Starting phenix.real_space_refine on Fri Jul 3 17:24:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9c_37364/07_2026/8w9c_37364.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9c_37364/07_2026/8w9c_37364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w9c_37364/07_2026/8w9c_37364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9c_37364/07_2026/8w9c_37364.map" model { file = "/net/cci-nas-00/data/ceres_data/8w9c_37364/07_2026/8w9c_37364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9c_37364/07_2026/8w9c_37364.cif" } resolution = 3.3 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= 0.009 sd= 0.092 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: 6 Type Number sf(0) Gaussians K 2 8.98 5 Zn 7 6.06 5 S 86 5.16 5 C 9769 2.51 5 N 2557 2.21 5 O 2857 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 200 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: 15278 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 5066 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 590} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2884 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 333} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3057 Classifications: {'peptide': 385} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 366} Chain: "C" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1483 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 175} Chain: "D" Number of atoms: 1497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1497 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 176} Chain: "F" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1282 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 147} Chain breaks: 1 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 1 Ad-hoc single atom residues: {' K': 2} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5538 SG CYS E 263 34.086 49.663 104.185 1.00 60.61 S ATOM 5555 SG CYS E 266 36.357 51.085 101.911 1.00 47.09 S ATOM 5708 SG CYS E 286 33.258 52.780 101.241 1.00 40.71 S ATOM 5619 SG CYS E 275 23.463 42.608 109.874 1.00 85.76 S ATOM 5640 SG CYS E 278 26.235 40.933 108.153 1.00 87.11 S ATOM 5843 SG CYS E 303 24.485 42.041 105.361 1.00 82.80 S ATOM 5866 SG CYS E 306 23.157 39.356 107.231 1.00 84.14 S ATOM 6956 SG CYS E 440 69.578 57.886 88.096 1.00 28.90 S ATOM 6982 SG CYS E 443 71.299 57.467 84.950 1.00 29.47 S ATOM 7170 SG CYS E 466 71.957 61.090 86.940 1.00 40.27 S ATOM 6795 SG CYS E 420 81.860 67.677 89.782 1.00 31.10 S ATOM 7051 SG CYS E 451 78.596 68.932 90.092 1.00 25.88 S ATOM 14235 SG CYS F 286 58.783 28.464 28.916 1.00 88.61 S ATOM 14146 SG CYS F 275 59.837 18.553 40.471 1.00 96.34 S ATOM 14393 SG CYS F 306 58.885 20.509 43.480 1.00 89.64 S Time building chain proxies: 3.10, per 1000 atoms: 0.20 Number of scatterers: 15278 At special positions: 0 Unit cell: (138.933, 116.316, 161.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 7 29.99 K 2 19.00 S 86 16.00 O 2857 8.00 N 2557 7.00 C 9769 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 649.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1000 " pdb="ZN ZN B1000 " - pdb=" ND1 HIS B 188 " pdb=" ZN E1000 " pdb="ZN ZN E1000 " - pdb=" ND1 HIS E 283 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 263 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 266 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 286 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 303 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 275 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 306 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 278 " pdb=" ZN E1002 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 443 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 440 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 466 " pdb=" ZN E1003 " pdb="ZN ZN E1003 " - pdb=" ND1 HIS E 448 " pdb="ZN ZN E1003 " - pdb=" SG CYS E 420 " pdb="ZN ZN E1003 " - pdb=" SG CYS E 451 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb=" ND1 HIS F 283 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 286 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 306 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 275 " Number of angles added : 9 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3572 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 10 sheets defined 55.0% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 665 through 677 Processing helix chain 'A' and