Starting phenix.real_space_refine on Sun Jul 5 09:16:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vja_65108/07_2026/9vja_65108.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vja_65108/07_2026/9vja_65108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vja_65108/07_2026/9vja_65108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vja_65108/07_2026/9vja_65108.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vja_65108/07_2026/9vja_65108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vja_65108/07_2026/9vja_65108.map" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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 180 5.49 5 S 64 5.16 5 C 16316 2.51 5 N 4424 2.21 5 O 5441 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26425 Number of models: 1 Model: "" Number of chains: 11 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: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2333 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} 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: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 586 Classifications: {'RNA': 28} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 4, 'rna3p_pur': 9, 'rna3p_pyr': 14} Link IDs: {'rna2p': 5, 'rna3p': 22} Chain: "t" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1322 Classifications: {'RNA': 62} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 10, 'rna3p_pur': 31, 'rna3p_pyr': 18} Link IDs: {'rna2p': 13, 'rna3p': 48} 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: "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: "S" Number of atoms: 10832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1323, 10832 Classifications: {'peptide': 1323} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 40, 'TRANS': 1282} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 5.53, per 1000 atoms: 0.21 Number of scatterers: 26425 At special positions: 0 Unit cell: (121.16, 163.1, 171.488, 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 64 16.00 P 180 15.00 O 5441 8.00 N 4424 7.00 C 16316 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: 2.26 Conformation dependent library (CDL) restraints added in 818.7 milliseconds 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 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: 114 helices and 26 sheets defined 50.9% alpha, 10.5% beta 60 base pairs and 108 stacking pairs defined. Time for finding SS restraints: 3.70 Creating SS restraints... Processing helix chain 'K' and resid 51 through 59 removed outlier: 4.122A pdb=" N ASP K 59 " --> pdb=" O LYS K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 94 Processing helix chain 'K' and resid 97 through 121 Processing helix chain 'K' and resid 126 through 135 Processing helix chain 'K' and resid 136 through 139 removed outlier: 4.034A pdb=" N LEU K 139 " --> pdb=" O ARG K 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 136 through 139' Processing helix chain 'K' and resid 142 through 145 removed outlier: 3.849A pdb=" N ALA K 145 " --> pdb=" O PHE K 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 142 through 145' Processing helix chain 'K' and resid 146 through 160 removed outlier: 3.603A pdb=" N HIS K 150 " --> pdb=" O ASN K 146 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU K 159 " --> pdb=" O TYR K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 170 through 195 removed outlier: 3.658A pdb=" N ALA K 174 " --> pdb=" O ASN K 170 " (cutoff:3.500A) Processing helix chain 'K' and resid 211 through 216 Processing helix chain 'K' and resid 218 through 220 No H-bonds generated for 'chain 'K' and resid 218 through 220' Processing helix chain 'K' and resid 221 through 232 removed outlier: 4.250A pdb=" N VAL K 225 " --> pdb=" O PHE K 221 " (cutoff:3.500A) Processing helix chain 'K' and resid 236 through 244 Processing helix chain 'K' and resid 245 through 249 removed outlier: 3.529A pdb=" N PHE K 248 " --> pdb=" O PHE K 245 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET K 249 " --> pdb=" O ALA K 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 245 through 249' Processing helix chain 'K' and resid 260 through 276 Processing helix chain 'L' and resid 51 through 60 Processing helix chain 'L' and resid 88 through 94 Processing helix chain 'L' and resid 97 through 122 removed outlier: 3.560A pdb=" N LEU L 120 " --> pdb=" O GLN L 116 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 138 removed outlier: 4.131A pdb=" N ALA L 130 " --> pdb=" O GLY L 126 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ALA L 131 " --> pdb=" O GLN L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 160 Processing helix chain 'L' and resid 172 through 195 removed outlier: 3.548A pdb=" N GLU L 190 " --> pdb=" O ILE L 186 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 216 Processing helix chain 'L' and resid 217 through 220 Proline residue: L 220 - end of helix No H-bonds generated for 'chain 'L' and resid 217 through 220' Processing helix chain 'L' and resid 221 through 232 removed outlier: 4.387A pdb=" N VAL L 225 " --> pdb=" O PHE L 221 " (cutoff:3.500A) Processing helix chain 'L' and resid 236 through 245 Processing helix chain 'L' and resid 261 through 276 Processing helix chain 'A' and resid 24 through 37 Processing helix chain 'A' and resid 55 through 57 No H-bonds generated for 'chain 'A' and resid 55 through 57' Processing helix chain 'A' and resid 64 through 68 removed outlier: 3.691A pdb=" N TYR A 68 " --> pdb=" O ILE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 90 removed outlier: 4.718A pdb=" N LEU A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 114 removed outlier: 3.508A pdb=" N LYS A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 143 through 158 Processing helix chain 'A' and resid 169 through 173 Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'B' and resid 24 through 37 Processing helix chain 'B' and resid 64 through 68 removed outlier: 3.596A pdb=" N TYR B 68 " --> pdb=" O ILE B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 90 Processing helix chain 'B' and resid 90 through 115 removed outlier: 4.195A pdb=" N MET B 96 " --> pdb=" O GLU B 92 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR B 110 " --> pdb=" O GLN B 106 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU B 111 " --> pdb=" O LEU B 107 " (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 174 through 189 removed outlier: 3.601A pdb=" N GLN B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 37 removed outlier: 3.692A pdb=" N PHE C 28 " --> pdb=" O ASP C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 68 removed outlier: 3.628A pdb=" N TYR C 68 " --> pdb=" O ILE C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 90 Processing helix chain 'C' and resid 90 through 113 removed outlier: 3.693A pdb=" N LYS C 94 " --> pdb=" O LYS C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 133 Processing helix chain 'C' and resid 143 through 158 removed outlier: 3.751A pdb=" N LYS C 147 " --> pdb=" O THR C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 173 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: 3.763A pdb=" N GLY D 67 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 3.541A 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: 3.596A pdb=" N LYS D 90 " --> pdb=" O GLN D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 115 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 'S' and resid 59 through 86 Processing helix chain 'S' and resid 87 through 92 removed outlier: 3.870A pdb=" N ASP S 92 " --> pdb=" O GLU S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 97 through 103 Processing helix chain 'S' and resid 121 through 132 Processing helix chain 'S' and resid 134 through 145 removed outlier: 3.767A 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 182 through 194 Processing helix chain 'S' and resid 223 through 235 removed outlier: 3.688A pdb=" N SER S 228 " --> pdb=" O ARG S 224 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN S 234 " --> pdb=" O LYS S 230 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE S 235 " --> pdb=" O VAL S 231 " (cutoff:3.500A) Processing helix chain 'S' and resid 241 through 253 removed outlier: 3.804A pdb=" N GLY S 245 " --> pdb=" O ASN S 241 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N PHE S 247 " --> pdb=" O LEU S 243 " (cutoff:3.500A) Processing helix chain 'S' and resid 276 through 289 Processing helix chain 'S' and resid 292 through 312 Processing helix chain 'S' and resid 313 through 315 No H-bonds generated for 'chain 'S' and resid 313 through 315' Processing helix chain 'S' and resid 321 through 349 removed outlier: 3.665A pdb=" N SER S 326 " --> pdb=" O LYS S 322 " (cutoff:3.500A) Processing helix chain 'S' and resid 350 through 352 No H-bonds generated for 'chain 'S' and resid 350 through 352' Processing helix chain 'S' and resid 353 through 358 Processing helix chain 'S' and resid 364 through 371 Processing helix chain 'S' and resid 376 through 388 removed outlier: 3.564A pdb=" N ILE S 388 " --> pdb=" O VAL S 384 " (cutoff:3.500A) Processing helix chain 'S' and resid 394 through 403 Processing helix chain 'S' and resid 419 through 435 removed outlier: 4.176A pdb=" N HIS S 423 " --> pdb=" O PRO S 419 " (cutoff:3.500A) Processing helix chain 'S' and resid 438 through 444 removed outlier: 3.740A pdb=" N LYS S 442 " --> pdb=" O TYR S 438 " (cutoff:3.500A) Processing helix chain 'S' and resid 444 through 454 removed outlier: 3.735A pdb=" N ILE S 448 " --> pdb=" O ASN S 444 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL S 452 " --> pdb=" O ILE S 448 " (cutoff:3.500A) Processing helix chain 'S' and resid 492 through 504 Processing helix chain 'S' and resid 521 through 535 removed outlier: 4.151A pdb=" N LYS S 535 " --> pdb=" O ASN S 531 " (cutoff:3.500A) Processing helix chain 'S' and resid 549 through 564 Processing helix chain 'S' and resid 568 through 581 Processing helix chain 'S' and resid 599 through 608 removed outlier: 3.870A 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 646 Processing helix chain 'S' and resid 652 through 662 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 removed outlier: 4.163A pdb=" N ALA S 723 " --> pdb=" O ALA S 719 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER S 725 " --> pdb=" O GLN S 721 " (cutoff:3.500A) Processing helix chain 'S' and resid 731 through 738 removed outlier: 3.508A pdb=" N VAL S 736 " --> pdb=" O LEU S 732 " (cutoff:3.500A) Processing helix chain 'S' and resid 742 through 764 Processing helix chain 'S' and resid 791 