K 89 GLN cc_start: 0.7086 (tp40) cc_final: 0.6698 (tp-100) REVERT: K 98 GLU cc_start: 0.8186 (tp30) cc_final: 0.7596 (mp0) REVERT: K 112 LYS cc_start: 0.8188 (tttp) cc_final: 0.7940 (tttm) REVERT: K 176 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6757 (mp) REVERT: K 250 ASN cc_start: 0.7079 (t0) cc_final: 0.6640 (t0) REVERT: K 280 GLU cc_start: 0.6200 (tm-30) cc_final: 0.5793 (tm-30) REVERT: L 4 ARG cc_start: 0.7539 (mmm-85) cc_final: 0.6902 (mtm-85) REVERT: L 13 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8277 (ttpp) REVERT: L 36 GLU cc_start: 0.7927 (pt0) cc_final: 0.7583 (pt0) REVERT: L 254 TYR cc_start: 0.6536 (t80) cc_final: 0.6166 (t80) REVERT: S 183 GLU cc_start: 0.7513 (tp30) cc_final: 0.7070 (tp30) REVERT: S 214 ILE cc_start: 0.7634 (OUTLIER) cc_final: 0.7130 (pp) REVERT: S 217 GLU cc_start: 0.8508 (mp0) cc_final: 0.8006 (mp0) REVERT: S 230 LYS cc_start: 0.8269 (mtpt) cc_final: 0.7759 (mtpt) REVERT: S 294 ASP cc_start: 0.7120 (p0) cc_final: 0.6902 (p0) REVERT: S 337 ASP cc_start: 0.8109 (m-30) cc_final: 0.7696 (m-30) REVERT: S 340 LYS cc_start: 0.8293 (mttt) cc_final: 0.7985 (mtmt) REVERT: S 395 GLU cc_start: 0.7160 (tp30) cc_final: 0.6735 (tp30) REVERT: S 454 PHE cc_start: 0.8608 (t80) cc_final: 0.7958 (t80) REVERT: S 465 LYS cc_start: 0.8724 (mttt) cc_final: 0.8500 (mttm) REVERT: S 619 ASP cc_start: 0.8177 (t0) cc_final: 0.7695 (t0) REVERT: S 657 LYS cc_start: 0.8549 (tttp) cc_final: 0.8218 (ttpp) REVERT: S 763 MET cc_start: 0.8361 (mmt) cc_final: 0.8073 (tpt) REVERT: S 832 ASP cc_start: 0.7404 (t70) cc_final: 0.7202 (t0) REVERT: S 890 MET cc_start: 0.7695 (tpp) cc_final: 0.7379 (tpp) REVERT: S 891 LYS cc_start: 0.7840 (tttt) cc_final: 0.7540 (tppp) REVERT: S 923 ASP cc_start: 0.5967 (OUTLIER) cc_final: 0.5757 (t0) REVERT: S 982 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7505 (mtp85) REVERT: S 1042 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7418 (mmm160) REVERT: S 1065 LYS cc_start: 0.8516 (ttmm) cc_final: 0.8227 (mmmm) REVERT: S 1107 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8348 (tptt) REVERT: S 1265 LYS cc_start: 0.7645 (mmtm) cc_final: 0.7142 (mmtm) REVERT: S 1268 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7551 (mp0) REVERT: S 1298 LYS cc_start: 0.8007 (mtpt) cc_final: 0.7499 (ttmm) REVERT: S 1303 ASP cc_start: 0.7998 (m-30) cc_final: 0.7550 (m-30) outliers start: 129 outliers final: 50 residues processed: 637 average time/residue: 0.6917 time to fit residues: 504.7874 Evaluate side-chains 605 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 542 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 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 126 VAL Chi-restraints excluded: chain C residue 205 GLN Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain A residue 58 GLU 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 283 VAL Chi-restraints excluded: chain L residue 13 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 240 MET Chi-restraints excluded: chain L residue 264 ILE 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 812 THR Chi-restraints excluded: chain S residue 863 LEU Chi-restraints excluded: chain S residue 923 ASP 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 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: 0.6980 chunk 59 optimal weight: 5.9990 chunk 84 optimal weight: 0.5980 chunk 240 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 ASN ** 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 157 ASN K 232 ASN L 18 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 116 GLN L 204 HIS L 250 ASN L 271 HIS ** L 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 102 GLN S 193 ASN S 547 ASN S 617 HIS S 650 GLN S 713 GLN S1202 ASN S1253 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.193973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.147345 restraints weight = 39023.716| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.13 r_work: 0.3468 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 27277 Z= 0.205 Angle : 0.618 12.357 37604 Z= 0.322 Chirality : 0.042 0.213 4303 Planarity : 0.004 0.052 4151 Dihedral : 19.491 178.609 5428 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.70 % Favored : 94.05 % Rotamer: Outliers : 5.05 % Allowed : 18.44 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.16), residues: 2755 helix: 1.43 (0.14), residues: 1355 sheet: -0.40 (0.34), residues: 248 loop : -1.54 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 71 TYR 0.022 0.002 TYR A 68 PHE 0.022 0.002 PHE C 130 TRP 0.023 0.002 TRP K 3 HIS 0.006 0.001 HIS K 28 Details of bonding type rmsd covalent geometry : bond 0.00469 (27277) covalent geometry : angle 0.61832 (37604) hydrogen bonds : bond 0.04380 ( 1267) hydrogen bonds : angle 4.31735 ( 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 679 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 553 time to evaluate : 0.899 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: 0.8247 (p0) cc_final: 0.7887 (p0) REVERT: B 60 PHE cc_start: 0.8198 (t80) cc_final: 0.7972 (t80) REVERT: B 149 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8208 (tpp) REVERT: B 158 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8191 (mm) REVERT: B 197 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7880 (tm130) REVERT: C 60 PHE cc_start: 0.7043 (t80) cc_final: 0.6582 (t80) REVERT: D 100 LEU cc_start: 0.5358 (tp) cc_final: 0.4751 (pp) REVERT: D 120 GLU cc_start: 0.7295 (mm-30) cc_final: 0.7061 (mp0) REVERT: D 137 ILE cc_start: 0.6355 (tt) cc_final: 0.6089 (mm) REVERT: D 142 ASP cc_start: 0.3525 (OUTLIER) cc_final: 0.3017 (t70) REVERT: D 149 MET cc_start: 0.6862 (mmm) cc_final: 0.6654 (mpt) REVERT: D 150 GLU cc_start: 0.6190 (mt-10) cc_final: 0.5694 (mt-10) REVERT: A 21 THR cc_start: 0.8579 (m) cc_final: 0.8331 (p) REVERT: A 58 GLU cc_start: 0.6460 (OUTLIER) cc_final: 0.6133 (pp20) REVERT: A 107 LEU cc_start: 0.7173 (pp) cc_final: 0.6806 (tp) REVERT: A 111 GLU cc_start: 0.6504 (mp0) cc_final: 0.5650 (mm-30) REVERT: A 188 ASN cc_start: 0.7958 (m-40) cc_final: 0.7737 (t0) REVERT: A 196 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7222 (mt-10) REVERT: A 200 VAL cc_start: 0.7937 (t) cc_final: 0.7420 (m) REVERT: K 32 ILE cc_start: 0.8541 (pt) cc_final: 0.8100 (mt) REVERT: K 41 LEU cc_start: 0.8735 (tp) cc_final: 0.8380 (tp) REVERT: K 43 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7267 (mp0) REVERT: K 98 GLU cc_start: 0.8189 (tp30) cc_final: 0.7571 (mp0) REVERT: K 176 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6821 (mp) REVERT: K 210 ASP cc_start: 0.7553 (t0) cc_final: 0.7340 (t0) REVERT: K 235 GLU cc_start: 0.7620 (mp0) cc_final: 0.6880 (mp0) REVERT: K 280 GLU cc_start: 0.6216 (tm-30) cc_final: 0.5796 (tm-30) REVERT: L 4 ARG cc_start: 0.7595 (mmm-85) cc_final: 0.6984 (mtm-85) REVERT: L 36 GLU cc_start: 0.7970 (pt0) cc_final: 0.7670 (pt0) REVERT: L 92 ARG cc_start: 0.6752 (mtm180) cc_final: 0.6411 (mtm180) REVERT: L 253 MET cc_start: 0.6333 (tpp) cc_final: 0.5956 (tpp) REVERT: S 102 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7993 (mm-40) REVERT: S 183 GLU cc_start: 0.7558 (tp30) cc_final: 0.7104 (tp30) REVERT: S 214 ILE cc_start: 0.7661 (OUTLIER) cc_final: 0.7176 (pp) REVERT: S 217 GLU cc_start: 0.8497 (mp0) cc_final: 0.7997 (mp0) REVERT: S 230 LYS cc_start: 0.8271 (mtpt) cc_final: 0.7754 (mtpt) REVERT: S 304 ASP cc_start: 0.7991 (m-30) cc_final: 0.7566 (m-30) REVERT: S 316 ASP cc_start: 0.7867 (t0) cc_final: 0.7638 (t0) REVERT: S 337 ASP cc_start: 0.8151 (m-30) cc_final: 0.7932 (m-30) REVERT: S 340 LYS cc_start: 0.8310 (mttt) cc_final: 0.7956 (mtmt) REVERT: S 395 GLU cc_start: 0.7203 (tp30) cc_final: 0.6742 (tp30) REVERT: S 454 PHE cc_start: 0.8582 (t80) cc_final: 0.7859 (t80) REVERT: S 564 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7805 (mtm-85) REVERT: S 566 LYS cc_start: 0.8577 (mmtt) cc_final: 0.8096 (ttmm) REVERT: S 594 GLN cc_start: 0.8176 (tt0) cc_final: 0.7835 (tt0) REVERT: S 619 ASP cc_start: 0.8216 (t0) cc_final: 0.7643 (t0) REVERT: S 657 LYS cc_start: 0.8634 (tttp) cc_final: 0.8315 (ttpp) REVERT: S 890 MET cc_start: 0.7615 (tpp) cc_final: 0.7295 (tpp) REVERT: S 891 LYS cc_start: 0.7895 (tttt) cc_final: 0.7472 (tppp) REVERT: S 970 SER cc_start: 0.8396 (t) cc_final: 0.8107 (m) REVERT: S 982 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7504 (mtp85) REVERT: S 1042 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7483 (mmm160) REVERT: S 1065 LYS cc_start: 0.8605 (ttmm) cc_final: 0.8346 (mmmm) REVERT: S 1107 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8178 (mmtm) REVERT: S 1169 ARG cc_start: 0.7739 (ttm110) cc_final: 0.7461 (ttm110) REVERT: S 1265 LYS cc_start: 0.7634 (mmtm) cc_final: 0.7117 (mmtm) REVERT: S 1268 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7601 (mp0) REVERT: S 1298 LYS cc_start: 0.8053 (mtpt) cc_final: 0.7540 (ttmm) REVERT: S 1303 ASP cc_start: 0.7982 (m-30) cc_final: 0.7528 (m-30) outliers start: 126 outliers final: 59 residues processed: 622 average time/residue: 0.6861 time to fit residues: 489.5169 Evaluate side-chains 617 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 544 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 149 MET Chi-restraints excluded: chain B residue 158 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 72 SER Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 116 GLU 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 10 GLU Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 161 LYS 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 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 275 VAL Chi-restraints excluded: chain K residue 283 VAL 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 240 MET Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain S residue 39 GLU Chi-restraints excluded: chain S residue 102 GLN 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 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 665 THR Chi-restraints excluded: chain S residue 697 VAL 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 981 VAL Chi-restraints excluded: chain S residue 982 ARG Chi-restraints excluded: chain S residue 1042 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 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=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: 1.9990 chunk 273 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 279 optimal weight: 0.0370 chunk 257 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 HIS B 188 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 ASN A 153 GLN A 197 GLN K 28 HIS ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 ASN K 157 ASN K 232 ASN L 18 ASN L 116 GLN L 271 HIS S 405 ASN S 617 HIS S 650 GLN S 713 GLN S 926 HIS ** S 931 GLN ** 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 = 0.4296 r_free = 0.4296 target = 0.191119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.144738 restraints weight = 38329.927| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.87 r_work: 0.3447 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.122 27277 Z= 0.341 Angle : 0.708 12.639 37604 Z= 0.369 Chirality : 0.047 0.290 4303 Planarity : 0.005 0.104 4151 Dihedral : 19.551 177.847 5420 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.57 % Favored : 93.18 % Rotamer: Outliers : 6.50 % Allowed : 18.89 % Favored : 74.62 % 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: -0.31 (0.16), residues: 2755 helix: 0.98 (0.14), residues: 1358 sheet: -0.36 (0.34), residues: 244 loop : -1.65 (0.17), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 71 TYR 0.026 0.002 TYR S 368 PHE 0.047 0.002 PHE C 130 TRP 0.025 0.002 TRP K 3 HIS 0.009 0.002 HIS S1253 Details of bonding type rmsd covalent geometry : bond 0.00795 (27277) covalent geometry : angle 0.70841 (37604) hydrogen bonds : bond 0.05199 ( 1267) hydrogen bonds : angle 4.54717 ( 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 734 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 572 time to evaluate : 0.899 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 15 GLU cc_start: 0.7699 (tp30) cc_final: 0.7430 (tp30) REVERT: B 39 ASP cc_start: 0.8228 (p0) cc_final: 0.7986 (p0) REVERT: B 145 PHE cc_start: 0.8555 (t80) cc_final: 0.8313 (t80) REVERT: B 149 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8659 (tpp) REVERT: B 158 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8217 (mm) REVERT: B 197 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7887 (tm130) REVERT: B 208 LEU cc_start: 0.8557 (tt) cc_final: 0.8131 (tp) REVERT: C 55 LYS cc_start: 0.7340 (OUTLIER) cc_final: 0.7021 (ttmm) REVERT: C 58 GLU cc_start: 0.6032 (OUTLIER) cc_final: 0.5817 (mm-30) REVERT: C 60 PHE cc_start: 0.7009 (t80) cc_final: 0.6664 (t80) REVERT: C 98 GLU cc_start: 0.7973 (pp20) cc_final: 0.7707 (pp20) REVERT: D 1 MET cc_start: 0.3995 (tmm) cc_final: 0.2860 (ppp) REVERT: D 120 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7110 (mp0) REVERT: A 19 PHE cc_start: 0.8632 (m-80) cc_final: 0.8429 (m-80) REVERT: A 21 THR cc_start: 0.8569 (m) cc_final: 0.8335 (p) REVERT: A 94 LYS cc_start: 0.7399 (ptpp) cc_final: 0.6888 (ptpp) REVERT: A 107 LEU cc_start: 0.7259 (pp) cc_final: 0.6978 (pp) REVERT: A 188 ASN cc_start: 0.8188 (m-40) cc_final: 0.7958 (t0) REVERT: A 196 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7207 (mt-10) REVERT: A 200 VAL cc_start: 0.7987 (t) cc_final: 0.7546 (m) REVERT: K 43 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7409 (mp0) REVERT: K 92 ARG cc_start: 0.8197 (ttm-80) cc_final: 0.7700 (ttm-80) REVERT: K 98 GLU cc_start: 0.8190 (tp30) cc_final: 0.7613 (mp0) REVERT: K 112 LYS cc_start: 0.8292 (tttm) cc_final: 0.7971 (tttm) REVERT: K 210 ASP cc_start: 0.7546 (t0) cc_final: 0.7307 (t0) REVERT: K 280 GLU cc_start: 0.6306 (tm-30) cc_final: 0.5856 (tm-30) REVERT: L 92 ARG cc_start: 0.6916 (mtm180) cc_final: 0.6516 (mtm180) REVERT: L 189 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.5184 (ttm170) REVERT: L 253 MET cc_start: 0.6540 (tpp) cc_final: 0.6313 (tpp) REVERT: S 76 ARG cc_start: 0.7993 (tpt170) cc_final: 0.7755 (tpt170) REVERT: S 102 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7804 (mm110) REVERT: S 173 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8145 (mtmm) REVERT: S 183 GLU cc_start: 0.7514 (tp30) cc_final: 0.7077 (tp30) REVERT: S 214 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7302 (pp) REVERT: S 217 GLU cc_start: 0.8468 (mp0) cc_final: 0.7992 (mp0) REVERT: S 230 LYS cc_start: 0.8293 (mtpt) cc_final: 0.7804 (mtpt) REVERT: S 304 ASP cc_start: 0.8013 (m-30) cc_final: 0.7577 (m-30) REVERT: S 340 LYS cc_start: 0.8342 (mttt) cc_final: 0.7990 (mtmt) REVERT: S 395 GLU cc_start: 0.7124 (tp30) cc_final: 0.6644 (tp30) REVERT: S 442 LYS cc_start: 0.8098 (ttpp) cc_final: 0.7883 (ttpp) REVERT: S 454 PHE cc_start: 0.8537 (t80) cc_final: 0.7864 (t80) REVERT: S 564 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7755 (mtm-85) REVERT: S 619 ASP cc_start: 0.8244 (t0) cc_final: 0.7721 (t0) REVERT: S 657 LYS cc_start: 0.8634 (tttp) cc_final: 0.8344 (ttpp) REVERT: S 715 SER cc_start: 0.8314 (p) cc_final: 0.8102 (m) REVERT: S 827 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7539 (mpp) REVERT: S 890 MET cc_start: 0.7630 (tpp) cc_final: 0.7270 (tpp) REVERT: S 982 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7584 (mtp85) REVERT: S 1065 LYS cc_start: 0.8696 (ttmm) cc_final: 0.8469 (mmmm) REVERT: S 1107 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8568 (mttt) REVERT: S 1169 ARG cc_start: 0.7683 (ttm110) cc_final: 0.7411 (ttm110) REVERT: S 1180 THR cc_start: 0.8603 (OUTLIER) cc_final: 0.8257 (m) REVERT: S 1268 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7465 (mp0) REVERT: S 1298 LYS cc_start: 0.8036 (mtpt) cc_final: 0.7599 (ttmm) REVERT: S 1303 ASP cc_start: 0.7977 (m-30) cc_final: 0.7526 (m-30) outliers start: 162 outliers final: 80 residues processed: 665 average time/residue: 0.6789 time to fit residues: 518.6282 Evaluate side-chains 661 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 564 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 149 MET Chi-restraints excluded: chain B residue 158 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 58 GLU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain D residue 61 VAL 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 9 GLU Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 60 PHE Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 167 ILE 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 38 ASP Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 157 ASN 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 21 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 189 ARG Chi-restraints excluded: chain L residue 197 PHE 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 21 MET Chi-restraints excluded: chain S residue 39 GLU Chi-restraints excluded: chain S residue 102 GLN 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 387 ILE 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 564 ARG Chi-restraints excluded: chain S residue 583 GLU Chi-restraints excluded: chain S residue 665 THR Chi-restraints excluded: chain S residue 792 LEU Chi-restraints excluded: chain S residue 824 LEU Chi-restraints excluded: chain S residue 827 MET Chi-restraints excluded: chain S residue 849 ILE 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 1042 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 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 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: 0.0980 chunk 89 optimal weight: 0.5980 chunk 254 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 199 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 204 optimal weight: 2.9990 chunk 224 optimal weight: 0.8980 chunk 181 optimal weight: 4.9990 chunk 230 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 4 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 GLN K 28 HIS ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 111 GLN K 115 ASN K 116 GLN K 157 ASN L 116 GLN L 271 HIS S 102 GLN S 405 ASN S 617 HIS S 650 GLN S 713 GLN S 926 HIS ** S 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.194203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.147820 restraints weight = 38396.536| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 1.84 r_work: 0.3493 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 27277 Z= 0.165 Angle : 0.628 11.827 37604 Z= 0.330 Chirality : 0.041 0.189 4303 Planarity : 0.004 0.055 4151 Dihedral : 19.451 177.581 5417 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.63 % Favored : 94.16 % Rotamer: Outliers : 5.29 % Allowed : 21.21 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.16), residues: 2755 helix: 1.24 (0.14), residues: 1356 sheet: -0.35 (0.35), residues: 236 loop : -1.57 (0.17), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG K 71 TYR 0.024 0.001 TYR L 254 PHE 0.056 0.001 PHE C 130 TRP 0.023 0.002 TRP K 3 HIS 0.007 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00373 (27277) covalent geometry : angle 0.62832 (37604) hydrogen bonds : bond 0.04204 ( 1267) hydrogen bonds : angle 4.32607 ( 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 694 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 562 time to evaluate : 0.881 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 15 GLU cc_start: 0.7596 (tp30) cc_final: 0.7320 (tp30) REVERT: B 138 GLU cc_start: 0.6670 (tm-30) cc_final: 0.6215 (tm-30) REVERT: B 145 PHE cc_start: 0.8478 (t80) cc_final: 0.8176 (t80) REVERT: B 150 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8388 (mt-10) REVERT: B 158 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8215 (mm) REVERT: B 179 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8206 (tp-100) REVERT: B 197 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7961 (tm130) REVERT: C 55 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.7131 (ttmm) REVERT: C 58 GLU cc_start: 0.6128 (OUTLIER) cc_final: 0.5662 (mm-30) REVERT: C 98 GLU cc_start: 0.8021 (pp20) cc_final: 0.7630 (pp20) REVERT: C 157 TYR cc_start: 0.6247 (t80) cc_final: 0.4003 (t80) REVERT: D 1 MET cc_start: 0.3623 (tmm) cc_final: 0.2627 (ppp) REVERT: D 58 GLU cc_start: 0.5821 (mt-10) cc_final: 0.5597 (mt-10) REVERT: D 66 LEU cc_start: 0.7239 (mm) cc_final: 0.6812 (tp) REVERT: D 96 MET cc_start: 0.6906 (ttp) cc_final: 0.6662 (ppp) REVERT: D 120 GLU cc_start: 0.7322 (mm-30) cc_final: 0.7075 (mp0) REVERT: D 130 PHE cc_start: 0.7098 (m-80) cc_final: 0.6689 (m-80) REVERT: A 21 THR cc_start: 0.8529 (m) cc_final: 0.8302 (p) REVERT: A 94 LYS cc_start: 0.7404 (ptpp) cc_final: 0.7049 (ptpp) REVERT: A 188 ASN cc_start: 0.8152 (m-40) cc_final: 0.7893 (t0) REVERT: A 196 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7171 (mt-10) REVERT: A 200 VAL cc_start: 0.7883 (t) cc_final: 0.7487 (m) REVERT: K 92 ARG cc_start: 0.8199 (ttm-80) cc_final: 0.7713 (ttp80) REVERT: K 98 GLU cc_start: 0.8187 (tp30) cc_final: 0.7633 (mp0) REVERT: K 176 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6688 (mp) REVERT: K 210 ASP cc_start: 0.7625 (t0) cc_final: 0.7351 (t0) REVERT: K 235 GLU cc_start: 0.7722 (mp0) cc_final: 0.6994 (mp0) REVERT: K 242 ARG cc_start: 0.7624 (mpp80) cc_final: 0.7339 (mpp80) REVERT: K 280 GLU cc_start: 0.6226 (tm-30) cc_final: 0.5763 (tm-30) REVERT: L 4 ARG cc_start: 0.7538 (mmm-85) cc_final: 0.6977 (mtm-85) REVERT: L 36 GLU cc_start: 0.8036 (pt0) cc_final: 0.7623 (pt0) REVERT: L 92 ARG cc_start: 0.6836 (mtm180) cc_final: 0.6458 (mtm180) REVERT: L 189 ARG cc_start: 0.7483 (ttm170) cc_final: 0.7175 (ttt180) REVERT: L 253 MET cc_start: 0.6407 (tpp) cc_final: 0.6112 (tpp) REVERT: S 173 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8131 (mtmm) REVERT: S 183 GLU cc_start: 0.7474 (tp30) cc_final: 0.7047 (tp30) REVERT: S 214 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7203 (pp) REVERT: S 217 GLU cc_start: 0.8414 (mp0) cc_final: 0.7885 (mp0) REVERT: S 230 LYS cc_start: 0.8280 (mtpt) cc_final: 0.7765 (mtpt) REVERT: S 304 ASP cc_start: 0.7981 (m-30) cc_final: 0.7560 (m-30) REVERT: S 337 ASP cc_start: 0.8173 (m-30) cc_final: 0.7945 (m-30) REVERT: S 340 LYS cc_start: 0.8275 (mttt) cc_final: 0.7932 (mtmt) REVERT: S 395 GLU cc_start: 0.7092 (tp30) cc_final: 0.6596 (tp30) REVERT: S 454 PHE cc_start: 0.8548 (t80) cc_final: 0.7911 (t80) REVERT: S 564 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7763 (mtm-85) REVERT: S 619 ASP cc_start: 0.8172 (t0) cc_final: 0.7662 (t0) REVERT: S 657 LYS cc_start: 0.8595 (tttp) cc_final: 0.8296 (ttpp) REVERT: S 890 MET cc_start: 0.7590 (tpp) cc_final: 0.7247 (tpp) REVERT: S 891 LYS cc_start: 0.7912 (tttt) cc_final: 0.7593 (tppp) REVERT: S 982 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7961 (mtt90) REVERT: S 1065 LYS cc_start: 0.8618 (ttmm) cc_final: 0.8371 (mmmm) REVERT: S 1068 LYS cc_start: 0.8610 (mtmm) cc_final: 0.8404 (mtmm) REVERT: S 1107 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8441 (mttt) REVERT: S 1169 ARG cc_start: 0.7643 (ttm110) cc_final: 0.7374 (ttm110) REVERT: S 1268 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7517 (mp0) REVERT: S 1298 LYS cc_start: 0.7973 (mtpt) cc_final: 0.7508 (ttmm) REVERT: S 1303 ASP cc_start: 