resid 679 through 694 Processing helix chain 'A' and resid 698 through 708 removed outlier: 3.882A pdb=" N PHE A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 724 Processing helix chain 'A' and resid 772 through 777 removed outlier: 3.519A pdb=" N GLU A 776 " --> pdb=" O ASP A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 839 removed outlier: 3.857A pdb=" N CYS A 830 " --> pdb=" O ARG A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 849 Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 872 through 886 Processing helix chain 'A' and resid 886 through 923 removed outlier: 4.032A pdb=" N THR A 890 " --> pdb=" O HIS A 886 " (cutoff:3.500A) Proline residue: A 892 - end of helix removed outlier: 4.454A pdb=" N VAL A 915 " --> pdb=" O GLU A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 928 Processing helix chain 'A' and resid 931 through 935 removed outlier: 3.908A pdb=" N PHE A 935 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 964 removed outlier: 4.277A pdb=" N ILE A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 999 removed outlier: 3.917A pdb=" N ASP A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1021 Processing helix chain 'A' and resid 1025 through 1038 Processing helix chain 'A' and resid 1065 through 1070 removed outlier: 3.505A pdb=" N HIS A1070 " --> pdb=" O LEU A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1081 removed outlier: 3.852A pdb=" N TYR A1074 " --> pdb=" O HIS A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1127 removed outlier: 3.644A pdb=" N GLN A1127 " --> pdb=" O GLU A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1174 removed outlier: 4.982A pdb=" N GLU A1166 " --> pdb=" O LYS A1162 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ARG A1167 " --> pdb=" O GLN A1163 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR A1174 " --> pdb=" O LYS A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1184 removed outlier: 3.533A pdb=" N LYS A1182 " --> pdb=" O VAL A1178 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU A1184 " --> pdb=" O PHE A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1194 removed outlier: 3.882A pdb=" N MET A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1217 removed outlier: 3.557A pdb=" N GLN A1206 " --> pdb=" O ASP A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1232 removed outlier: 3.552A pdb=" N TYR A1232 " --> pdb=" O LEU A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1242 removed outlier: 3.834A pdb=" N LEU A1239 " --> pdb=" O ALA A1236 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR A1241 " --> pdb=" O LYS A1238 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A1242 " --> pdb=" O LEU A1239 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1259 removed outlier: 3.928A pdb=" N MET A1257 " --> pdb=" O ALA A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1275 removed outlier: 3.563A pdb=" N ALA A1275 " --> pdb=" O LYS A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1292 Processing helix chain 'A' and resid 1329 through 1341 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 303 through 312 Processing helix chain 'E' and resid 315 through 330 removed outlier: 3.643A pdb=" N LEU E 319 " --> pdb=" O SER E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 337 Processing helix chain 'E' and resid 338 through 343 removed outlier: 3.544A pdb=" N ILE E 343 " --> pdb=" O LEU E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.564A pdb=" N LYS E 358 " --> pdb=" O PRO E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 389 Processing helix chain 'E' and resid 430 through 434 removed outlier: 3.665A pdb=" N SER E 434 " --> pdb=" O PRO E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 579 Processing helix chain 'B' and resid 28 through 32 removed outlier: 4.102A pdb=" N TYR B 32 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 55 removed outlier: 3.913A pdb=" N ARG B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 removed outlier: 3.780A pdb=" N LYS B 59 " --> pdb=" O GLY B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 removed outlier: 3.876A pdb=" N CYS B 75 " --> pdb=" O LYS B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 89 Processing helix chain 'B' and resid 92 through 97 removed outlier: 4.352A pdb=" N GLU B 95 " --> pdb=" O ASP B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 104 removed outlier: 3.791A pdb=" N LYS B 103 " --> pdb=" O ARG