through 803 Processing helix chain 'S' and resid 815 through 818 removed outlier: 3.619A pdb=" N ARG S 818 " --> pdb=" O GLU S 815 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 815 through 818' Processing helix chain 'S' and resid 819 through 828 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 900 Processing helix chain 'S' and resid 904 through 917 removed outlier: 3.782A pdb=" N PHE S 908 " --> pdb=" O SER S 904 " (cutoff:3.500A) Processing helix chain 'S' and resid 920 through 933 Processing helix chain 'S' and resid 936 through 951 removed outlier: 3.571A pdb=" N LYS S 940 " --> pdb=" O ARG S 936 " (cutoff:3.500A) Processing helix chain 'S' and resid 967 through 975 Processing helix chain 'S' and resid 987 through 1007 Processing helix chain 'S' and resid 1010 through 1014 Processing helix chain 'S' and resid 1023 through 1035 Processing helix chain 'S' and resid 1061 through 1072 Processing helix chain 'S' and resid 1150 through 1157 Processing helix chain 'S' and resid 1157 through 1164 Processing helix chain 'S' and resid 1207 through 1222 removed outlier: 3.794A pdb=" N LEU S1221 " --> pdb=" O ALA S1217 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU S1222 " --> pdb=" O LYS S1218 " (cutoff:3.500A) Processing helix chain 'S' and resid 1227 through 1235 Processing helix chain 'S' and resid 1236 through 1253 removed outlier: 4.048A pdb=" N GLN S1240 " --> pdb=" O GLN S1236 " (cutoff:3.500A) Processing helix chain 'S' and resid 1256 through 1269 Processing helix chain 'S' and resid 1274 through 1289 removed outlier: 3.940A pdb=" N ASN S1289 " --> pdb=" O LEU S1285 " (cutoff:3.500A) Processing helix chain 'S' and resid 1312 through 1317 removed outlier: 3.979A pdb=" N PHE S1316 " --> pdb=" O LYS S1313 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 4 through 7 removed outlier: 7.679A pdb=" N ARG K 4 " --> pdb=" O ASP K 38 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU K 40 " --> pdb=" O ARG K 4 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL K 6 " --> pdb=" O LEU K 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'K' and resid 29 through 33 removed outlier: 3.550A pdb=" N SER K 15 " --> pdb=" O VAL K 22 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS K 13 " --> pdb=" O LYS K 24 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TYR K 16 " --> pdb=" O THR K 50 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR L 50 " --> pdb=" O LEU L 14 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N TYR L 16 " --> pdb=" O THR L 50 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER L 15 " --> pdb=" O VAL L 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 66 through 67 removed outlier: 3.770A pdb=" N GLY K 75 " --> pdb=" O PHE K 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 252 through 253 Processing sheet with id=AA5, first strand: chain 'L' and resid 39 through 41 Processing sheet with id=AA6, first strand: chain 'L' and resid 251 through 254 Processing sheet with id=AA7, first strand: chain 'A' and resid 12 through 13 Processing sheet with id=AA8, first strand: chain 'A' and resid 59 through 62 removed outlier: 6.421A pdb=" N PHE A 60 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ILE A 167 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL A 62 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU A 164 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU A 195 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE A 166 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR A 18 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLU A 196 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU A 20 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N ALA A 17 " --> pdb=" O PHE A 204 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N TYR A 206 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N PHE A 19 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N LEU A 208 " --> pdb=" O PHE A 19 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR A 21 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU A 217 " --> pdb=" O GLN A 205 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AB1, first strand: chain 'B' and resid 12 through 13 Processing sheet with id=AB2, first strand: chain 'B' and resid 59 through 62 removed outlier: 6.732A pdb=" N PHE B 60 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE B 167 " --> pdb=" O PHE B 60 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL B 62 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU B 164 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU B 195 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N PHE B 166 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 22 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N ALA B 17 " --> pdb=" O PHE B 204 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N TYR B 206 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE B 19 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N LEU B 208 " --> pdb=" O PHE B 19 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR B 21 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 136 through 137 Processing sheet with id=AB4, first strand: chain 'C' and resid 12 through 13 removed outlier: 3.537A pdb=" N PHE C 47 " --> pdb=" O ARG C 2 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 17 through 21 removed outlier: 7.372A pdb=" N THR C 18 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N GLU C 196 " --> pdb=" O THR C 18 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU C 20 " --> pdb=" O GLU C 196 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 204 through 208 Processing sheet with id=AB7, first strand: chain 'D' and resid 12 through 13 Processing sheet with id=AB8, first strand: chain 'D' and resid 59 through 62 removed outlier: 3.849A pdb=" N PHE D 60 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR D 18 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLU D 196 " --> pdb=" O THR D 18 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU D 20 " --> pdb=" O GLU D 196 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N ALA D 17 " --> pdb=" O PHE D 204 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N TYR D 206 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N PHE D 19 " --> pdb=" O TYR D 206 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU D 208 " --> pdb=" O PHE D 19 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR D 21 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG D 203 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER D 215 " --> pdb=" O ILE D 207 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'S' and resid 26 through 27 removed outlier: 3.885A pdb=" N GLN S 26 " --> pdb=" O THR S 22 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TYR S 5 " --> pdb=" O ARG S 769 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N VAL S 771 " --> pdb=" O TYR S 5 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE S 7 " --> pdb=" O VAL S 771 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N GLU S 773 " --> pdb=" O ILE S 7 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU S 9 " --> pdb=" O GLU S 773 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE S 770 " --> pdb=" O ILE S 962 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'S' and resid 26 through 27 removed outlier: 3.885A pdb=" N GLN S 26 " --> pdb=" O THR S 22 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'S' and resid 42 through 46 removed outlier: 10.272A pdb=" N GLU S1330 " --> pdb=" O LYS S 31 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ARG S1332 " --> pdb=" O PRO S 33 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TYR S 35 " --> pdb=" O ARG S1332 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LYS S1334 " --> pdb=" O TYR S 35 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU S1181 " --> pdb=" O ILE S1321 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR S1180 " --> pdb=" O LEU S1192 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'S' and resid 256 through 257 removed outlier: 3.514A pdb=" N ALA S 256 " --> pdb=" O ILE S 270 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'S' and resid 516 through 518 removed outlier: 4.749A pdb=" N LEU S 517 " --> pdb=" O GLY S 668 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'S' and resid 545 through 546 removed outlier: 3.933A pdb=" N ALA S 546 " --> pdb=" O TYR S 538 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR S 538 " --> pdb=" O ALA S 546 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'S' and resid 848 through 851 removed outlier: 3.665A pdb=" N ASP S 848 " --> pdb=" O VAL S 869 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL S 869 " --> pdb=" O ASP S 848 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'S' and resid 1139 through 1147 removed outlier: 3.545A pdb=" N MET S1174 " --> pdb=" O LEU S1128 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR S1130 " --> pdb=" O VAL S1172 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL S1172 " --> pdb=" O THR S1130 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N GLU S1132 " --> pdb=" O PRO S1170 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'S' and resid 1297 through 1298 1062 hydrogen bonds defined for protein. 3084 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 145 hydrogen bonds 274 hydrogen bond angles 0 basepair planarities 60 basepair parallelities 108 stacking parallelities Total time for adding SS restraints: 6.25 Time building geometry restraints manager: 3.02 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: 5398 1.33 - 1.45: 6873 1.45 - 1.57: 14546 1.57 - 1.69: 356 1.69 - 1.81: 116 Bond restraints: 27289 Sorted by residual: bond pdb=" C3' DC N 5 " pdb=" C2' DC N 5 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.40e+01 bond pdb=" C3' DC T 32 " pdb=" C2' DC T 32 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.29e+01 bond pdb=" C3' DA T 22 " pdb=" C2' DA T 22 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DC N -34 " pdb=" C2' DC N -34 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DA N -23 " pdb=" C2' DA N -23 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.68e+00 ... (remaining 27284 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 36833 1.97 - 3.95: 714 3.95 - 5.92: 71 5.92 - 7.89: 11 7.89 - 9.87: 2 Bond angle restraints: 37631 Sorted by residual: angle pdb=" O4' DA T 14 " pdb=" C4' DA T 14 " pdb=" C3' DA T 14 " ideal model delta sigma weight residual 106.00 103.31 2.69 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N1 C g 19 " pdb=" C2 C g 19 " pdb=" O2 C g 19 " ideal model delta sigma weight residual 118.90 121.