0.7964 (m-30) cc_final: 0.7511 (m-30) outliers start: 132 outliers final: 62 residues processed: 635 average time/residue: 0.6844 time to fit residues: 499.0324 Evaluate side-chains 623 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 549 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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 131 LYS Chi-restraints excluded: chain B residue 158 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 58 GLU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 93 VAL 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 7 LEU Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 60 PHE 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 K residue 143 ASP Chi-restraints excluded: chain K residue 157 ASN 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 39 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 206 ASN 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 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 665 THR Chi-restraints excluded: chain S residue 773 GLU 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 233 optimal weight: 0.0000 chunk 271 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 255 optimal weight: 0.8980 chunk 237 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 HIS ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 GLN C 180 GLN D 37 GLN A 197 GLN K 28 HIS ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 111 GLN K 115 ASN ** K 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 157 ASN K 232 ASN L 18 ASN 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.194457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.148487 restraints weight = 38486.052| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.84 r_work: 0.3502 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27277 Z= 0.161 Angle : 0.621 12.170 37604 Z= 0.326 Chirality : 0.041 0.199 4303 Planarity : 0.004 0.063 4151 Dihedral : 19.362 177.191 5408 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.77 % Favored : 94.01 % Rotamer: Outliers : 5.29 % Allowed : 21.97 % Favored : 72.73 % 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: 1.34 (0.14), residues: 1357 sheet: -0.37 (0.35), residues: 236 loop : -1.56 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG K 71 TYR 0.020 0.001 TYR S1019 PHE 0.056 0.001 PHE C 130 TRP 0.026 0.002 TRP K 3 HIS 0.005 0.001 HIS C 155 Details of bonding type rmsd covalent geometry : bond 0.00365 (27277) covalent geometry : angle 0.62124 (37604) hydrogen bonds : bond 0.04054 ( 1267) hydrogen bonds : angle 4.23396 ( 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 699 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 567 time to evaluate : 0.880 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 15 GLU cc_start: 0.7589 (tp30) cc_final: 0.7245 (tp30) REVERT: B 23 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8188 (mtpp) REVERT: B 128 GLU cc_start: 0.7933 (mp0) cc_final: 0.7319 (pm20) REVERT: B 158 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8282 (mm) REVERT: B 179 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8210 (tp-100) REVERT: B 197 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7924 (tm130) REVERT: C 55 LYS cc_start: 0.7489 (OUTLIER) cc_final: 0.7197 (ttmm) REVERT: C 58 GLU cc_start: 0.5990 (OUTLIER) cc_final: 0.5677 (mm-30) REVERT: C 60 PHE cc_start: 0.7454 (t80) cc_final: 0.7027 (t80) REVERT: C 66 LEU cc_start: 0.2547 (pp) cc_final: 0.2343 (pp) REVERT: D 1 MET cc_start: 0.3339 (tmm) cc_final: 0.2603 (ppp) REVERT: D 66 LEU cc_start: 0.7272 (mm) cc_final: 0.6805 (tp) REVERT: D 77 LYS cc_start: 0.8183 (mmtp) cc_final: 0.7893 (mmtp) REVERT: D 120 GLU cc_start: 0.7356 (mm-30) cc_final: 0.7107 (mp0) REVERT: D 127 GLN cc_start: 0.8140 (mm110) cc_final: 0.7744 (mm-40) REVERT: A 21 THR cc_start: 0.8523 (m) cc_final: 0.8293 (p) REVERT: A 111 GLU cc_start: 0.6290 (OUTLIER) cc_final: 0.5627 (pt0) REVERT: A 167 ILE cc_start: 0.8254 (mp) cc_final: 0.8036 (mm) REVERT: A 188 ASN cc_start: 0.8135 (m-40) cc_final: 0.7898 (t0) REVERT: A 196 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7168 (mt-10) REVERT: A 200 VAL cc_start: 0.7838 (t) cc_final: 0.7376 (m) REVERT: K 98 GLU cc_start: 0.8087 (tp30) cc_final: 0.7528 (mp0) REVERT: K 112 LYS cc_start: 0.8036 (tttm) cc_final: 0.7640 (ttpp) REVERT: K 176 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6784 (mp) REVERT: K 210 ASP cc_start: 0.7649 (t0) cc_final: 0.7378 (t0) REVERT: K 235 GLU cc_start: 0.7693 (mp0) cc_final: 0.6938 (mp0) REVERT: K 280 GLU cc_start: 0.6257 (tm-30) cc_final: 0.5841 (tm-30) REVERT: L 4 ARG cc_start: 0.7502 (mmm-85) cc_final: 0.6982 (mtm-85) REVERT: L 36 GLU cc_start: 0.8080 (pt0) cc_final: 0.7671 (pt0) REVERT: L 92 ARG cc_start: 0.6827 (mtm180) cc_final: 0.6443 (mtm180) REVERT: L 189 ARG cc_start: 0.7407 (ttm170) cc_final: 0.7179 (ttt180) REVERT: L 253 MET cc_start: 0.6389 (tpp) cc_final: 0.6150 (tpp) REVERT: S 87 GLU cc_start: 0.7804 (tt0) cc_final: 0.7415 (tm-30) REVERT: S 173 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8148 (mtmm) REVERT: S 183 GLU cc_start: 0.7473 (tp30) cc_final: 0.7021 (tp30) REVERT: S 214 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7190 (pp) REVERT: S 217 GLU cc_start: 0.8388 (mp0) cc_final: 0.7866 (mp0) REVERT: S 230 LYS cc_start: 0.8265 (mtpt) cc_final: 0.7744 (mtpt) REVERT: S 270 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.7329 (tp) REVERT: S 304 ASP cc_start: 0.7949 (m-30) cc_final: 0.7534 (m-30) REVERT: S 340 LYS cc_start: 0.8255 (mttt) cc_final: 0.7920 (mtmt) REVERT: S 395 GLU cc_start: 0.7094 (tp30) cc_final: 0.6622 (tp30) REVERT: S 454 PHE cc_start: 0.8553 (t80) cc_final: 0.7886 (t80) REVERT: S 488 GLN cc_start: 0.8035 (mm110) cc_final: 0.7658 (mm-40) REVERT: S 564 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7702 (mtm-85) REVERT: S 566 LYS cc_start: 0.8437 (mmmt) cc_final: 0.8174 (ttmm) REVERT: S 619 ASP cc_start: 0.8171 (t0) cc_final: 0.7653 (t0) REVERT: S 657 LYS cc_start: 0.8556 (tttp) cc_final: 0.8274 (ttpp) REVERT: S 724 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7537 (mp10) REVERT: S 738 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7468 (mm-30) REVERT: S 890 MET cc_start: 0.7516 (tpp) cc_final: 0.7217 (tpp) REVERT: S 891 LYS cc_start: 0.7912 (tttt) cc_final: 0.7603 (tppp) REVERT: S 970 SER cc_start: 0.8410 (t) cc_final: 0.8146 (m) REVERT: S 982 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7971 (mtt90) REVERT: S 1065 LYS cc_start: 0.8564 (ttmm) cc_final: 0.8315 (mmmm) REVERT: S 1169 ARG cc_start: 0.7643 (ttm110) cc_final: 0.7343 (ttm110) REVERT: S 1268 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: S 1298 LYS cc_start: 0.7957 (mtpt) cc_final: 0.7503 (ttmm) REVERT: S 1303 ASP cc_start: 0.7945 (m-30) cc_final: 0.7485 (m-30) outliers start: 132 outliers final: 69 residues processed: 638 average time/residue: 0.6800 time to fit residues: 498.1469 Evaluate side-chains 642 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 558 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 131 LYS Chi-restraints excluded: chain B residue 158 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 C residue 55 LYS Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain D residue 61 VAL 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 9 GLU Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 157 ASN 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 39 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 133 LEU 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 270 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 387 ILE 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 637 ARG Chi-restraints excluded: chain S residue 697 VAL Chi-restraints excluded: chain S residue 715 SER Chi-restraints excluded: chain S residue 724 GLN 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 904 SER Chi-restraints excluded: chain S residue 930 ARG 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 135 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 199 optimal weight: 0.6980 chunk 281 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 GLN K 28 HIS K 93 GLN K 115 ASN ** K 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 157 ASN ** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 232 ASN L 18 ASN L 258 GLN L 271 HIS S 102 GLN S 617 HIS S 650 GLN S 713 GLN S 926 HIS ** S 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.193959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.148005 restraints weight = 38324.801| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.91 r_work: 0.3494 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 27277 Z= 0.185 Angle : 0.644 11.968 37604 Z= 0.337 Chirality : 0.042 0.208 4303 Planarity : 0.004 0.067 4151 Dihedral : 19.327 176.892 5401 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.88 % Favored : 93.90 % Rotamer: Outliers : 5.33 % Allowed : 22.49 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.16), residues: 2755 helix: 1.26 (0.14), residues: 1360 sheet: -0.37 (0.34), residues: 245 loop : -1.55 (0.17), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG K 71 TYR 0.021 0.002 TYR S1019 PHE 0.059 0.002 PHE C 130 TRP 0.031 0.002 TRP K 3 HIS 0.006 0.001 HIS S 420 Details of bonding type rmsd covalent geometry : bond 0.00427 (27277) covalent geometry : angle 0.64373 (37604) hydrogen bonds : bond 0.04231 ( 1267) hydrogen bonds : angle 4.26882 ( 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 690 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 557 time to evaluate : 0.809 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: B 15 GLU cc_start: 0.7660 (tp30) cc_final: 0.7315 (tp30) REVERT: B 96 MET cc_start: 0.7144 (OUTLIER) cc_final: 0.6817 (tpt) REVERT: B 145 PHE cc_start: 0.8471 (t80) cc_final: 0.8101 (t80) REVERT: B 179 GLN cc_start: 0.8404 (mm-40) cc_final: 0.8163 (tp-100) REVERT: B 197 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7934 (tm130) REVERT: C 55 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.7138 (ttmm) REVERT: C 58 GLU cc_start: 0.6017 (OUTLIER) cc_final: 0.5694 (mm-30) REVERT: C 60 PHE cc_start: 0.7418 (t80) cc_final: 0.7037 (t80) REVERT: C 96 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.6495 (pp-130) REVERT: C 98 GLU cc_start: 0.7859 (pp20) cc_final: 0.7550 (pp20) REVERT: D 1 MET cc_start: 0.3118 (tmm) cc_final: 0.2539 (pp-130) REVERT: D 66 LEU cc_start: 0.7290 (mm) cc_final: 0.6920 (tp) REVERT: D 77 LYS cc_start: 0.8224 (mmtp) cc_final: 0.7896 (mmtp) REVERT: D 120 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7179 (mp0) REVERT: A 21 THR cc_start: 0.8519 (m) cc_final: 0.8301 (p) REVERT: A 33 LYS cc_start: 0.8314 (tttp) cc_final: 0.7939 (tmtt) REVERT: A 167 ILE cc_start: 0.8269 (mp) cc_final: 0.8050 (mm) REVERT: A 188 ASN cc_start: 0.8164 (m-40) cc_final: 0.7930 (t0) REVERT: A 196 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7181 (mt-10) REVERT: K 98 GLU cc_start: 0.8087 (tp30) cc_final: 0.7555 (mp0) REVERT: K 140 ARG cc_start: 0.7224 (mtp-110) cc_final: 0.6630 (mtp-110) REVERT: K 176 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6798 (mp) REVERT: K 210 ASP cc_start: 0.7659 (t0) cc_final: 0.7362 (t0) REVERT: K 235 GLU cc_start: 0.7715 (mp0) cc_final: 0.6975 (mp0) REVERT: K 242 ARG cc_start: 0.7642 (tpp80) cc_final: 0.7280 (mpp80) REVERT: K 280 GLU cc_start: 0.6282 (tm-30) cc_final: 0.5895 (tm-30) REVERT: L 4 ARG cc_start: 0.7565 (mmm-85) cc_final: 0.7089 (mtm-85) REVERT: L 36 GLU cc_start: 0.8142 (pt0) cc_final: 0.7718 (pt0) REVERT: L 92 ARG cc_start: 0.6837 (mtm180) cc_final: 0.6444 (mtm180) REVERT: L 189 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.7144 (ttt180) REVERT: L 253 MET cc_start: 0.6398 (tpp) cc_final: 0.6181 (tpp) REVERT: S 173 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8122 (mtmm) REVERT: S 183 GLU cc_start: 0.7488 (tp30) cc_final: 0.7030 (tp30) REVERT: S 214 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7243 (pp) REVERT: S 217 GLU cc_start: 0.8414 (mp0) cc_final: 0.7885 (mp0) REVERT: S 230 LYS cc_start: 0.8279 (mtpt) cc_final: 0.7762 (mtpt) REVERT: S 270 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7352 (tp) REVERT: S 296 PHE cc_start: 0.7507 (m-80) cc_final: 0.7215 (m-80) REVERT: S 304 ASP cc_start: 0.7952 (m-30) cc_final: 0.7543 (m-30) REVERT: S 340 LYS cc_start: 0.8270 (mttt) cc_final: 0.7938 (mtmt) REVERT: S 395 GLU cc_start: 0.7143 (tp30) cc_final: 0.6666 (tp30) REVERT: S 454 PHE cc_start: 0.8541 (t80) cc_final: 0.7888 (t80) REVERT: S 488 GLN cc_start: 0.8041 (mm110) cc_final: 0.7691 (mm-40) REVERT: S 564 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7707 (mtm-85) REVERT: S 594 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7635 (mm-40) REVERT: S 619 ASP cc_start: 0.8170 (t0) cc_final: 0.7654 (t0) REVERT: S 657 LYS cc_start: 0.8550 (tttp) cc_final: 0.8273 (ttpp) REVERT: S 724 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7569 (mp10) REVERT: S 738 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7465 (mm-30) REVERT: S 891 LYS cc_start: 0.7947 (tttt) cc_final: 0.7575 (tppp) REVERT: S 970 SER cc_start: 0.8417 (t) cc_final: 0.8146 (m) REVERT: S 982 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7983 (mtt90) REVERT: S 1065 LYS cc_start: 0.8563 (ttmm) cc_final: 0.8306 (mmmm) REVERT: S 1086 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8623 (pttp) REVERT: S 1169 ARG cc_start: 0.7666 (ttm110) cc_final: 0.7395 (ttm110) REVERT: S 1298 LYS cc_start: 0.7972 (mtpt) cc_final: 0.7521 (ttmm) REVERT: S 1303 ASP cc_start: 0.7954 (m-30) cc_final: 0.7506 (m-30) outliers start: 133 outliers final: 72 residues processed: 633 average time/residue: 0.6812 time to fit residues: 494.9146 Evaluate side-chains 640 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 552 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 96 MET Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 161 LYS 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 49 LEU Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 157 ASN 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 39 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 189 ARG Chi-restraints excluded: chain L residue 197 PHE 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 270 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 534 THR Chi-restraints excluded: chain S residue 549 SER Chi-restraints excluded: chain S residue 564 ARG Chi-restraints excluded: chain S residue 583 GLU Chi-restraints excluded: chain S residue 594 GLN Chi-restraints excluded: chain S residue 637 ARG Chi-restraints excluded: chain S residue 665 THR Chi-restraints excluded: chain S residue 697 VAL Chi-restraints excluded: chain S residue 715 SER Chi-restraints excluded: chain S residue 724 GLN Chi-restraints excluded: chain S residue 773 GLU 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 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 1086 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 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: 1.9990 chunk 14 optimal weight: 1.9990 chunk 230 optimal weight: 0.9980 chunk 225 optimal weight: 0.2980 chunk 125 optimal weight: 0.8980 chunk 169 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 210 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 GLN C 205 GLN D 37 GLN D 180 GLN A 197 GLN K 28 HIS K 115 ASN K 157 ASN ** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 232 ASN L 18 