B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 137 removed outlier: 3.725A pdb=" N GLY B 137 " --> pdb=" O ARG B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 175 removed outlier: 3.576A pdb=" N LEU B 168 " --> pdb=" O ASN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 196 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 243 through 262 Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 287 through 302 removed outlier: 4.727A pdb=" N CYS B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL B 295 " --> pdb=" O HIS B 291 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE B 301 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLY B 302 " --> pdb=" O VAL B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 330 removed outlier: 3.651A pdb=" N VAL B 318 " --> pdb=" O THR B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 347 Processing helix chain 'B' and resid 365 through 381 Processing helix chain 'C' and resid 225 through 240 Processing helix chain 'C' and resid 253 through 266 Processing helix chain 'C' and resid 271 through 297 removed outlier: 3.771A pdb=" N GLN C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLY C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASN C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 316 removed outlier: 3.557A pdb=" N TYR C 306 " --> pdb=" O GLU C 302 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP C 316 " --> pdb=" O LYS C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 325 removed outlier: 3.700A pdb=" N ARG C 324 " --> pdb=" O VAL C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 345 removed outlier: 4.047A pdb=" N LEU C 331 " --> pdb=" O GLY C 327 " (cutoff:3.500A) Proline residue: C 339 - end of helix removed outlier: 3.795A pdb=" N THR C 345 " --> pdb=" O LEU C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 374 removed outlier: 4.126A pdb=" N CYS C 352 " --> pdb=" O ASP C 348 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ASP C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLU C 372 " --> pdb=" O MET C 368 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR C 373 " --> pdb=" O HIS C 369 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 399 removed outlier: 3.537A pdb=" N LEU C 399 " --> pdb=" O GLU C 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 241 removed outlier: 3.548A pdb=" N LYS D 229 " --> pdb=" O PRO D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 266 Processing helix chain 'D' and resid 267 through 269 No H-bonds generated for 'chain 'D' and resid 267 through 269' Processing helix chain 'D' and resid 271 through 297 removed outlier: 5.748A pdb=" N GLY D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ASN D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 316 Processing helix chain 'D' and resid 321 through 325 removed outlier: 3.962A pdb=" N ILE D 325 " --> pdb=" O PRO D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 344 Proline residue: D 339 - end of helix Processing helix chain 'D' and resid 348 through 369 Processing helix chain 'D' and resid 391 through 399 removed outlier: 4.087A pdb=" N LEU D 399 " --> pdb=" O GLU D 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 287 No H-bonds generated for 'chain 'F' and resid 285 through 287' Processing helix chain 'F' and resid 303 through 313 Processing helix chain 'F' and resid 315 through 330 Processing helix chain 'F' and resid 333 through 335 No H-bonds generated for 'chain 'F' and resid 333 through 335' Processing helix chain 'F' and resid 336 through 344 removed outlier: 3.961A pdb=" N ASN F 342 " --> pdb=" O LYS F 338 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE F 343 " --> pdb=" O LEU F 339 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP F 344 " --> pdb=" O LEU F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 576 Processing sheet with id=AA1, first strand: chain 'A' and resid 756 through 757 Processing sheet with id=AA2, first strand: chain 'A' and resid 975 through 978 Processing sheet with id=AA3, first strand: chain 'E' and resid 177 through 179 removed outlier: 6.081A pdb=" N GLU E 177 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA B 22 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL B 308 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU B 269 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU B 181 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N GLN B 270 