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT N -17 " pdb=" C4 DT N -17 " pdb=" O4 DT N -17 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" C1' U g 34 " pdb=" N1 U g 34 " pdb=" C2 U g 34 " ideal model delta sigma weight residual 117.70 122.94 -5.24 1.20e+00 6.94e-01 1.91e+01 angle pdb=" C1' U g 8 " pdb=" N1 U g 8 " pdb=" C2 U g 8 " ideal model delta sigma weight residual 117.70 122.80 -5.10 1.20e+00 6.94e-01 1.81e+01 ... (remaining 37626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.42: 15350 32.42 - 64.84: 1034 64.84 - 97.26: 54 97.26 - 129.68: 1 129.68 - 162.10: 3 Dihedral angle restraints: 16442 sinusoidal: 8253 harmonic: 8189 Sorted by residual: dihedral pdb=" O4' U g 34 " pdb=" C1' U g 34 " pdb=" N1 U g 34 " pdb=" C2 U g 34 " ideal model delta sinusoidal sigma weight residual 200.00 37.90 162.10 1 1.50e+01 4.44e-03 8.33e+01 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 49.09 150.91 1 1.50e+01 4.44e-03 8.00e+01 dihedral pdb=" CA ALA S 59 " pdb=" C ALA S 59 " pdb=" N GLU S 60 " pdb=" CA GLU S 60 " ideal model delta harmonic sigma weight residual -180.00 -155.58 -24.42 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 16439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3228 0.045 - 0.090: 869 0.090 - 0.135: 201 0.135 - 0.181: 13 0.181 - 0.226: 1 Chirality restraints: 4312 Sorted by residual: chirality pdb=" CB VAL K 64 " pdb=" CA VAL K 64 " pdb=" CG1 VAL K 64 " pdb=" CG2 VAL K 64 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB VAL S1336 " pdb=" CA VAL S1336 " pdb=" CG1 VAL S1336 " pdb=" CG2 VAL S1336 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.77e-01 chirality pdb=" CA GLU L 219 " pdb=" N GLU L 219 " pdb=" C GLU L 219 " pdb=" CB GLU L 219 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.54e-01 ... (remaining 4309 not shown) Planarity restraints: 4149 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP S 558 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.17e+00 pdb=" C ASP S 558 " 0.046 2.00e-02 2.50e+03 pdb=" O ASP S 558 " -0.017 2.00e-02 2.50e+03 pdb=" N TYR S 559 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG K 222 " -0.033 5.00e-02 4.00e+02 4.94e-02 3.90e+00 pdb=" N PRO K 223 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO K 223 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO K 223 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA T 14 " -0.025 2.00e-02 2.50e+03 1.15e-02 3.64e+00 pdb=" N9 DA T 14 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DA T 14 " 0.006 2.00e-02 2.50e+03 pdb=" N7 DA T 14 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA T 14 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA T 14 " -0.005 2.00e-02 2.50e+03 pdb=" N6 DA T 14 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DA T 14 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DA T 14 " 0.011 2.00e-02 2.50e+03 pdb=" N3 DA T 14 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DA T 14 " 0.001 2.00e-02 2.50e+03 ... (remaining 4146 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2231 2.74 - 3.28: 26232 3.28 - 3.82: 46488 3.82 - 4.36: 55618 4.36 - 4.90: 89669 Nonbonded interactions: 220238 Sorted by model distance: nonbonded pdb=" O2' A t 35 " pdb=" O LEU S 101 " model vdw 2.196 3.040 nonbonded pdb=" O THR K 198 " pdb=" OG1 THR K 198 " model vdw 2.196 3.040 nonbonded pdb=" OG1 THR B 143 " pdb=" OE1 GLU B 146 " model vdw 2.199 3.040 nonbonded pdb=" O PHE S 530 " pdb=" OG1 THR S 534 " model vdw 2.200 3.040 nonbonded pdb=" O VAL K 273 " pdb=" ND2 ASN K 277 " model vdw 2.217 3.120 ... (remaining 220233 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' and resid 4 through 288) selection = chain 'L' } 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: 5.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 26.820 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 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 0.046 27289 Z= 0.288 Angle : 0.655 9.868 37631 Z= 0.447 Chirality : 0.043 0.226 4312 Planarity : 0.004 0.061 4149 Dihedral : 18.451 162.104 11140 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.15 % Favored : 92.59 % Rotamer: Outliers : 6.99 % Allowed : 10.89 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.16), residues: 2754 helix: 0.40 (0.14), residues: 1307 sheet: -0.43 (0.33), residues: 264 loop : -2.01 (0.17), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 71 TYR 0.015 0.002 TYR S 155 PHE 0.019 0.002 PHE S 86 TRP 0.010 0.001 TRP S 113 HIS 0.006 0.001 HIS S 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.29 (27289) covalent geometry : angle 0.65492 / 0.45 (37631) hydrogen bonds : bond 0.15026 / 10.00 ( 1206) hydrogen bonds : angle 5.90292 / 4.30 ( 3358) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 459 time to evaluate : 0.777 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: K 28 HIS cc_start: 0.5866 (p90) cc_final: 0.5174 (p90) REVERT: K 140 ARG cc_start: 0.6534 (mmp-170) cc_final: 0.6043 (mmp-170) REVERT: K 142 PHE cc_start: 0.3336 (OUTLIER) cc_final: 0.1961 (p90) REVERT: K 191 LEU cc_start: 0.6258 (OUTLIER) cc_final: 0.6041 (tt) REVERT: K 276 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6690 (tp) REVERT: A 7 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.6716 (tp) REVERT: A 77 LYS cc_start: 0.5479 (OUTLIER) cc_final: 0.5263 (mtmm) REVERT: C 216 TYR cc_start: 0.1274 (t80) cc_final: 0.0964 (t80) REVERT: S 301 ASN cc_start: 0.8953 (m-40) cc_final: 0.8705 (m110) REVERT: S 307 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8265 (mm-30) REVERT: S 467 ASP cc_start: 0.7697 (p0) cc_final: 0.7470 (p0) REVERT: S 690 TYR cc_start: 0.7671 (OUTLIER) cc_final: 0.6246 (m-80) REVERT: S 846 HIS cc_start: 0.7645 (m-70) cc_final: 0.7294 (m90) REVERT: S 890 MET cc_start: 0.7214 (tpt) cc_final: 0.5626 (ttt) outliers start: 174 outliers final: 45 residues processed: 594 average time/residue: 0.1290 time to fit residues: 117.3283 Evaluate side-chains 286 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 235 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 123 ARG Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 160 PHE Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 123 ARG Chi-restraints excluded: chain L residue 166 ARG Chi-restraints excluded: chain L residue 206 ASN Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 230 TYR Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain S residue 179 ILE Chi-restraints excluded: chain S residue 181 VAL Chi-restraints excluded: chain S residue 214 ILE Chi-restraints excluded: chain S residue 218 LEU Chi-restraints excluded: chain S residue 248 LEU Chi-restraints excluded: chain S residue 260 LYS Chi-restraints excluded: chain S residue 455 ARG Chi-restraints excluded: chain S residue 463 LEU Chi-restraints excluded: chain S residue 487 LEU Chi-restraints excluded: chain S residue 509 THR Chi-restraints excluded: chain S residue 690 TYR Chi-restraints excluded: chain S residue 701 TYR Chi-restraints excluded: chain S residue 717 LYS Chi-restraints excluded: chain S residue 808 LYS Chi-restraints excluded: chain S residue 841 LEU Chi-restraints excluded: chain S residue 843 ARG Chi-restraints excluded: chain S residue 853 ILE Chi-restraints excluded: chain S residue 871 SER Chi-restraints excluded: chain S residue 920 THR Chi-restraints excluded: chain S residue 933 VAL Chi-restraints excluded: chain S residue 1064 LEU Chi-restraints excluded: chain S residue 1160 LEU Chi-restraints excluded: chain S residue 1176 LEU Chi-restraints excluded: chain S residue 1255 LEU Chi-restraints excluded: chain S residue 1299 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.0470 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.1980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 overall best weight: 0.5882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 11 HIS K 103 GLN ** K 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 232 ASN L 89 GLN L 207 GLN L 232 ASN ** L 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 277 ASN A 30 HIS ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN C 4 ASN C 153 GLN C 180 GLN C 188 ASN ** D 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN S 37 ASN S 77 ASN S 178 ASN S 186 GLN S 377 GLN S 403 GLN S 477 GLN S 638 GLN S 721 GLN S 929 GLN S 937 GLN S1202 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.171734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.117470 restraints weight = 55696.857| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.64 r_work: 0.3111 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27289 Z= 0.155 Angle : 0.654 10.648 37631 Z= 0.354 Chirality : 0.043 0.209 4312 Planarity : 0.004 0.056 4149 Dihedral : 19.889 160.009 5492 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.97 % Favored : 92.77 % Rotamer: Outliers : 3.86 % Allowed : 15.95 % Favored : 80.19 % 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: -0.80 (0.16), residues: 2754 helix: 0.66 (0.14), residues: 1325 sheet: -0.52 (0.32), residues: 258 loop : -1.96 (0.17), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 233 TYR 0.027 0.002 TYR A 80 PHE 0.026 0.002 PHE C 204 TRP 0.007 0.001 TRP S 113 HIS 0.014 0.001 HIS L 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (27289) covalent geometry : angle 0.65392 / 0.35 (37631) hydrogen bonds : bond 0.05057 / 3.39 ( 1206) hydrogen bonds : angle 4.80467 / 3.42 ( 3358) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 274 time to evaluate : 1.140 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: K 28 HIS cc_start: 0.6976 (p90) cc_final: 0.6741 (p90) REVERT: K 140 ARG cc_start: 0.7250 (mmp-170) cc_final: 0.6813 (mmp-170) REVERT: K 142 PHE cc_start: 0.4147 (OUTLIER) cc_final: 0.3376 (p90) REVERT: K 170 ASN cc_start: 0.5464 (OUTLIER) cc_final: 0.5128 (p0) REVERT: K 172 ILE cc_start: 0.5804 (mt) cc_final: 0.5391 (mt) REVERT: K 222 ARG cc_start: 0.5252 (ptp90) cc_final: 0.5036 (mtt180) REVERT: L 66 PHE cc_start: 0.6103 (m-80) cc_final: 0.5883 (m-80) REVERT: L 240 MET cc_start: 0.3461 (mtt) cc_final: 0.0106 (tmm) REVERT: A 7 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6839 (tp) REVERT: A 80 TYR cc_start: 0.5655 (m-10) cc_final: 0.5122 (m-80) REVERT: A 212 PHE cc_start: 0.7755 (m-10) cc_final: 0.7530 (m-80) REVERT: B 39 ASP cc_start: 0.8622 (p0) cc_final: 0.8296 (p0) REVERT: B 42 ASN cc_start: 0.8384 (m-40) cc_final: 0.8172 (m-40) REVERT: S 178 ASN cc_start: 0.8001 (t0) cc_final: 0.7772 (t0) REVERT: S 301 ASN cc_start: 0.8901 (m-40) cc_final: 0.8611 (m110) REVERT: S 307 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8523 (mm-30) REVERT: S 455 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8759 (ttp-170) REVERT: S 467 ASP cc_start: 0.8153 (p0) cc_final: 0.7886 (p0) REVERT: S 690 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.6093 (m-80) REVERT: S 703 ARG cc_start: 0.6626 (mpp80) cc_final: 0.6093 (mtm180) REVERT: S 846 HIS cc_start: 0.8148 (m-70) cc_final: 0.7919 (m90) REVERT: S 890 MET cc_start: 0.7152 (tpt) cc_final: 0.5628 (ttt) REVERT: S 893 TYR cc_start: 0.8165 (t80) cc_final: 0.7551 (t80) REVERT: S 930 ARG cc_start: 0.8514 (mtp85) cc_final: 0.8310 (mtp85) REVERT: S 1277 GLU cc_start: 0.6969 (tp30) cc_final: 0.6575 (tp30) outliers start: 96 outliers final: 48 residues processed: 358 average time/residue: 0.1772 time to fit residues: 99.5170 Evaluate side-chains 268 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 215 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 10 LYS Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 170 ASN Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 52 MET Chi-restraints excluded: chain L residue 166 ARG Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain S residue 14 ASN Chi-restraints excluded: chain S residue 179 ILE Chi-restraints excluded: chain S residue 214 ILE Chi-restraints excluded: chain S residue 248 LEU Chi-restraints excluded: chain S residue 314 ASP Chi-restraints excluded: chain S residue 455 ARG Chi-restraints excluded: chain S residue 463 LEU Chi-restraints excluded: chain S residue 487 LEU Chi-restraints excluded: chain S residue 509 THR Chi-restraints excluded: chain S residue 690 TYR Chi-restraints excluded: chain S residue 700 HIS Chi-restraints excluded: chain S residue 701 TYR Chi-restraints excluded: chain S residue 717 LYS Chi-restraints excluded: chain S residue 793 LYS Chi-restraints excluded: chain S residue 820 THR Chi-restraints excluded: chain S residue 853 ILE Chi-restraints excluded: chain S residue 920 THR Chi-restraints excluded: chain S residue 933 VAL Chi-restraints excluded: chain S residue 1064 LEU Chi-restraints excluded: chain S residue 1160 LEU Chi-restraints excluded: chain S residue 1176 LEU Chi-restraints excluded: chain S residue 1255 LEU Chi-restraints excluded: chain S residue 1285 LEU Chi-restraints excluded: chain S residue 1299 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 149 optimal weight: 10.0000 chunk 174 optimal weight: 6.9990 chunk 176 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 251 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 84 HIS L 212 ASN A 26 GLN A 50 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN B 211 ASN ** C 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 ASN S 116 HIS S 320 HIS S 477 GLN S 581 ASN S 937 GLN S1262 GLN S1323 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.165104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.107944 restraints weight = 55231.303| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.95 r_work: 0.2932 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.111 27289 Z= 0.517 Angle : 0.867 10.682 37631 Z= 0.460 Chirality : 0.055 0.297 4312 Planarity : 0.006 0.064 4149 Dihedral : 20.045 157.041 5442 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.21 % Favored : 91.47 % Rotamer: Outliers : 5.22 % Allowed : 17.40 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.16), residues: 2754 helix: 0.42 (0.14), residues: 1314 sheet: -0.86 (0.33), residues: 252 loop : -2.02 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG L 123 TYR 0.039 0.003 TYR S 950 PHE 0.036 0.003 PHE S1022 TRP 0.013 0.002 TRP S 48 HIS 0.014 0.002 HIS S 167 Details of bonding type rmsd/Z covalent geometry : bond 0.01161 / 0.52 (27289) covalent geometry : angle 0.86668 / 0.46 (37631) hydrogen bonds : bond 0.06667 / 4.48 ( 1206) hydrogen bonds : angle 5.03102 / 3.57 ( 3358) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 225 time to evaluate : 0.902 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: K 140 ARG cc_start: 0.7258 (mmp-170) cc_final: 0.6902 (mmp-170) REVERT: K 142 PHE cc_start: 0.4404 (OUTLIER) cc_final: 0.3418 (p90) REVERT: K 160 PHE cc_start: 0.7515 (m-80) cc_final: 0.6932 (t80) REVERT: K 233 ARG cc_start: 0.4258 (OUTLIER) cc_final: 0.3819 (tpm170) REVERT: L 66 PHE cc_start: 0.6022 (m-80) cc_final: 0.5777 (m-80) REVERT: L 210 ASP cc_start: 0.6705 (OUTLIER) cc_final: 0.6312 (t0) REVERT: L 218 MET cc_start: 0.6356 (ppp) cc_final: 0.5596 (ppp) REVERT: A 80 TYR cc_start: 0.5536 (m-10) cc_final: 0.5161 (m-80) REVERT: B 39 ASP cc_start: 0.8654 (p0) cc_final: 0.8303 (p0) REVERT: B 42 ASN cc_start: 0.8399 (m-40) cc_final: 0.8134 (m-40) REVERT: B 83 LEU cc_start: 0.5904 (OUTLIER) cc_final: 0.5394 (mt) REVERT: C 1 MET cc_start: 0.2515 (tpt) cc_final: 0.1939 (tpt) REVERT: C 213 TYR cc_start: 0.6923 (t80) cc_final: 0.6213 (m-80) REVERT: S 76 ARG cc_start: 0.9383 (OUTLIER) cc_final: 0.8318 (tpm170) REVERT: S 178 ASN cc_start: 0.8378 (t0) cc_final: 0.8081 (t0) REVERT: S 307 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8356 (mt-10) REVERT: S 408 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8403 (ptm160) REVERT: S 455 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8848 (ttt180) REVERT: S 690 TYR cc_start: 0.7265 (OUTLIER) cc_final: 0.6228 (m-80) REVERT: S 706 MET cc_start: 0.8482 (mmm) cc_final: 0.8267 (mmt) REVERT: S 815 GLU cc_start: 0.8818 (mp0) cc_final: 0.8568 (mp0) REVERT: S 846 HIS cc_start: 0.8065 (m-70) cc_final: 0.7795 (m90) REVERT: S 855 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7956 (mp10) REVERT: S 890 MET cc_start: 0.6885 (tpt) cc_final: 0.5306 (ttt) REVERT: S 893 TYR cc_start: 0.8220 (t80) cc_final: 0.7435 (t80) REVERT: S 930 ARG cc_start: 0.8604 (mtp85) cc_final: 0.8369 (mtp85) REVERT: S 1202 ASN cc_start: 0.9260 (OUTLIER) cc_final: 0.8899 (m110) REVERT: S 1277 GLU cc_start: 0.7517 (tp30) cc_final: 0.7299 (tp30) outliers start: 130 outliers final: 74 residues processed: 335 average time/residue: 0.1682 time to fit residues: 89.1263 Evaluate side-chains 287 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 203 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 233 ARG Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 67 CYS Chi-restraints excluded: chain L residue 164 PHE Chi-restraints excluded: chain L residue 166 ARG Chi-restraints excluded: chain L residue 210 ASP Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 230 TYR Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain S residue 14 ASN Chi-restraints excluded: chain S residue 76 ARG Chi-restraints excluded: chain S residue 109 GLU Chi-restraints excluded: chain S residue 151 LEU Chi-restraints excluded: chain S residue 179 ILE Chi-restraints excluded: chain S residue 181 VAL Chi-restraints excluded: chain S residue 208 LEU Chi-restraints excluded: chain S residue 214 ILE Chi-restraints excluded: chain S residue 218 LEU Chi-restraints excluded: chain S residue 248 LEU Chi-restraints excluded: chain S residue 398 LEU Chi-restraints excluded: chain S residue 408 ARG Chi-restraints excluded: chain S residue 455 ARG Chi-restraints excluded: chain S residue 463 LEU Chi-restraints excluded: chain S residue 487 LEU Chi-restraints excluded: chain S residue 509 THR Chi-restraints excluded: chain S residue 594 GLN Chi-restraints excluded: chain S residue 606 LEU Chi-restraints excluded: chain S residue 642 THR Chi-restraints excluded: chain S residue 690 TYR Chi-restraints excluded: chain S residue 701 TYR Chi-restraints excluded: chain S residue 717 LYS Chi-restraints excluded: chain S residue 729 GLU Chi-restraints excluded: chain S residue 793 LYS Chi-restraints excluded: chain S residue 808 LYS Chi-restraints excluded: chain S residue 820 THR Chi-restraints excluded: chain S residue 841 LEU Chi-restraints excluded: chain S residue 853 ILE Chi-restraints excluded: chain S residue 855 GLN Chi-restraints excluded: chain S residue 871 SER Chi-restraints excluded: chain S residue 879 ASP Chi-restraints excluded: chain S residue 920 THR Chi-restraints excluded: chain S residue 933 VAL Chi-restraints excluded: chain S residue 1064 LEU Chi-restraints excluded: chain S residue 1160 LEU Chi-restraints excluded: chain S residue 1168 LEU Chi-restraints excluded: chain S residue 1176 LEU Chi-restraints excluded: chain S residue 1202 ASN Chi-restraints excluded: chain S residue 1255 LEU Chi-restraints excluded: chain S residue 1266 LEU Chi-restraints excluded: chain S residue 1285 LEU Chi-restraints excluded: chain S residue 1299 PHE Chi-restraints excluded: chain S residue 1335 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 220 optimal weight: 0.9990 chunk 82 optimal weight: 40.0000 chunk 253 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 205 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 261 optimal weight: 0.9980 chunk 83 optimal weight: 20.0000 chunk 232 optimal weight: 0.6980 chunk 170 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 11 HIS ** K 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 26 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 ASN ** D 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 581 ASN S1287 GLN S1301 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.168684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.114730 restraints weight = 55216.793| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.64 r_work: 0.3038 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27289 Z= 0.149 Angle : 0.632 9.381 37631 Z= 0.343 Chirality : 0.042 0.260 4312 Planarity : 0.004 0.075 4149 Dihedral : 20.021 156.177 5437 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.50 % Favored : 93.25 % Rotamer: Outliers : 3.98 % Allowed : 18.52 % Favored : 77.50 % 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: -0.79 (0.16), residues: 2754 helix: 0.71 (0.14), residues: 1320 sheet: -0.93 (0.32), residues: 264 loop : -1.89 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 203 TYR 0.029 0.002 TYR C 157 PHE 0.025 0.002 PHE A 212 TRP 0.009 0.001 TRP S1059 HIS 0.012 0.001 HIS K 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (27289) covalent geometry : angle 0.63249 / 0.34 (37631) hydrogen bonds : bond 0.04655 / 3.12 ( 1206) hydrogen bonds : angle 4.62435 / 3.29 ( 3358) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 226 time to evaluate : 0.947 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: K 43 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.6454 (mm-30) REVERT: K 140 ARG cc_start: 0.7222 (mmp-170) cc_final: 0.6875 (mmp-170) REVERT: K 142 PHE