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.194243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.148435 restraints weight = 38631.170| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.86 r_work: 0.3498 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 27277 Z= 0.182 Angle : 0.671 14.725 37604 Z= 0.345 Chirality : 0.043 0.467 4303 Planarity : 0.004 0.072 4151 Dihedral : 19.302 176.635 5398 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.92 % Favored : 93.90 % Rotamer: Outliers : 4.85 % Allowed : 23.50 % 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: -0.06 (0.16), residues: 2755 helix: 1.24 (0.14), residues: 1359 sheet: -0.33 (0.34), residues: 243 loop : -1.55 (0.17), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG K 71 TYR 0.021 0.001 TYR S1019 PHE 0.059 0.002 PHE C 130 TRP 0.034 0.002 TRP K 3 HIS 0.005 0.001 HIS S 420 Details of bonding type rmsd covalent geometry : bond 0.00421 (27277) covalent geometry : angle 0.67085 (37604) hydrogen bonds : bond 0.04230 ( 1267) hydrogen bonds : angle 4.31911 ( 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 676 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 555 time to evaluate : 0.929 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: B 15 GLU cc_start: 0.7674 (tp30) cc_final: 0.7323 (tp30) REVERT: B 23 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8179 (mtpp) REVERT: B 58 GLU cc_start: 0.7810 (mp0) cc_final: 0.7576 (mp0) REVERT: B 96 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.6823 (tpt) REVERT: B 145 PHE cc_start: 0.8480 (t80) cc_final: 0.8179 (t80) REVERT: B 184 TYR cc_start: 0.7898 (t80) cc_final: 0.7589 (t80) REVERT: B 197 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7938 (tm130) REVERT: C 55 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.7144 (ttmm) REVERT: C 58 GLU cc_start: 0.6119 (OUTLIER) cc_final: 0.5752 (mm-30) REVERT: C 60 PHE cc_start: 0.7445 (t80) cc_final: 0.7045 (t80) REVERT: C 96 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6487 (pp-130) REVERT: D 1 MET cc_start: 0.2960 (tmm) cc_final: 0.2413 (pp-130) REVERT: D 66 LEU cc_start: 0.7236 (mm) cc_final: 0.6765 (tp) REVERT: D 77 LYS cc_start: 0.8285 (mmtp) cc_final: 0.7931 (mmtp) REVERT: D 84 GLU cc_start: 0.7184 (tp30) cc_final: 0.6532 (tp30) REVERT: D 117 MET cc_start: 0.7020 (tpp) cc_final: 0.6462 (tpp) REVERT: D 120 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7128 (mp0) REVERT: A 21 THR cc_start: 0.8539 (m) cc_final: 0.8303 (p) REVERT: A 167 ILE cc_start: 0.8258 (mp) cc_final: 0.8033 (mm) REVERT: A 188 ASN cc_start: 0.8182 (m-40) cc_final: 0.7944 (t0) REVERT: A 196 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7205 (mt-10) REVERT: K 98 GLU cc_start: 0.8110 (tp30) cc_final: 0.7535 (mp0) REVERT: K 140 ARG cc_start: 0.7161 (mtp-110) cc_final: 0.6578 (mtp-110) REVERT: K 176 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6717 (mp) REVERT: K 210 ASP cc_start: 0.7659 (t0) cc_final: 0.7342 (t0) REVERT: K 235 GLU cc_start: 0.7704 (mp0) cc_final: 0.6937 (mp0) REVERT: K 242 ARG cc_start: 0.7671 (tpp80) cc_final: 0.7280 (mpp80) REVERT: K 280 GLU cc_start: 0.6255 (tm-30) cc_final: 0.5864 (tm-30) REVERT: L 4 ARG cc_start: 0.7554 (mmm-85) cc_final: 0.7058 (mtm-85) REVERT: L 36 GLU cc_start: 0.8127 (pt0) cc_final: 0.7684 (pt0) REVERT: L 92 ARG cc_start: 0.6821 (mtm180) cc_final: 0.6414 (mtm180) REVERT: L 189 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.7097 (ttt180) REVERT: S 173 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8179 (mtmm) REVERT: S 183 GLU cc_start: 0.7512 (tp30) cc_final: 0.7060 (tp30) REVERT: S 217 GLU cc_start: 0.8416 (mp0) cc_final: 0.7897 (mp0) REVERT: S 230 LYS cc_start: 0.8288 (mtpt) cc_final: 0.7769 (mtpt) REVERT: S 270 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7338 (tp) REVERT: S 294 ASP cc_start: 0.7424 (p0) cc_final: 0.7220 (p0) REVERT: S 296 PHE cc_start: 0.7520 (m-80) cc_final: 0.7243 (m-80) REVERT: S 304 ASP cc_start: 0.7981 (m-30) cc_final: 0.7566 (m-30) REVERT: S 340 LYS cc_start: 0.8269 (mttt) cc_final: 0.7930 (mtmt) REVERT: S 395 GLU cc_start: 0.7092 (tp30) cc_final: 0.6618 (tp30) REVERT: S 446 GLU cc_start: 0.7792 (pm20) cc_final: 0.7489 (pm20) REVERT: S 454 PHE cc_start: 0.8543 (t80) cc_final: 0.7893 (t80) REVERT: S 488 GLN cc_start: 0.8044 (mm110) cc_final: 0.7685 (mm-40) REVERT: S 564 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7684 (mtm-85) REVERT: S 619 ASP cc_start: 0.8171 (t0) cc_final: 0.7656 (t0) REVERT: S 657 LYS cc_start: 0.8539 (tttp) cc_final: 0.8255 (ttpp) REVERT: S 724 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7611 (mp10) REVERT: S 738 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7476 (mm-30) REVERT: S 891 LYS cc_start: 0.7937 (tttt) cc_final: 0.7671 (tppp) REVERT: S 970 SER cc_start: 0.8404 (t) cc_final: 0.8128 (m) REVERT: S 982 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.8015 (mtt90) REVERT: S 1065 LYS cc_start: 0.8539 (ttmm) cc_final: 0.8282 (mmmm) REVERT: S 1086 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8620 (pttp) REVERT: S 1169 ARG cc_start: 0.7628 (ttm110) cc_final: 0.7352 (ttm110) REVERT: S 1298 LYS cc_start: 0.7954 (mtpt) cc_final: 0.7500 (ttmm) REVERT: S 1303 ASP cc_start: 0.7937 (m-30) cc_final: 0.7485 (m-30) outliers start: 121 outliers final: 73 residues processed: 619 average time/residue: 0.7014 time to fit residues: 497.9311 Evaluate side-chains 633 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 545 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 96 MET 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 C residue 55 LYS Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 205 GLN Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 157 ASN 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 39 VAL Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 189 ARG Chi-restraints excluded: chain L residue 197 PHE Chi-restraints excluded: chain L residue 240 MET Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain S residue 13 THR 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 270 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 534 THR Chi-restraints excluded: chain S residue 549 SER Chi-restraints excluded: chain S residue 564 ARG Chi-restraints excluded: chain S residue 583 GLU Chi-restraints excluded: chain S residue 637 ARG Chi-restraints excluded: chain S residue 662 LYS Chi-restraints excluded: chain S residue 665 THR Chi-restraints excluded: chain S residue 697 VAL Chi-restraints excluded: chain S residue 724 GLN Chi-restraints excluded: chain S residue 773 GLU 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 1045 THR Chi-restraints excluded: chain S residue 1060 SER Chi-restraints excluded: chain S residue 1076 MET Chi-restraints excluded: chain S residue 1086 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 1283 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 273 optimal weight: 0.7980 chunk 123 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 122 optimal weight: 0.5980 chunk 108 optimal weight: 0.5980 chunk 184 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 0 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 HIS B 179 GLN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 GLN D 180 GLN A 197 GLN K 28 HIS K 115 ASN K 157 ASN ** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 232 ASN L 271 HIS S 102 GLN S 617 HIS S 650 GLN S 713 GLN S 926 HIS ** S 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.193503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.147666 restraints weight = 38614.746| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.99 r_work: 0.3494 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 27277 Z= 0.185 Angle : 0.683 13.962 37604 Z= 0.351 Chirality : 0.043 0.368 4303 Planarity : 0.004 0.072 4151 