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE B 183 " --> pdb=" O GLN B 270 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL B 234 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N THR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL B 236 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER B 207 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU B 238 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS B 209 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 273 through 274 Processing sheet with id=AA5, first strand: chain 'E' and resid 437 through 439 Processing sheet with id=AA6, first strand: chain 'E' and resid 505 through 506 removed outlier: 5.833A pdb=" N GLN E 521 " --> pdb=" O ILE E 542 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 244 through 246 Processing sheet with id=AA8, first strand: chain 'D' and resid 244 through 246 Processing sheet with id=AA9, first strand: chain 'F' and resid 260 through 263 removed outlier: 6.954A pdb=" N GLU F 260 " --> pdb=" O SER F 281 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N HIS F 283 " --> pdb=" O GLU F 260 " (cutoff:3.500A) removed outlier: 11.188A pdb=" N PHE F 262 " --> pdb=" O HIS F 283 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 364 through 366 700 hydrogen bonds defined for protein. 2022 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 2546 1.26 - 1.40: 3878 1.40 - 1.53: 8709 1.53 - 1.67: 354 1.67 - 1.81: 128 Bond restraints: 15615 Sorted by residual: bond pdb=" CE1 HIS E 469 " pdb=" NE2 HIS E 469 " ideal model delta sigma weight residual 1.321 1.215 0.106 1.00e-02 1.00e+04 1.12e+02 bond pdb=" C PRO E 471 " pdb=" O PRO E 471 " ideal model delta sigma weight residual 1.233 1.121 0.112 1.18e-02 7.18e+03 9.08e+01 bond pdb=" CG HIS E 469 " pdb=" ND1 HIS E 469 " ideal model delta sigma weight residual 1.378 1.302 0.076 1.10e-02 8.26e+03 4.72e+01 bond pdb=" N ASN E 517 " pdb=" CA ASN E 517 " ideal model delta sigma weight residual 1.457 1.544 -0.087 1.29e-02 6.01e+03 4.50e+01 bond pdb=" CA GLY E 518 " pdb=" C GLY E 518 " ideal model delta sigma weight residual 1.514 1.435 0.079 1.41e-02 5.03e+03 3.17e+01 ... (remaining 15610 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.30: 20997 4.30 - 8.60: 66 8.60 - 12.90: 7 12.90 - 17.19: 4 17.19 - 21.49: 1 Bond angle restraints: 21075 Sorted by residual: angle pdb=" C HIS E 469 " pdb=" N SER E 470 " pdb=" CA SER E 470 " ideal model delta sigma weight residual 120.49 137.08 -16.59 1.42e+00 4.96e-01 1.36e+02 angle pdb=" N PRO E 471 " pdb=" CA PRO E 471 " pdb=" C PRO E 471 " ideal model delta sigma weight residual 111.41 125.55 -14.14 1.50e+00 4.44e-01 8.88e+01 angle pdb=" N GLY E 518 " pdb=" CA GLY E 518 " pdb=" C GLY E 518 " ideal model delta sigma weight residual 113.18 91.69 21.49 2.37e+00 1.78e-01 8.22e+01 angle pdb=" CA ASN E 517 " pdb=" CB ASN E 517 " pdb=" CG ASN E 517 " ideal model delta sigma weight residual 112.60 104.68 7.92 1.00e+00 1.00e+00 6.27e+01 angle pdb=" CA THR E 472 " pdb=" C THR E 472 " pdb=" O THR E 472 " ideal model delta sigma weight residual 120.55 111.40 9.15 1.21e+00 6.83e-01 5.71e+01 ... (remaining 21070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 7944 17.87 - 35.74: 1104 35.74 - 53.62: 314 53.62 - 71.49: 70 71.49 - 89.36: 17 Dihedral angle restraints: 9449 sinusoidal: 3930 harmonic: 5519 Sorted by residual: dihedral pdb=" C ASN E 517 " pdb=" N ASN E 517 " pdb=" CA ASN E 517 " pdb=" CB ASN E 517 " ideal model delta harmonic sigma weight residual -122.60 -160.57 37.97 0 2.50e+00 1.60e-01 2.31e+02 dihedral pdb=" N ASN E 517 " pdb=" C ASN E 517 " pdb=" CA ASN E 517 " pdb=" CB ASN E 517 " ideal model delta harmonic sigma weight residual 122.80 160.71 -37.91 0 2.50e+00 1.60e-01 2.30e+02 dihedral pdb=" N THR E 472 " pdb=" C THR E 472 " pdb=" CA THR E 472 " pdb=" CB THR E 472 " ideal model delta harmonic sigma weight residual 123.40 141.04 -17.64 0 2.50e+00 1.60e-01 4.98e+01 ... (remaining 9446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.320: 2273 0.320 - 0.641: 2 0.641 - 0.961: 1 0.961 - 1.281: 0 1.281 - 1.601: 1 Chirality restraints: 2277 Sorted by residual: chirality pdb=" CA ASN E 517 " pdb=" N ASN E 517 " pdb=" C ASN E 517 " pdb=" CB ASN E 517 " both_signs ideal model delta sigma weight residual False 2.51 0.91 1.60 2.00e-01 2.50e+01 6.41e+01 chirality pdb=" CA THR E 472 " pdb=" N THR E 472 " pdb=" C THR E 472 " pdb=" CB THR E 472 " both_signs ideal model delta sigma weight residual