cc_start: 0.4204 (OUTLIER) cc_final: 0.3302 (p90) REVERT: K 240 MET cc_start: 0.6525 (OUTLIER) cc_final: 0.6239 (ppp) REVERT: L 66 PHE cc_start: 0.6046 (m-80) cc_final: 0.5844 (m-80) REVERT: L 210 ASP cc_start: 0.6535 (OUTLIER) cc_final: 0.6118 (t0) REVERT: L 218 MET cc_start: 0.6219 (ppp) cc_final: 0.5560 (ppp) REVERT: A 80 TYR cc_start: 0.5298 (m-10) cc_final: 0.4880 (m-80) REVERT: A 130 PHE cc_start: 0.6188 (OUTLIER) cc_final: 0.5928 (t80) REVERT: B 39 ASP cc_start: 0.8516 (p0) cc_final: 0.8133 (p0) REVERT: B 42 ASN cc_start: 0.8401 (m-40) cc_final: 0.8122 (m-40) REVERT: B 83 LEU cc_start: 0.5878 (OUTLIER) cc_final: 0.5580 (mp) REVERT: C 1 MET cc_start: 0.2326 (tpt) cc_final: 0.1839 (tpt) REVERT: C 112 LEU cc_start: 0.5914 (mt) cc_final: 0.5081 (tt) REVERT: C 213 TYR cc_start: 0.6947 (t80) cc_final: 0.6277 (m-80) REVERT: S 178 ASN cc_start: 0.8302 (t0) cc_final: 0.7993 (t0) REVERT: S 307 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8567 (mm-30) REVERT: S 690 TYR cc_start: 0.7129 (OUTLIER) cc_final: 0.6006 (m-80) REVERT: S 815 GLU cc_start: 0.8765 (mp0) cc_final: 0.8479 (mp0) REVERT: S 890 MET cc_start: 0.6889 (tpt) cc_final: 0.5476 (ttt) REVERT: S 893 TYR cc_start: 0.7817 (t80) cc_final: 0.7061 (t80) REVERT: S 909 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8414 (mm-40) REVERT: S 930 ARG cc_start: 0.8602 (mtp85) cc_final: 0.8279 (mtp85) REVERT: S 1037 TYR cc_start: 0.7338 (p90) cc_final: 0.7091 (t80) REVERT: S 1277 GLU cc_start: 0.7059 (tp30) cc_final: 0.6682 (tp30) outliers start: 99 outliers final: 56 residues processed: 311 average time/residue: 0.1766 time to fit residues: 86.1318 Evaluate side-chains 264 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 201 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 240 MET Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 52 MET Chi-restraints excluded: chain L residue 166 ARG Chi-restraints excluded: chain L residue 210 ASP Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain S residue 14 ASN Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain S residue 179 ILE Chi-restraints excluded: chain S residue 181 VAL Chi-restraints excluded: chain S residue 208 LEU Chi-restraints excluded: chain S residue 214 ILE Chi-restraints excluded: chain S residue 248 LEU Chi-restraints excluded: chain S residue 260 LYS Chi-restraints excluded: chain S residue 314 ASP Chi-restraints excluded: chain S residue 463 LEU Chi-restraints excluded: chain S residue 487 LEU Chi-restraints excluded: chain S residue 509 THR Chi-restraints excluded: chain S residue 606 LEU Chi-restraints excluded: chain S residue 690 TYR Chi-restraints excluded: chain S residue 700 HIS Chi-restraints excluded: chain S residue 701 TYR Chi-restraints excluded: chain S residue 717 LYS Chi-restraints excluded: chain S residue 793 LYS Chi-restraints excluded: chain S residue 808 LYS Chi-restraints excluded: chain S residue 820 THR Chi-restraints excluded: chain S residue 841 LEU Chi-restraints excluded: chain S residue 853 ILE Chi-restraints excluded: chain S residue 879 ASP Chi-restraints excluded: chain S residue 920 THR Chi-restraints excluded: chain S residue 933 VAL Chi-restraints excluded: chain S residue 1040 LEU Chi-restraints excluded: chain S residue 1064 LEU Chi-restraints excluded: chain S residue 1160 LEU Chi-restraints excluded: chain S residue 1176 LEU Chi-restraints excluded: chain S residue 1255 LEU Chi-restraints excluded: chain S residue 1266 LEU Chi-restraints excluded: chain S residue 1299 PHE Chi-restraints excluded: chain S residue 1301 GLN Chi-restraints excluded: chain S residue 1331 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 135 optimal weight: 30.0000 chunk 27 optimal weight: 3.9990 chunk 50 optimal weight: 20.0000 chunk 79 optimal weight: 8.9990 chunk 258 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 105 optimal weight: 30.0000 chunk 115 optimal weight: 20.0000 chunk 192 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 11 HIS K 29 GLN ** K 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN ** D 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1028 ASN S1202 ASN S1287 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.166520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.109995 restraints weight = 54790.285| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.11 r_work: 0.2971 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 27289 Z= 0.304 Angle : 0.680 11.474 37631 Z= 0.365 Chirality : 0.045 0.260 4312 Planarity : 0.004 0.066 4149 Dihedral : 19.948 154.902 5432 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.59 % Favored : 92.16 % Rotamer: Outliers : 4.66 % Allowed : 18.68 % Favored : 76.66 % 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: -0.84 (0.16), residues: 2754 helix: 0.69 (0.14), residues: 1317 sheet: -0.99 (0.31), residues: 273 loop : -1.93 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 843 TYR 0.029 0.002 TYR D 157 PHE 0.044 0.002 PHE D 130 TRP 0.008 0.001 TRP S1059 HIS 0.007 0.002 HIS S 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00682 / 0.30 (27289) covalent geometry : angle 0.67977 / 0.37 (37631) hydrogen bonds : bond 0.05108 / 3.41 ( 1206) hydrogen bonds : angle 4.63743 / 3.29 ( 3358) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 206 time to evaluate : 0.917 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: K 52 MET cc_start: 0.6455 (ttt) cc_final: 0.6080 (tmm) REVERT: K 140 ARG cc_start: 0.7255 (mmp-170) cc_final: 0.6856 (mmp-170) REVERT: K 142 PHE cc_start: 0.4377 (OUTLIER) cc_final: 0.3343 (p90) REVERT: K 240 MET cc_start: 0.6590 (OUTLIER) cc_final: 0.6225 (ppp) REVERT: L 210 ASP cc_start: 0.6568 (OUTLIER) cc_final: 0.6125 (t0) REVERT: L 218 MET cc_start: 0.6189 (ppp) cc_final: 0.5326 (ppp) REVERT: A 80 TYR cc_start: 0.5294 (m-10) cc_final: 0.4954 (m-80) REVERT: B 39 ASP cc_start: 0.8596 (p0) cc_final: 0.8235 (p0) REVERT: B 42 ASN cc_start: 0.8482 (m-40) cc_final: 0.8221 (m-40) REVERT: B 83 LEU cc_start: 0.5872 (OUTLIER) cc_final: 0.5569 (mp) REVERT: C 1 MET cc_start: 0.2472 (tpt) cc_final: 0.1942 (tpt) REVERT: C 112 LEU cc_start: 0.5919 (mt) cc_final: 0.5100 (tt) REVERT: C 213 TYR cc_start: 0.6908 (t80) cc_final: 0.6214 (m-80) REVERT: S 51 ARG cc_start: 0.9350 (OUTLIER) cc_final: 0.7689 (ttm170) REVERT: S 178 ASN cc_start: 0.8346 (t0) cc_final: 0.8020 (t0) REVERT: S 307 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8627 (mm-30) REVERT: S 408 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8270 (ptm160) REVERT: S 690 TYR cc_start: 0.7249 (OUTLIER) cc_final: 0.6088 (m-80) REVERT: S 717 LYS cc_start: 0.6935 (OUTLIER) cc_final: 0.6732 (mptt) REVERT: S 739 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9283 (mp) REVERT: S 815 GLU cc_start: 0.8827 (mp0) cc_final: 0.8555 (mp0) REVERT: S 890 MET cc_start: 0.6946 (tpt) cc_final: 0.5451 (ttt) REVERT: S 893 TYR cc_start: 0.7930 (t80) cc_final: 0.7161 (t80) REVERT: S 904 SER cc_start: 0.9345 (t) cc_final: 0.9100 (m) REVERT: S 1037 TYR cc_start: 0.7575 (p90) cc_final: 0.7216 (t80) REVERT: S 1255 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9010 (pp) REVERT: S 1277 GLU cc_start: 0.7181 (tp30) cc_final: 0.6751 (tp30) REVERT: S 1301 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7979 (mp10) outliers start: 116 outliers final: 70 residues processed: 302 average time/residue: 0.1752 time to fit residues: 83.8312 Evaluate side-chains 283 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 202 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 240 MET Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain L residue 164 PHE Chi-restraints excluded: chain L residue 166 ARG Chi-restraints excluded: chain L residue 210 ASP Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain S residue 14 ASN Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain S residue 109 GLU Chi-restraints excluded: chain S residue 151 LEU Chi-restraints excluded: chain S residue 179 ILE Chi-restraints excluded: chain S residue 181 VAL Chi-restraints excluded: chain S residue 208 LEU Chi-restraints excluded: chain S residue 214 ILE Chi-restraints excluded: chain S residue 218 LEU Chi-restraints excluded: chain S residue 248 LEU Chi-restraints excluded: chain S residue 408 ARG Chi-restraints excluded: chain S residue 463 LEU Chi-restraints excluded: chain S residue 487 LEU Chi-restraints excluded: chain S residue 509 THR Chi-restraints excluded: chain S residue 567 VAL Chi-restraints excluded: chain S residue 606 LEU Chi-restraints excluded: chain S residue 611 THR Chi-restraints excluded: chain S residue 642 THR Chi-restraints excluded: chain S residue 690 TYR Chi-restraints excluded: chain S residue 701 TYR Chi-restraints excluded: chain S residue 717 LYS Chi-restraints excluded: chain S residue 729 GLU Chi-restraints excluded: chain S residue 739 LEU Chi-restraints excluded: chain S residue 793 LYS Chi-restraints excluded: chain S residue 808 LYS Chi-restraints excluded: chain S residue 820 THR Chi-restraints excluded: chain S residue 841 LEU Chi-restraints excluded: chain S residue 853 ILE Chi-restraints excluded: chain S residue 863 LEU Chi-restraints excluded: chain S residue 920 THR Chi-restraints excluded: chain S residue 933 VAL Chi-restraints excluded: chain S residue 1040 LEU Chi-restraints excluded: chain S residue 1052 THR Chi-restraints excluded: chain S residue 1064 LEU Chi-restraints excluded: chain S residue 1160 LEU Chi-restraints excluded: chain S residue 1176 LEU Chi-restraints excluded: chain S residue 1247 VAL Chi-restraints excluded: chain S residue 1255 LEU Chi-restraints excluded: chain S residue 1266 LEU Chi-restraints excluded: chain S residue 1285 LEU Chi-restraints excluded: chain S residue 1299 PHE Chi-restraints excluded: chain S residue 1301 GLN Chi-restraints excluded: chain S residue 1331 THR Chi-restraints excluded: chain S residue 1335 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 161 optimal weight: 0.8980 chunk 140 optimal weight: 20.0000 chunk 42 optimal weight: 0.0870 chunk 258 optimal weight: 2.9990 chunk 225 optimal weight: 9.9990 chunk 255 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 160 optimal weight: 0.5980 chunk 233 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 57 optimal weight: 50.0000 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 11 HIS ** K 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 9 ASN ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 HIS ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 GLN S1202 ASN S1224 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.168880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.115484 