Dihedral : 19.290 176.442 5396 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.17 % Favored : 93.65 % Rotamer: Outliers : 4.45 % Allowed : 24.18 % Favored : 71.37 % 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: -0.09 (0.16), residues: 2755 helix: 1.20 (0.14), residues: 1360 sheet: -0.49 (0.33), residues: 255 loop : -1.54 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG K 71 TYR 0.023 0.002 TYR S1019 PHE 0.062 0.002 PHE C 130 TRP 0.037 0.002 TRP K 3 HIS 0.006 0.001 HIS S 420 Details of bonding type rmsd covalent geometry : bond 0.00429 (27277) covalent geometry : angle 0.68261 (37604) hydrogen bonds : bond 0.04261 ( 1267) hydrogen bonds : angle 4.33421 ( 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 654 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 543 time to evaluate : 0.940 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 15 GLU cc_start: 0.7716 (tp30) cc_final: 0.7344 (tp30) REVERT: B 23 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8207 (mtpp) REVERT: B 66 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.6937 (mt) REVERT: B 96 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6827 (tpt) REVERT: B 145 PHE cc_start: 0.8474 (t80) cc_final: 0.8163 (t80) REVERT: B 197 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7942 (tm130) REVERT: C 55 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.7177 (ttmm) REVERT: C 58 GLU cc_start: 0.6194 (OUTLIER) cc_final: 0.5818 (mm-30) REVERT: C 60 PHE cc_start: 0.7446 (t80) cc_final: 0.7080 (t80) REVERT: C 96 MET cc_start: 0.7271 (OUTLIER) cc_final: 0.6516 (pp-130) REVERT: C 98 GLU cc_start: 0.7825 (pp20) cc_final: 0.7534 (pp20) REVERT: C 153 GLN cc_start: 0.8094 (pt0) cc_final: 0.7837 (pm20) REVERT: D 1 MET cc_start: 0.2839 (tmm) cc_final: 0.2298 (pp-130) REVERT: D 77 LYS cc_start: 0.8308 (mmtp) cc_final: 0.7972 (mmtp) REVERT: D 84 GLU cc_start: 0.7240 (tp30) cc_final: 0.6540 (tp30) REVERT: D 117 MET cc_start: 0.6962 (tpp) cc_final: 0.6659 (tpp) REVERT: A 21 THR cc_start: 0.8529 (m) cc_final: 0.8310 (p) REVERT: A 167 ILE cc_start: 0.8265 (mp) cc_final: 0.8042 (mm) REVERT: A 188 ASN cc_start: 0.8176 (m-40) cc_final: 0.7775 (t160) REVERT: A 201 GLN cc_start: 0.5954 (mp10) cc_final: 0.5636 (mp10) REVERT: K 98 GLU cc_start: 0.8147 (tp30) cc_final: 0.7546 (mp0) REVERT: K 176 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6772 (mp) REVERT: K 210 ASP cc_start: 0.7675 (t0) cc_final: 0.7371 (t0) REVERT: K 235 GLU cc_start: 0.7712 (mp0) cc_final: 0.6932 (mp0) REVERT: K 242 ARG cc_start: 0.7659 (tpp80) cc_final: 0.7295 (mpp80) REVERT: K 280 GLU cc_start: 0.6249 (tm-30) cc_final: 0.5889 (tm-30) REVERT: L 4 ARG cc_start: 0.7598 (mmm-85) cc_final: 0.7091 (mtm-85) REVERT: L 36 GLU cc_start: 0.8157 (pt0) cc_final: 0.7727 (pt0) REVERT: L 92 ARG cc_start: 0.6819 (mtm180) cc_final: 0.6431 (mtm180) REVERT: L 189 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.7112 (ttt180) REVERT: S 173 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8140 (mtmm) REVERT: S 182 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7253 (pmmt) REVERT: S 183 GLU cc_start: 0.7476 (tp30) cc_final: 0.6995 (tp30) REVERT: S 215 GLU cc_start: 0.7491 (tt0) cc_final: 0.6632 (tt0) REVERT: S 217 GLU cc_start: 0.8423 (mp0) cc_final: 0.7859 (mp0) REVERT: S 230 LYS cc_start: 0.8268 (mtpt) cc_final: 0.7747 (mtpt) REVERT: S 270 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.7302 (tp) REVERT: S 296 PHE cc_start: 0.7549 (m-80) cc_final: 0.7268 (m-80) REVERT: S 304 ASP cc_start: 0.7976 (m-30) cc_final: 0.7563 (m-30) REVERT: S 340 LYS cc_start: 0.8282 (mttt) cc_final: 0.7943 (mtmt) REVERT: S 395 GLU cc_start: 0.7128 (tp30) cc_final: 0.6641 (tp30) REVERT: S 454 PHE cc_start: 0.8547 (t80) cc_final: 0.7897 (t80) REVERT: S 488 GLN cc_start: 0.8064 (mm110) cc_final: 0.7695 (mm-40) REVERT: S 564 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7705 (mtm-85) REVERT: S 619 ASP cc_start: 0.8182 (t0) cc_final: 0.7660 (t0) REVERT: S 657 LYS cc_start: 0.8576 (tttp) cc_final: 0.8210 (ttpp) REVERT: S 724 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7658 (mp10) REVERT: S 738 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7477 (mm-30) REVERT: S 890 MET cc_start: 0.7757 (tpp) cc_final: 0.7297 (tpp) REVERT: S 891 LYS cc_start: 0.7953 (tttt) cc_final: 0.7643 (tppp) REVERT: S 970 SER cc_start: 0.8405 (t) cc_final: 0.8130 (m) REVERT: S 982 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8020 (mtt90) REVERT: S 1065 LYS cc_start: 0.8544 (ttmm) cc_final: 0.8289 (mmmm) REVERT: S 1086 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8624 (pttp) REVERT: S 1169 ARG cc_start: 0.7685 (ttm110) cc_final: 0.7405 (ttm110) REVERT: S 1174 MET cc_start: 0.8442 (ptm) cc_final: 0.8202 (ptm) REVERT: S 1298 LYS cc_start: 0.7956 (mtpt) cc_final: 0.7488 (ttmm) REVERT: S 1303 ASP cc_start: 0.7962 (m-30) cc_final: 0.7516 (m-30) outliers start: 111 outliers final: 72 residues processed: 606 average time/residue: 0.6968 time to fit residues: 483.7115 Evaluate side-chains 630 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 542 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 96 MET 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 C residue 55 LYS Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 96 MET 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 D residue 180 GLN Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 157 ASN Chi-restraints excluded: chain K residue 176 LEU Chi-restraints excluded: chain K residue 186 ILE 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 39 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 189 ARG Chi-restraints excluded: chain L residue 197 PHE 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 13 THR 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 270 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 534 THR Chi-restraints excluded: chain S residue 549 SER Chi-restraints excluded: chain S residue 564 ARG Chi-restraints excluded: chain S residue 583 GLU Chi-restraints excluded: chain S residue 637 ARG Chi-restraints excluded: chain S residue 662 LYS Chi-restraints excluded: chain S residue 665 THR Chi-restraints excluded: chain S residue 697 VAL 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 1045 THR Chi-restraints excluded: chain S residue 1060 SER Chi-restraints excluded: chain S residue 1076 MET Chi-restraints excluded: chain S residue 1086 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 1246 VAL 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: 1.9990 chunk 115 optimal weight: 0.8980 chunk 121 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 233 optimal weight: 0.7980 chunk 269 optimal weight: 0.8980 chunk 210 optimal weight: 0.2980 chunk 260 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 GLN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN D 180 GLN A 197 GLN K 28 HIS K 115 ASN K 157 ASN ** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 232 ASN L 28 HIS L 258 GLN L 271 HIS S 102 GLN S 617 HIS S 650 GLN S 713 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.193165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.147236 restraints weight = 38631.866| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.92 r_work: 0.3491 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 27277 Z= 0.188 Angle : 0.704 12.702 37604 Z= 0.360 Chirality : 0.043 0.292 4303 Planarity : 0.004 0.074 4151 Dihedral : 19.289 176.299 5394 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.35 % Favored : 93.47 % Rotamer: Outliers : 4.01 % Allowed : 25.18 % Favored : 70.81 % 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: -0.13 (0.16), residues: 2755 helix: 1.20 (0.14), residues: 1357 sheet: -0.70 (0.33), residues: 259 loop : -1.55 (0.17), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG K 71 TYR 0.029 0.002 TYR L 254 PHE 0.045 0.002 PHE D 130 TRP 0.039 0.002 TRP K 3 HIS 0.005 0.001 HIS S 420 Details of bonding type rmsd covalent geometry : bond 0.00438 (27277) covalent geometry : angle 0.70410 (37604) hydrogen bonds : bond 0.04274 ( 1267) hydrogen bonds : angle 4.36735 ( 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 646 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 546 time to evaluate : 0.944 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: B 15 GLU cc_start: 0.7610 (tp30) cc_final: 0.7307 (tp30) REVERT: B 23 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8172 (mtpp) REVERT: B 58 GLU cc_start: 0.7622 (mp0) cc_final: 0.7373 (mp0) REVERT: B 145 PHE cc_start: 0.8468 (t80) cc_final: 0.8195 (t80) REVERT: B 197 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7927 (tm130) REVERT: C 55 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.7219 (ttmm) REVERT: C 58 GLU cc_start: 0.6218 (OUTLIER) cc_final: 0.5801 (mm-30) REVERT: C 60 PHE cc_start: 0.7509 (t80) cc_final: 0.7151 (t80) REVERT: C 90 LYS cc_start: 0.5751 (pmtt) cc_final: 0.5520 (pmtt) REVERT: C 96 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.6685 (pp-130) REVERT: C 98 GLU cc_start: 0.7823 (pp20) cc_final: 0.7520 (pp20) REVERT: D 1 MET cc_start: 0.2806 (tmm) cc_final: 0.2422 (tmm) REVERT: D 77 LYS cc_start: 0.8312 (mmtp) cc_final: 0.7977 (mmtp) REVERT: D 84 GLU cc_start: 0.7163 (tp30) cc_final: 0.6472 (tp30) REVERT: D 177 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6191 (mm-30) REVERT: A 21 THR cc_start: 0.8539 (m) cc_final: 0.8322 (p) REVERT: A 24 ASP cc_start: 0.8004 (t0) cc_final: 0.7501 (t70) REVERT: A 167 ILE cc_start: 0.8229 (mp) cc_final: 0.7996 (mm) REVERT: A 201 GLN cc_start: 0.6024 (mp10) cc_final: 0.5680 (mp10) REVERT: K 98 GLU cc_start: 0.8210 (tp30) cc_final: 0.7547 (mp0) REVERT: K 176 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6759 (mp) REVERT: K 210 ASP cc_start: 0.7628 (t0) cc_final: 0.7316 (t0) REVERT: K 235 GLU cc_start: 0.7655 (mp0) cc_final: 0.6933 (mp0) REVERT: K 242 ARG cc_start: 0.7747 (tpp80) cc_final: 0.7368 (mpp80) REVERT: K 280 GLU cc_start: 0.6167 (tm-30) cc_final: 0.5818 (tm-30) REVERT: L 4 ARG cc_start: 0.7552 (mmm-85) cc_final: 0.7049 (mtm-85) REVERT: L 36 GLU cc_start: 0.8218 (pt0) cc_final: 0.7799 (pt0) REVERT: L 92 ARG cc_start: 0.6855 (mtm180) cc_final: 0.6481 (mtm180) REVERT: L 189 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.7167 (ttt180) REVERT: S 173 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8150 (mtmm) REVERT: S 182 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7240 (pmmt) REVERT: S 183 GLU cc_start: 0.7500 (tp30) cc_final: 0.7033 (tp30) REVERT: S 215 GLU cc_start: 0.7532 (tt0) cc_final: 0.6663 (tt0) REVERT: S 217 GLU cc_start: 0.8416 (mp0) cc_final: 0.7880 (mp0) REVERT: S 230 LYS cc_start: 0.8301 (mtpt) cc_final: 0.7786 (mtpt) REVERT: S 270 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.7314 (tp) REVERT: S 296 PHE cc_start: 0.7581 (m-80) cc_final: 0.7279 (m-80) REVERT: S 304 ASP cc_start: 0.7976 (m-30) cc_final: 0.7589 (m-30) REVERT: S 340 LYS cc_start: 0.8292 (mttt) cc_final: 0.7962 (mtmt) REVERT: S 395 GLU cc_start: 0.7181 (tp30) cc_final: 0.6724 (tp30) REVERT: S 454 PHE cc_start: 0.8542 (t80) cc_final: 0.7903 (t80) REVERT: S 488 GLN cc_start: 0.8094 (mm110) cc_final: 0.7734 (mm-40) REVERT: S 564 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7674 (mtm-85) REVERT: S 619 ASP cc_start: 0.8131 (t0) cc_final: 0.7569 (t0) REVERT: S 657 LYS cc_start: 0.8590 (tttp) cc_final: 0.8241 (ttpp) REVERT: S 724 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7662 (mp10) REVERT: S 738 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7544 (mm-30) REVERT: S 891 LYS cc_start: 0.7931 (tttt) cc_final: 0.7640 (tppp) REVERT: S 970 SER cc_start: 0.8363 (t) cc_final: 0.8087 (m) REVERT: S 982 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7961 (mtt90) REVERT: S 1065 LYS cc_start: 0.8473 (ttmm) cc_final: 0.8240 (mmmm) REVERT: S 1086 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8604 (pttp) REVERT: S 1169 ARG cc_start: 0.7700 (ttm110) cc_final: 0.7423 (ttm110) REVERT: S 1174 MET cc_start: 0.8433 (ptm) cc_final: 0.8199 (ptm) REVERT: S 1298 LYS cc_start: 0.7984 (mtpt) cc_final: 0.7523 (ttmm) REVERT: S 1303 ASP cc_start: 0.7920 (m-30) cc_final: 0.7476 (m-30) outliers start: 100 outliers final: 72 residues processed: 600 average time/residue: 0.7213 time to fit residues: 494.4768 Evaluate side-chains 628 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 541 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 57 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 70 VAL 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 C residue 55 LYS Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 205 GLN Chi-restraints excluded: chain D residue 96 MET 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 D residue 177 GLU Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 157 ASN Chi-restraints excluded: chain K residue 176 LEU Chi-restraints excluded: chain K residue 186 ILE 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 39 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 189 ARG Chi-restraints excluded: chain L residue 197 PHE 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 13 THR 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 270 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 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 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 697 VAL 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 1045 THR Chi-restraints excluded: chain S residue 1060 SER Chi-restraints excluded: chain S residue 1076 MET Chi-restraints excluded: chain S residue 1086 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 1283 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 138 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 147 optimal weight: 8.9990 chunk 55 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 167 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 chunk 269 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 GLN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 GLN C 180 GLN C 205 GLN A 197 GLN K 28 HIS K 115 ASN K 157 ASN ** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 212 ASN K 232 ASN L 18 ASN L 28 HIS ** L 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 102 GLN S 193 ASN S 617 HIS S 650 GLN S 713 GLN S 926 HIS ** S 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.190634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.144681 restraints weight = 38451.653| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.06 r_work: 0.3444 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.116 27277 Z= 0.319 Angle : 0.767 14.018 37604 Z= 0.396 Chirality : 0.048 0.306 4303 Planarity : 0.005 0.084 4151 Dihedral : 19.372 176.137 5393 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.01 % Favored : 92.81 % Rotamer: Outliers : 3.69 % Allowed : 25.54 % Favored : 70.77 % 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: -0.43 (0.16), residues: 2755 helix: 0.86 (0.14), residues: 1362 sheet: -0.87 (0.31), residues: 289 loop : -1.56 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG K 71 TYR 0.029 0.002 TYR S1019 PHE 0.045 0.002 PHE D 130 TRP 0.045 0.003 TRP K 3 HIS 0.009 0.001 HIS K 11 Details of bonding type rmsd covalent geometry : bond 0.00747 (27277) covalent geometry : angle 0.76719 (37604) hydrogen bonds : bond 0.05041 ( 1267) hydrogen bonds : angle 4.60016 ( 3512) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13454.22 seconds wall clock time: 228 minutes 31.10 seconds (13711.10 seconds total)