False 2.53 1.79 0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" CA PRO E 471 " pdb=" N PRO E 471 " pdb=" C PRO E 471 " pdb=" CB PRO E 471 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.43 2.00e-01 2.50e+01 4.56e+00 ... (remaining 2274 not shown) Planarity restraints: 2694 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS E 469 " -0.053 2.00e-02 2.50e+03 4.65e-02 3.24e+01 pdb=" CG HIS E 469 " 0.083 2.00e-02 2.50e+03 pdb=" ND1 HIS E 469 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS E 469 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 HIS E 469 " 0.009 2.00e-02 2.50e+03 pdb=" NE2 HIS E 469 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 470 " -0.021 2.00e-02 2.50e+03 4.09e-02 1.67e+01 pdb=" C SER E 470 " 0.071 2.00e-02 2.50e+03 pdb=" O SER E 470 " -0.025 2.00e-02 2.50e+03 pdb=" N PRO E 471 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 471 " 0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C PRO E 471 " -0.065 2.00e-02 2.50e+03 pdb=" O PRO E 471 " 0.025 2.00e-02 2.50e+03 pdb=" N THR E 472 " 0.021 2.00e-02 2.50e+03 ... (remaining 2691 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.60: 186 2.60 - 3.23: 15432 3.23 - 3.87: 29121 3.87 - 4.50: 39218 4.50 - 5.14: 63639 Nonbonded interactions: 147596 Sorted by model distance: nonbonded pdb=" N GLY E 518 " pdb=" N ASN E 519 " model vdw 1.965 2.560 nonbonded pdb=" OD2 ASP B 274 " pdb="ZN ZN B1000 " model vdw 1.981 2.230 nonbonded pdb=" OD1 ASP B 186 " pdb="ZN ZN B1000 " model vdw 2.038 2.230 nonbonded pdb=" O THR E 472 " pdb=" OG1 THR E 472 " model vdw 2.061 3.040 nonbonded pdb=" O LEU E 171 " pdb=" OG1 THR E 172 " model vdw 2.086 3.040 ... (remaining 147591 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 'C' selection = (chain 'D' and resid 219 through 401) } 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: 0.010 Normalize map: mean=0, sd=1: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.600 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 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 : 0.010 0.632 15634 Z= 0.390 Angle : 0.883 38.479 21084 Z= 0.473 Chirality : 0.058 1.601 2277 Planarity : 0.005 0.072 2694 Dihedral : 18.159 89.361 5877 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.14 % Favored : 93.64 % Rotamer: Outliers : 7.42 % Allowed : 19.10 % Favored : 73.48 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.11 (0.16), residues: 1840 helix: -1.40 (0.14), residues: 924 sheet: -2.00 (0.55), residues: 86 loop : -2.84 (0.18), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 136 TYR 0.018 0.001 TYR E 356 PHE 0.027 0.002 PHE C 374 TRP 0.028 0.002 TRP E 492 HIS 0.035 0.001 HIS E 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.27 (15615) covalent geometry : angle 0.78867 / 0.47 (21075) hydrogen bonds : bond 0.13518 / 8.95 ( 700) hydrogen bonds : angle 5.86930 / 4.21 ( 2022) metal coordination : bond 0.24323 / 12.06 ( 19) metal coordination : angle 19.24830 / 16.18 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 304 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 679 LYS cc_start: 0.6075 (mmtt) cc_final: 0.5817 (pttp) REVERT: A 1256 LEU cc_start: 0.7187 (OUTLIER) cc_final: 0.6961 (tt) REVERT: A 1337 TYR cc_start: -0.2315 (OUTLIER) cc_final: -0.3763 (t80) REVERT: E 107 LYS cc_start: 0.6088 (OUTLIER) cc_final: 0.5673 (tptp) REVERT: E 262 PHE cc_start: 0.5551 (m-80) cc_final: 0.4830 (m-80) REVERT: E 287 LEU cc_start: 0.6995 (mt) cc_final: 0.6721 (mt) REVERT: E 345 SER cc_start: 0.8436 (m) cc_final: 0.7519 (t) REVERT: E 490 LYS cc_start: 0.7578 (pttp) cc_final: 0.6780 (mmtm) REVERT: B 72 GLN cc_start: 0.7593 (tt0) cc_final: 0.7248 (mm-40) REVERT: B 114 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.7037 (m-30) REVERT: B 248 ARG cc_start: 0.6650 (ttt180) cc_final: 0.6391 (ttt90) REVERT: D 223 GLN cc_start: 0.7824 (tm-30) cc_final: 0.7512 (tm-30) REVERT: D 228 LEU cc_start: 0.6574 (OUTLIER) cc_final: 0.6339 (mp) REVERT: D 315 LYS cc_start: 0.7158 (pttt) cc_final: 0.6800 (tppt) REVERT: D 350 GLN cc_start: 0.6929 (OUTLIER) cc_final: 0.6528 (tt0) REVERT: D 356 ILE cc_start: 0.7956 (pp) cc_final: 0.7513 (pp) REVERT: F 285 LEU cc_start: 0.7224 (mt) cc_final: 0.6425 (tt) REVERT: F 560 MET cc_start: 0.7888 (tpt) cc_final: 0.7603 (tpt) outliers start: 127 outliers final: 83 residues processed: 417 average time/residue: 0.1319 time to fit residues: 80.0940 Evaluate side-chains 319 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 