restraints weight = 55170.077| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.59 r_work: 0.3068 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27289 Z= 0.133 Angle : 0.606 13.099 37631 Z= 0.326 Chirality : 0.042 0.270 4312 Planarity : 0.004 0.052 4149 Dihedral : 19.929 154.161 5432 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.57 % Favored : 93.17 % Rotamer: Outliers : 3.62 % Allowed : 19.85 % Favored : 76.54 % 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: -0.64 (0.16), residues: 2754 helix: 0.86 (0.14), residues: 1315 sheet: -1.01 (0.31), residues: 281 loop : -1.80 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 156 TYR 0.020 0.001 TYR C 38 PHE 0.046 0.002 PHE D 130 TRP 0.008 0.001 TRP S 473 HIS 0.011 0.001 HIS K 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (27289) covalent geometry : angle 0.60638 / 0.33 (37631) hydrogen bonds : bond 0.04273 / 2.86 ( 1206) hydrogen bonds : angle 4.41296 / 3.13 ( 3358) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 214 time to evaluate : 0.900 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: K 43 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6674 (mm-30) REVERT: K 44 THR cc_start: 0.6099 (OUTLIER) cc_final: 0.5818 (p) REVERT: K 140 ARG cc_start: 0.7206 (mmp-170) cc_final: 0.6734 (mmp-170) REVERT: K 142 PHE cc_start: 0.4339 (OUTLIER) cc_final: 0.3295 (p90) REVERT: K 240 MET cc_start: 0.6585 (OUTLIER) cc_final: 0.6268 (ppp) REVERT: L 210 ASP cc_start: 0.6582 (OUTLIER) cc_final: 0.6113 (t0) REVERT: L 218 MET cc_start: 0.6334 (ppp) cc_final: 0.5434 (ppp) REVERT: A 130 PHE cc_start: 0.6546 (t80) cc_final: 0.5973 (t80) REVERT: A 206 TYR cc_start: 0.7629 (m-10) cc_final: 0.7305 (m-10) REVERT: A 212 PHE cc_start: 0.7772 (m-80) cc_final: 0.7422 (m-80) REVERT: B 36 TYR cc_start: 0.8706 (m-80) cc_final: 0.8428 (m-80) REVERT: B 39 ASP cc_start: 0.8506 (p0) cc_final: 0.8160 (p0) REVERT: B 42 ASN cc_start: 0.8436 (m-40) cc_final: 0.8193 (m-40) REVERT: B 83 LEU cc_start: 0.5952 (OUTLIER) cc_final: 0.5698 (mp) REVERT: B 186 SER cc_start: 0.8773 (m) cc_final: 0.8528 (p) REVERT: C 1 MET cc_start: 0.2342 (tpt) cc_final: 0.1831 (tpt) REVERT: C 213 TYR cc_start: 0.6933 (t80) cc_final: 0.6251 (m-80) REVERT: S 178 ASN cc_start: 0.8280 (t0) cc_final: 0.8056 (t0) REVERT: S 307 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8834 (mm-30) REVERT: S 408 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8271 (ptm160) REVERT: S 815 GLU cc_start: 0.8906 (mp0) cc_final: 0.8590 (mp0) REVERT: S 890 MET cc_start: 0.6779 (tpt) cc_final: 0.5367 (ttt) REVERT: S 893 TYR cc_start: 0.8006 (t80) cc_final: 0.7370 (t80) REVERT: S 930 ARG cc_start: 0.8589 (mtp85) cc_final: 0.8334 (mtp85) REVERT: S 1037 TYR cc_start: 0.7402 (p90) cc_final: 0.7162 (t80) REVERT: S 1277 GLU cc_start: 0.7137 (tp30) cc_final: 0.6909 (tp30) outliers start: 90 outliers final: 61 residues processed: 293 average time/residue: 0.1660 time to fit residues: 77.3627 Evaluate side-chains 273 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 205 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 211 PHE Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 240 MET Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain L residue 166 ARG Chi-restraints excluded: chain L residue 210 ASP Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain S residue 14 ASN Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain S residue 109 GLU Chi-restraints excluded: chain S residue 179 ILE Chi-restraints excluded: chain S residue 208 LEU Chi-restraints excluded: chain S residue 214 ILE Chi-restraints excluded: chain S residue 218 LEU Chi-restraints excluded: chain S residue 248 LEU Chi-restraints excluded: chain S residue 260 LYS Chi-restraints excluded: chain S residue 408 ARG Chi-restraints excluded: chain S residue 463 LEU Chi-restraints excluded: chain S residue 487 LEU Chi-restraints excluded: chain S residue 509 THR Chi-restraints excluded: chain S residue 567 VAL Chi-restraints excluded: chain S residue 611 THR Chi-restraints excluded: chain S residue 701 TYR Chi-restraints excluded: chain S residue 717 LYS Chi-restraints excluded: chain S residue 793 LYS Chi-restraints excluded: chain S residue 808 LYS Chi-restraints excluded: chain S residue 820 THR Chi-restraints excluded: chain S residue 841 LEU Chi-restraints excluded: chain S residue 853 ILE Chi-restraints excluded: chain S residue 879 ASP Chi-restraints excluded: chain S residue 903 ILE Chi-restraints excluded: chain S residue 920 THR Chi-restraints excluded: chain S residue 933 VAL Chi-restraints excluded: chain S residue 1040 LEU Chi-restraints excluded: chain S residue 1064 LEU Chi-restraints excluded: chain S residue 1160 LEU Chi-restraints excluded: chain S residue 1176 LEU Chi-restraints excluded: chain S residue 1220 CYS Chi-restraints excluded: chain S residue 1255 LEU Chi-restraints excluded: chain S residue 1266 LEU Chi-restraints excluded: chain S residue 1299 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 143 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 215 optimal weight: 0.0370 chunk 4 optimal weight: 9.9990 chunk 168 optimal weight: 3.9990 chunk 62 optimal weight: 50.0000 chunk 264 optimal weight: 1.9990 chunk 253 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 11 HIS ** K 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 HIS ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1301 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.166852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.109033 restraints weight = 54786.375| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 3.16 r_work: 0.2964 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 27289 Z= 0.264 Angle : 0.650 12.430 37631 Z= 0.348 Chirality : 0.044 0.284 4312 Planarity : 0.004 0.049 4149 Dihedral : 19.890 153.079 5430 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.23 % Favored : 92.52 % Rotamer: Outliers : 3.74 % Allowed : 19.93 % Favored : 76.34 % 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: -0.67 (0.16), residues: 2754 helix: 0.84 (0.14), residues: 1315 sheet: -0.92 (0.32), residues: 273 loop : -1.86 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 156 TYR 0.035 0.002 TYR S1019 PHE 0.041 0.002 PHE D 130 TRP 0.009 0.001 TRP S 48 HIS 0.017 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.26 (27289) covalent geometry : angle 0.65011 / 0.35 (37631) hydrogen bonds : bond 0.04768 / 3.18 ( 1206) hydrogen bonds : angle 4.47731 / 3.18 ( 3358) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 208 time to evaluate : 0.887 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: K 43 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6540 (mm-30) REVERT: K 44 THR cc_start: 0.5928 (OUTLIER) cc_final: 0.5644 (p) REVERT: K 52 MET cc_start: 0.6285 (ttt) cc_final: 0.5987 (tmm) REVERT: K 140 ARG cc_start: 0.7183 (mmp-170) cc_final: 0.6838 (mmp-170) REVERT: K 142 PHE cc_start: 0.4493 (OUTLIER) cc_final: 0.3346 (p90) REVERT: K 240 MET cc_start: 0.6534 (OUTLIER) cc_final: 0.6229 (ppp) REVERT: L 210 ASP cc_start: 0.6491 (OUTLIER) cc_final: 0.6149 (t0) REVERT: L 218 MET cc_start: 0.6297 (ppp) cc_final: 0.5298 (ppp) REVERT: L 249 MET cc_start: 0.2824 (pmm) cc_final: 0.2241 (pmm) REVERT: A 191 ASP cc_start: 0.5740 (OUTLIER) cc_final: 0.5493 (t0) REVERT: A 206 TYR cc_start: 0.7613 (m-10) cc_final: 0.7347 (m-10) REVERT: B 36 TYR cc_start: 0.8684 (m-80) cc_final: 0.8443 (m-80) REVERT: B 39 ASP cc_start: 0.8584 (p0) cc_final: 0.8238 (p0) REVERT: B 42 ASN cc_start: 0.8463 (m-40) cc_final: 0.8206 (m-40) REVERT: B 83 LEU cc_start: 0.5834 (OUTLIER) cc_final: 0.5549 (mp) REVERT: B 117 MET cc_start: 0.4866 (pmm) cc_final: 0.3728 (ttt) REVERT: B 186 SER cc_start: 0.8753 (m) cc_final: 0.8521 (p) REVERT: C 1 MET cc_start: 0.2543 (tpt) cc_final: 0.1992 (tpt) REVERT: C 213 TYR cc_start: 0.6860 (t80) cc_final: 0.6109 (m-80) REVERT: S 51 ARG cc_start: 0.9342 (OUTLIER) cc_final: 0.7703 (ttm170) REVERT: S 76 ARG cc_start: 0.9292 (OUTLIER) cc_final: 0.8350 (tpm170) REVERT: S 178 ASN cc_start: 0.8347 (t0) cc_final: 0.8029 (t0) REVERT: S 214 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7352 (pp) REVERT: S 307 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8600 (mm-30) REVERT: S 408 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8232 (ptm160) REVERT: S 815 GLU cc_start: 0.8950 (mp0) cc_final: 0.8652 (mp0) REVERT: S 890 MET cc_start: 0.6698 (tpt) cc_final: 0.5343 (ttt) REVERT: S 893 TYR cc_start: 0.8112 (t80) cc_final: 0.7410 (t80) REVERT: S 904 SER cc_start: 0.9253 (t) cc_final: 0.8997 (m) REVERT: S 930 ARG cc_start: 0.8520 (mtp85) cc_final: 0.8242 (mtp85) REVERT: S 1037 TYR cc_start: 0.7537 (p90) cc_final: 0.7218 (t80) REVERT: S 1255 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.8972 (pp) outliers start: 93 outliers final: 67 residues processed: 287 average time/residue: 0.1680 time to fit residues: 76.4955 Evaluate side-chains 280 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 201 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 240 MET Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain L residue 164 PHE Chi-restraints excluded: chain L residue 166 ARG Chi-restraints excluded: chain L residue 210 ASP Chi-restraints excluded: chain L residue 239 ILE Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain S residue 14 ASN Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain S residue 76 ARG Chi-restraints excluded: chain S residue 179 ILE Chi-restraints excluded: chain S residue 208 LEU Chi-restraints excluded: chain S residue 214 ILE Chi-restraints excluded: chain S residue 218 LEU Chi-restraints excluded: chain S residue 248 LEU Chi-restraints excluded: chain S residue 260 LYS Chi-restraints excluded: chain S residue 408 ARG Chi-restraints excluded: chain S residue 463 LEU Chi-restraints excluded: chain S residue 487 LEU Chi-restraints excluded: chain S residue 509 THR Chi-restraints excluded: chain S residue 560 LEU Chi-restraints excluded: chain S residue 567 VAL Chi-restraints excluded: chain S residue 611 THR Chi-restraints excluded: chain S residue 642 THR Chi-restraints excluded: chain S residue 701 TYR Chi-restraints excluded: chain S residue 717 LYS Chi-restraints excluded: chain S residue 772 VAL Chi-restraints excluded: chain S residue 793 LYS Chi-restraints excluded: chain S residue 808 LYS Chi-restraints excluded: chain S residue 820 THR Chi-restraints excluded: chain S residue 841 LEU Chi-restraints excluded: chain S residue 853 ILE Chi-restraints excluded: chain S residue 863 LEU Chi-restraints excluded: chain S residue 879 ASP Chi-restraints excluded: chain S residue 903 ILE Chi-restraints excluded: chain S residue 920 THR Chi-restraints excluded: chain S residue 933 VAL Chi-restraints excluded: chain S residue 1040 LEU Chi-restraints excluded: chain S residue 1064 LEU Chi-restraints excluded: chain S residue 1160 LEU Chi-restraints excluded: chain S residue 1176 LEU Chi-restraints excluded: chain S residue 1220 CYS Chi-restraints excluded: chain S residue 1255 LEU Chi-restraints excluded: chain S residue 1266 LEU Chi-restraints excluded: chain S residue 1299 PHE Chi-restraints excluded: chain S residue 1301 GLN Chi-restraints excluded: chain S residue 1331 THR Chi-restraints excluded: chain S residue 1335 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 47 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 235 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 169 optimal weight: 0.6980 chunk 42 optimal weight: 50.0000 chunk 41 optimal weight: 3.9990 chunk 257 optimal weight: 0.7980 chunk 225 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 203 optimal weight: 0.6980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 11 HIS ** K 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 HIS ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.167673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.113594 restraints weight = 55042.856| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.65 r_work: 0.3028 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 27289 Z= 0.185 Angle : 0.622 12.753 37631 Z= 0.331 Chirality : 0.042 0.247 4312 Planarity : 0.004 0.046 4149 Dihedral : 19.908 152.647 5430 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.97 % Favored : 92.77 % Rotamer: Outliers : 3.70 % Allowed : 20.33 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.16), residues: 2754 helix: 0.90 (0.14), residues: 1316 sheet: -1.05 (0.31), residues: 288 loop : -1.85 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 930 TYR 0.035 0.002 TYR S1019 PHE 0.044 0.002 PHE D 130 TRP 0.008 0.001 TRP S1059 HIS 0.005 0.001 HIS K 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.19 (27289) covalent geometry : angle 0.62194 / 0.33 (37631) hydrogen bonds : bond 0.04395 / 2.93 ( 1206) hydrogen bonds : angle 4.39606 / 3.13 ( 3358) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 204 time to evaluate : 0.850 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: K 43 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6520 (mm-30) REVERT: K 44 THR cc_start: 0.5965 (OUTLIER) cc_final: 0.5672 (p) REVERT: K 52 MET cc_start: 0.6401 (ttt) cc_final: 0.6092 (tmm) REVERT: K 140 ARG cc_start: 0.7168 (mmp-170) cc_final: 0.6744 (mmp-170) REVERT: K 142 PHE cc_start: 0.4478 (OUTLIER) cc_final: 0.3325 (p90) REVERT: K 240 MET cc_start: 0.6598 (OUTLIER) cc_final: 0.6279 (ppp) REVERT: L 210 ASP cc_start: 0.6505 (OUTLIER) cc_final: 0.6090 (t0) REVERT: L 218 MET cc_start: 0.6620 (ppp) cc_final: 0.6048 (ppp) REVERT: L 249 MET cc_start: 0.2794 (pmm) cc_final: 0.2270 (pmm) REVERT: A 130 PHE cc_start: 0.6701 (t80) cc_final: 0.6022 (t80) REVERT: A 191 ASP cc_start: 0.5541 (OUTLIER) cc_final: 0.5275 (t0) REVERT: A 206 TYR cc_start: 0.7608 (m-80) cc_final: 0.7324 (m-10) REVERT: A 212 PHE cc_start: 0.7767 (m-80) cc_final: 0.7501 (m-80) REVERT: B 36 TYR cc_start: 0.8688 (m-80) cc_final: 0.8416 (m-80) REVERT: B 39 ASP cc_start: 0.8499 (p0) cc_final: 0.8152 (p0) REVERT: B 42 ASN cc_start: 0.8443 (m-40) cc_final: 0.8235 (m-40) REVERT: B 83 LEU cc_start: 0.5793 (OUTLIER) cc_final: 0.5507 (mp) REVERT: B 117 MET cc_start: 0.4907 (pmm) cc_final: 0.3635 (ttt) REVERT: B 149 MET cc_start: 0.8267 (mmm) cc_final: 0.7993 (mmm) REVERT: B 186 SER cc_start: 0.8703 (m) cc_final: 0.8481 (p) REVERT: C 1 MET cc_start: 0.2430 (tpt) cc_final: 0.1873 (tpt) REVERT: C 213 TYR cc_start: 0.6852 (t80) cc_final: 0.6114 (m-80) REVERT: S 178 ASN cc_start: 0.8251 (t0) cc_final: 0.7993 (t0) REVERT: S 214 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7451 (pp) REVERT: S 307 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8565 (mm-30) REVERT: S 408 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8179 (ptm160) REVERT: S 690 TYR cc_start: 0.7249 (OUTLIER) cc_final: 0.5916 (m-80) REVERT: S 739 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9275 (mp) REVERT: S 815 GLU cc_start: 0.8847 (mp0) cc_final: 0.8572 (mp0) REVERT: S 890 MET cc_start: 0.6825 (tpt) cc_final: 0.5367 (ttt) REVERT: S 893 TYR cc_start: 0.7773 (t80) cc_final: 0.7110 (t80) REVERT: S 904 SER cc_start: 0.9279 (t) cc_final: 0.9063 (m) REVERT: S 930 ARG cc_start: 0.8511 (mtp85) cc_final: 0.8248 (mtp85) REVERT: S 1037 TYR cc_start: 0.7496 (p90) cc_final: 0.7243 (t80) REVERT: S 1255 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.8985 (pp) outliers start: 92 outliers final: 67 residues processed: 283 average time/residue: 0.1674 time to fit residues: 75.4823 Evaluate side-chains 280 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 201 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 240 MET Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain L residue 164 PHE Chi-restraints excluded: chain L residue 166 ARG Chi-restraints excluded: chain L residue 210 ASP Chi-restraints excluded: chain L residue 239 ILE Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain S residue 14 ASN Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain S residue 109 GLU Chi-restraints excluded: chain S residue 179 ILE Chi-restraints excluded: chain S residue 208 LEU Chi-restraints excluded: chain S residue 214 ILE Chi-restraints excluded: chain S residue 218 LEU Chi-restraints excluded: chain S residue 248 LEU Chi-restraints excluded: chain S residue 260 LYS Chi-restraints excluded: chain S residue 408 ARG Chi-restraints excluded: chain S residue 463 LEU Chi-restraints excluded: chain S residue 487 LEU Chi-restraints excluded: chain S residue 494 ASP Chi-restraints excluded: chain S residue 509 THR Chi-restraints excluded: chain S residue 567 VAL Chi-restraints excluded: chain S residue 611 THR Chi-restraints excluded: chain S residue 690 TYR Chi-restraints excluded: chain S residue 701 TYR Chi-restraints excluded: chain S residue 717 LYS Chi-restraints excluded: chain S residue 739 LEU Chi-restraints excluded: chain S residue 793 LYS Chi-restraints excluded: chain S residue 808 LYS Chi-restraints excluded: chain S residue 820 THR Chi-restraints excluded: chain S residue 841 LEU Chi-restraints excluded: chain S residue 853 ILE Chi-restraints excluded: chain S residue 879 ASP Chi-restraints excluded: chain S residue 903 ILE Chi-restraints excluded: chain S residue 920 THR Chi-restraints excluded: chain S residue 933 VAL Chi-restraints excluded: chain S residue 1040 LEU Chi-restraints excluded: chain S residue 1064 LEU Chi-restraints excluded: chain S residue 1160 LEU Chi-restraints excluded: chain S residue 1176 LEU Chi-restraints excluded: chain S residue 1220 CYS Chi-restraints excluded: chain S residue 1255 LEU Chi-restraints excluded: chain S residue 1266 LEU Chi-restraints excluded: chain S residue 1299 PHE Chi-restraints excluded: chain S residue 1331 THR Chi-restraints excluded: chain S residue 1335 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 232 optimal weight: 0.9990 chunk 111 optimal weight: 9.9990 chunk 251 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 236 optimal weight: 9.9990 chunk 166 optimal weight: 0.9980 chunk 209 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 250 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 175 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1202 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.168490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.114322 restraints weight = 55183.065| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.54 r_work: 0.3050 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27289 Z= 0.141 Angle : 0.603 12.911 37631 Z= 0.321 Chirality : 0.041 0.230 4312 Planarity : 0.004 0.046 4149 Dihedral : 19.869 152.373 5430 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.68 % Favored : 93.06 % Rotamer: Outliers : 3.21 % Allowed : 20.89 % Favored : 75.89 % 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: -0.57 (0.16), residues: 2754 helix: 0.97 (0.14), residues: 1318 sheet: -1.07 (0.30), residues: 298 loop : -1.81 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 637 TYR 0.016 0.001 TYR S 950 PHE 0.048 0.001 PHE D 130 TRP 0.007 0.001 TRP S1059 HIS 0.004 0.001 HIS S 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (27289) covalent geometry : angle 0.60253 / 0.32 (37631) hydrogen bonds : bond 0.04106 / 2.74 ( 1206) hydrogen bonds : angle 4.29682 / 3.06 ( 3358) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 211 time to evaluate : 1.014 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: K 43 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6629 (mm-30) REVERT: K 44 THR cc_start: 0.5991 (OUTLIER) cc_final: 0.5678 (p) REVERT: K 52 MET cc_start: 0.6467 (ttt) cc_final: 0.6146 (tmm) REVERT: K 140 ARG cc_start: 0.7126 (mmp-170) cc_final: 0.6652 (mmp-170) REVERT: K 142 PHE cc_start: 0.4416 (OUTLIER) cc_final: 0.3292 (p90) REVERT: K 240 MET cc_start: 0.6528 (OUTLIER) cc_final: 0.6196 (ppp) REVERT: L 210 ASP cc_start: 0.6510 (OUTLIER) cc_final: 0.6061 (t0) REVERT: L 218 MET cc_start: 0.6649 (ppp) cc_final: 0.6054 (ppp) REVERT: L 249 MET cc_start: 0.2935 (pmm) cc_final: 0.2448 (pmm) REVERT: A 92 GLU cc_start: 0.7406 (mp0) cc_final: 0.6818 (pm20) REVERT: A 191 ASP cc_start: 0.5552 (OUTLIER) cc_final: 0.5326 (t0) REVERT: A 206 TYR cc_start: 0.7597 (m-80) cc_final: 0.7262 (m-10) REVERT: B 36 TYR cc_start: 0.8690 (m-80) cc_final: 0.8411 (m-80) REVERT: B 39 ASP cc_start: 0.8648 (p0) cc_final: 0.8372 (p0) REVERT: B 42 ASN cc_start: 0.8552 (m-40) cc_final: 0.8287 (m-40) REVERT: B 83 LEU cc_start: 0.5818 (OUTLIER) cc_final: 0.5543 (mp) REVERT: B 117 MET cc_start: 0.4998 (pmm) cc_final: 0.3703 (ttt) REVERT: B 149 MET cc_start: 0.8395 (mmm) cc_final: 0.7838 (mmm) REVERT: B 186 SER cc_start: 0.8773 (m) cc_final: 0.8547 (p) REVERT: C 1 MET cc_start: 0.2266 (tpt) cc_final: 0.1759 (tpt) REVERT: C 213 TYR cc_start: 0.6844 (t80) cc_final: 0.6134 (m-80) REVERT: S 178 ASN cc_start: 0.8218 (t0) cc_final: 0.7987 (t0) REVERT: S 214 ILE cc_start: 0.7883 (OUTLIER) cc_final: 0.7373 (pp) REVERT: S 307 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8845 (mm-30) REVERT: S 408 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8213 (ptm160) REVERT: S 739 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9287 (mp) REVERT: S 815 GLU cc_start: 0.8951 (mp0) cc_final: 0.8654 (mp0) REVERT: S 890 MET cc_start: 0.6728 (tpt) cc_final: 0.5373 (ttt) REVERT: S 893 TYR cc_start: 0.7864 (t80) cc_final: 0.7333 (t80) REVERT: S 904 SER cc_start: 0.9231 (t) cc_final: 0.8996 (m) REVERT: S 930 ARG cc_start: 0.8613 (mtp85) cc_final: 0.8354 (mtp85) REVERT: S 1037 TYR cc_start: 0.7460 (p90) cc_final: 0.7239 (t80) REVERT: S 1255 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.8985 (pp) REVERT: S 1301 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7810 (mp10) outliers start: 80 outliers final: 57 residues processed: 282 average time/residue: 0.1688 time to fit residues: 75.7923 Evaluate side-chains 272 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 203 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 240 MET Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain L residue 166 ARG Chi-restraints excluded: chain L residue 210 ASP Chi-restraints excluded: chain L residue 239 ILE Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain S residue 14 ASN Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain S residue 109 GLU Chi-restraints excluded: chain S residue 179 ILE Chi-restraints excluded: chain S residue 208 LEU Chi-restraints excluded: chain S residue 214 ILE Chi-restraints excluded: chain S residue 218 LEU Chi-restraints excluded: chain S residue 248 LEU Chi-restraints excluded: chain S residue 260 LYS Chi-restraints excluded: chain S residue 408 ARG Chi-restraints excluded: chain S residue 463 LEU Chi-restraints excluded: chain S residue 487 LEU Chi-restraints excluded: chain S residue 509 THR Chi-restraints excluded: chain S residue 567 VAL Chi-restraints excluded: chain S residue 611 THR Chi-restraints excluded: chain S residue 701 TYR Chi-restraints excluded: chain S residue 717 LYS Chi-restraints excluded: chain S residue 739 LEU Chi-restraints excluded: chain S residue 808 LYS Chi-restraints excluded: chain S residue 820 THR Chi-restraints excluded: chain S residue 841 LEU Chi-restraints excluded: chain S residue 853 ILE Chi-restraints excluded: chain S residue 879 ASP Chi-restraints excluded: chain S residue 903 ILE Chi-restraints excluded: chain S residue 920 THR Chi-restraints excluded: chain S residue 933 VAL Chi-restraints excluded: chain S residue 1040 LEU Chi-restraints excluded: chain S residue 1064 LEU Chi-restraints excluded: chain S residue 1220 CYS Chi-restraints excluded: chain S residue 1255 LEU Chi-restraints excluded: chain S residue 1266 LEU Chi-restraints excluded: chain S residue 1291 MET Chi-restraints excluded: chain S residue 1299 PHE Chi-restraints excluded: chain S residue 1301 GLN Chi-restraints excluded: chain S residue 1331 THR Chi-restraints excluded: chain S residue 1335 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 9 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 186 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 92 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 276 optimal weight: 0.1980 chunk 72 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 284 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 overall best weight: 2.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 11 HIS ** K 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 828 GLN ** S1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.167032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.113475 restraints weight = 54823.875| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.62 r_work: 0.3015 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 27289 Z= 0.239 Angle : 0.653 13.009 37631 Z= 0.346 Chirality : 0.044 0.239 4312 Planarity : 0.004 0.044 4149 Dihedral : 19.848 151.860 5426 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.44 % Favored : 92.30 % Rotamer: Outliers : 3.42 % Allowed : 21.09 % Favored : 75.49 % 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: -0.58 (0.16), residues: 2754 helix: 0.95 (0.14), residues: 1315 sheet: -0.95 (0.31), residues: 278 loop : -1.83 (0.18), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG S 411 TYR 0.038 0.002 TYR S1019 PHE 0.048 0.002 PHE D 130 TRP 0.010 0.001 TRP S 48 HIS 0.006 0.001 HIS S 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.24 (27289) covalent geometry : angle 0.65270 / 0.35 (37631) hydrogen bonds : bond 0.04575 / 3.04 ( 1206) hydrogen bonds : angle 4.40266 / 3.13 ( 3358) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 206 time to evaluate : 0.950 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: K 43 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6724 (mm-30) REVERT: K 44 THR cc_start: 0.6050 (OUTLIER) cc_final: 0.5776 (p) REVERT: K 67 CYS cc_start: 0.5813 (m) cc_final: 0.5138 (t) REVERT: K 140 ARG cc_start: 0.7183 (mmp-170) cc_final: 0.6732 (mmp-170) REVERT: K 142 PHE cc_start: 0.4502 (OUTLIER) cc_final: 0.3316 (p90) REVERT: K 240 MET cc_start: 0.6544 (OUTLIER) cc_final: 0.6245 (ppp) REVERT: L 218 MET cc_start: 0.6548 (ppp) cc_final: 0.5987 (ppp) REVERT: L 249 MET cc_start: 0.3010 (pmm) cc_final: 0.2509 (pmm) REVERT: A 2 ARG cc_start: 0.8350 (mpt180) cc_final: 0.8043 (mmm-85) REVERT: A 191 ASP cc_start: 0.5623 (OUTLIER) cc_final: 0.5410 (t0) REVERT: B 39 ASP cc_start: 0.8607 (p0) cc_final: 0.8304 (p0) REVERT: B 42 ASN cc_start: 0.8413 (m-40) cc_final: 0.8195 (m-40) REVERT: B 83 LEU cc_start: 0.5688 (OUTLIER) cc_final: 0.5450 (mp) REVERT: B 149 MET cc_start: 0.8376 (mmm) cc_final: 0.7884 (mmm) REVERT: B 186 SER cc_start: 0.8789 (m) cc_final: 0.8555 (p) REVERT: C 1 MET cc_start: 0.2418 (tpt) cc_final: 0.1859 (tpt) REVERT: C 213 TYR cc_start: 0.6867 (t80) cc_final: 0.6117 (m-80) REVERT: D 116 GLU cc_start: 0.3999 (tt0) cc_final: 0.3442 (pm20) REVERT: S 51 ARG cc_start: 0.9429 (OUTLIER) cc_final: 0.7752 (ttm170) REVERT: S 178 ASN cc_start: 0.8307 (t0) cc_final: 0.8081 (t0) REVERT: S 214 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7368 (pp) REVERT: S 307 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8702 (mm-30) REVERT: S 408 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8295 (ptm160) REVERT: S 739 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9275 (mp) REVERT: S 890 MET cc_start: 0.6706 (tpt) cc_final: 0.5334 (ttt) REVERT: S 904 SER cc_start: 0.9273 (t) cc_final: 0.9042 (m) REVERT: S 930 ARG cc_start: 0.8649 (mtp85) cc_final: 0.8393 (mtp85) REVERT: S 1037 TYR cc_start: 0.7505 (p90) cc_final: 0.7272 (t80) REVERT: S 1255 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9005 (pp) outliers start: 85 outliers final: 63 residues processed: 278 average time/residue: 0.1689 time to fit residues: 74.5649 Evaluate side-chains 277 residues out of total 2494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 203 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 37 ILE Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 240 MET Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain L residue 166 ARG Chi-restraints excluded: chain L residue 239 ILE Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain S residue 14 ASN Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain S residue 109 GLU Chi-restraints excluded: chain S residue 179 ILE Chi-restraints excluded: chain S residue 208 LEU Chi-restraints excluded: chain S residue 214 ILE Chi-restraints excluded: chain S residue 218 LEU Chi-restraints excluded: chain S residue 248 LEU Chi-restraints excluded: chain S residue 260 LYS Chi-restraints excluded: chain S residue 408 ARG Chi-restraints excluded: chain S residue 463 LEU Chi-restraints excluded: chain S residue 487 LEU Chi-restraints excluded: chain S residue 494 ASP Chi-restraints excluded: chain S residue 509 THR Chi-restraints excluded: chain S residue 567 VAL Chi-restraints excluded: chain S residue 611 THR Chi-restraints excluded: chain S residue 701 TYR Chi-restraints excluded: chain S residue 717 LYS Chi-restraints excluded: chain S residue 729 GLU Chi-restraints excluded: chain S residue 739 LEU Chi-restraints excluded: chain S residue 808 LYS Chi-restraints excluded: chain S residue 820 THR Chi-restraints excluded: chain S residue 841 LEU Chi-restraints excluded: chain S residue 853 ILE Chi-restraints excluded: chain S residue 863 LEU Chi-restraints excluded: chain S residue 879 ASP Chi-restraints excluded: chain S residue 903 ILE Chi-restraints excluded: chain S residue 920 THR Chi-restraints excluded: chain S residue 933 VAL Chi-restraints excluded: chain S residue 1040 LEU Chi-restraints excluded: chain S residue 1064 LEU Chi-restraints excluded: chain S residue 1092 GLU Chi-restraints excluded: chain S residue 1220 CYS Chi-restraints excluded: chain S residue 1255 LEU Chi-restraints excluded: chain S residue 1266 LEU Chi-restraints excluded: chain S residue 1291 MET Chi-restraints excluded: chain S residue 1299 PHE Chi-restraints excluded: chain S residue 1331 THR Chi-restraints excluded: chain S residue 1335 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 276 optimal weight: 0.3980 chunk 232 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 58 optimal weight: 50.0000 chunk 149 optimal weight: 6.9990 chunk 244 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 chunk 166 optimal weight: 0.5980 chunk 247 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 206 ASN ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 HIS ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 GLN ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.168806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.115715 restraints weight = 55128.667| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.59 r_work: 0.3064 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27289 Z= 0.129 Angle : 0.615 12.965 37631 Z= 0.327 Chirality : 0.041 0.217 4312 Planarity : 0.004 0.046 4149 Dihedral : 19.849 152.174 5424 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.54 % Favored : 93.21 % Rotamer: Outliers : 2.61 % Allowed : 21.66 % Favored : 75.73 % 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: -0.53 (0.16), residues: 2754 helix: 0.98 (0.14), residues: 1316 sheet: -0.97 (0.30), residues: 294 loop : -1.79 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 156 TYR 0.032 0.001 TYR B 184 PHE 0.048 0.001 PHE D 130 TRP 0.009 0.001 TRP S 473 HIS 0.004 0.001 HIS K 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (27289) covalent geometry : angle 0.61521 / 0.33 (37631) hydrogen bonds : bond 0.04084 / 2.73 ( 1206) hydrogen bonds : angle 4.29205 / 3.06 ( 3358) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10060.10 seconds wall clock time: 186 minutes 17.80 seconds (11177.80 seconds total)