230 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 836 ASN Chi-restraints excluded: chain A residue 907 ARG Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 953 SER Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain A residue 1235 LYS Chi-restraints excluded: chain A residue 1241 THR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1262 THR Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1299 ASN Chi-restraints excluded: chain A residue 1313 SER Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 371 GLN Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 454 ARG Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 543 ASP Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 350 GLN Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 353 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 GLN A 961 ASN A1039 ASN A1075 GLN A1216 ASN A1247 GLN E 352 GLN E 376 ASN E 433 ASN ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 521 GLN E 541 GLN E 580 ASN ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 HIS B 235 ASN B 317 ASN B 364 ASN C 305 GLN C 358 GLN D 350 GLN D 358 GLN D 375 ASN D 380 ASN F 259 ASN F 331 ASN F 355 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.217391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.175366 restraints weight = 17759.431| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 2.70 r_work: 0.3903 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15634 Z= 0.145 Angle : 0.660 11.285 21084 Z= 0.345 Chirality : 0.043 0.235 2277 Planarity : 0.005 0.106 2694 Dihedral : 9.542 67.538 2184 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.87 % Favored : 94.08 % Rotamer: Outliers : 5.61 % Allowed : 21.20 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.64 (0.18), residues: 1840 helix: -0.11 (0.16), residues: 955 sheet: -1.57 (0.56), residues: 80 loop : -2.27 (0.19), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 799 TYR 0.015 0.001 TYR C 326 PHE 0.025 0.002 PHE E 387 TRP 0.023 0.002 TRP E 428 HIS 0.005 0.001 HIS B 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (15615) covalent geometry : angle 0.65161 / 0.34 (21075) hydrogen bonds : bond 0.04616 / 2.99 ( 700) hydrogen bonds : angle 4.55991 / 3.26 ( 2022) metal coordination : bond 0.00875 / 0.54 ( 19) metal coordination : angle 4.97052 / 3.67 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 259 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 679 LYS cc_start: 0.5987 (mmtt) cc_final: 0.5350 (ptmm) REVERT: A 912 TRP cc_start: 0.5677 (OUTLIER) cc_final: 0.4952 (t-100) REVERT: A 1256 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6610 (tt) REVERT: A 1294 MET cc_start: 0.5489 (OUTLIER) cc_final: 0.5251 (ptt) REVERT: A 1337 TYR cc_start: -0.2856 (OUTLIER) cc_final: -0.3709 (t80) REVERT: E 107 LYS cc_start: 0.5911 (OUTLIER) cc_final: 0.5465 (tptp) REVERT: E 287 LEU cc_start: 0.7310 (mt) cc_final: 0.7109 (mt) REVERT: E 345 SER cc_start: 0.8536 (m) cc_final: 0.8150 (t) REVERT: E 490 LYS cc_start: 0.7634 (pttp) cc_final: 0.6379 (mmtm) REVERT: E 491 VAL cc_start: 0.7253 (OUTLIER) cc_final: 0.6756 (p) REVERT: E 570 GLN cc_start: 0.8307 (pt0) cc_final: 0.8036 (pt0) REVERT: B 72 GLN cc_start: 0.8261 (tt0) cc_final: 0.7412 (mm-40) REVERT: B 114 ASP cc_start: 0.7500 (OUTLIER) cc_final: 0.6880 (m-30) REVERT: B 116 LEU cc_start: 0.8051 (tp) cc_final: 0.7784 (tt) REVERT: B 248 ARG cc_start: 0.7500 (ttt180) cc_final: 0.7216 (ttt90) REVERT: C 358 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.6702 (mt0) REVERT: D 247 ARG cc_start: 0.7379 (ptp90) cc_final: 0.6845 (ptp90) REVERT: D 296 MET cc_start: 0.7577 (ptp) cc_final: 0.7240 (pmm) REVERT: D 315 LYS cc_start: 0.7443 (pttt) cc_final: 0.6892 (tppt) REVERT: F 285 LEU cc_start: 0.7480 (mt) cc_final: 0.6923 (pt) REVERT: F 309 LYS cc_start: 0.8101 (mmmt) cc_final: 0.7687 (mttt) outliers start: 96 outliers final: 53 residues processed: 333 average time/residue: 0.1174 time to fit residues: 58.5358 Evaluate side-chains 285 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 224 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 836 ASN Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 907 ARG Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1299 ASN Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 358 GLN Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 353 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 139 optimal weight: 0.7980 chunk 160 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 161 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 857 HIS A1299 ASN ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 HIS B 317 ASN B 330 ASN C 375 ASN ** F 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.216223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.175799 restraints weight = 17733.224| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 2.57 r_work: 0.3919 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 15634 Z= 0.157 Angle : 0.651 9.523 21084 Z= 0.341 Chirality : 0.043 0.232 2277 Planarity : 0.005 0.049 2694 Dihedral : 8.272 59.634 2100 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.03 % Favored : 93.91 % Rotamer: Outliers : 5.78 % Allowed : 22.37 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.08 (0.19), residues: 1840 helix: 0.38 (0.16), residues: 955 sheet: -1.40 (0.56), residues: 80 loop : -2.03 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 814 TYR 0.021 0.001 TYR A1240 PHE 0.029 0.002 PHE E 387 TRP 0.021 0.002 TRP E 492 HIS 0.006 0.001 HIS B 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (15615) covalent geometry : angle 0.64624 / 0.34 (21075) hydrogen bonds : bond 0.04491 / 2.89 ( 700) hydrogen bonds : angle 4.38965 / 3.14 ( 2022) metal coordination : bond 0.00673 / 0.41 ( 19) metal coordination : angle 4.00279 / 2.83 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 238 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 679 LYS cc_start: 0.6012 (mmtt) cc_final: 0.5395 (ptmm) REVERT: A 690 ASN cc_start: 0.7686 (OUTLIER) cc_final: 0.5228 (t0) REVERT: A 912 TRP cc_start: 0.5742 (OUTLIER) cc_final: 0.4993 (t-100) REVERT: A 1287 ARG cc_start: 0.6843 (tmt170) cc_final: 0.6532 (tmt170) REVERT: A 1294 MET cc_start: 0.5439 (OUTLIER) cc_final: 0.5202 (ptt) REVERT: A 1316 TYR cc_start: 0.8344 (OUTLIER) cc_final: 0.7783 (t80) REVERT: A 1337 TYR cc_start: -0.2721 (OUTLIER) cc_final: -0.3543 (t80) REVERT: E 107 LYS cc_start: 0.5686 (OUTLIER) cc_final: 0.5220 (tptp) REVERT: E 115 LEU cc_start: 0.5541 (OUTLIER) cc_final: 0.4964 (mp) REVERT: E 287 LEU cc_start: 0.7398 (mt) cc_final: 0.7176 (mt) REVERT: E 342 ASN cc_start: 0.7205 (OUTLIER) cc_final: 0.6750 (m110) REVERT: E 490 LYS cc_start: 0.7655 (pttp) cc_final: 0.6467 (mmtm) REVERT: E 491 VAL cc_start: 0.7314 (OUTLIER) cc_final: 0.6847 (p) REVERT: E 514 TYR cc_start: 0.7571 (OUTLIER) cc_final: 0.6914 (t80) REVERT: E 570 GLN cc_start: 0.8118 (pt0) cc_final: 0.7898 (pt0) REVERT: B 72 GLN cc_start: 0.8206 (tt0) cc_final: 0.7421 (mm-40) REVERT: B 114 ASP cc_start: 0.7512 (m-30) cc_final: 0.6867 (m-30) REVERT: B 116 LEU cc_start: 0.7996 (tp) cc_final: 0.7792 (tt) REVERT: B 248 ARG cc_start: 0.7543 (ttt180) cc_final: 0.7207 (ttt90) REVERT: B 252 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6924 (mt-10) REVERT: C 285 LEU cc_start: 0.6010 (OUTLIER) cc_final: 0.5733 (tp) REVERT: D 247 ARG cc_start: 0.7474 (ptp90) cc_final: 0.6982 (ptp90) REVERT: F 285 LEU cc_start: 0.7507 (mt) cc_final: 0.6922 (pt) outliers start: 99 outliers final: 57 residues processed: 318 average time/residue: 0.1216 time to fit residues: 58.0221 Evaluate side-chains 290 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 222 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 836 ASN Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 907 ARG Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 914 LYS Chi-restraints excluded: chain A residue 1134 SER Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1316 TYR Chi-restraints excluded: chain A residue 1325 LYS Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 342 ASN Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 514 TYR Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 353 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 60 optimal weight: 0.0870 chunk 71 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 171 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 330 ASN C 295 ASN C 350 GLN C 375 ASN ** F 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.219314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.179075 restraints weight = 17674.598| |-----------------------------------------------------------------------------| r_work (start): 0.4222 rms_B_bonded: 2.56 r_work: 0.3940 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15634 Z= 0.126 Angle : 0.604 10.033 21084 Z= 0.318 Chirality : 0.042 0.223 2277 Planarity : 0.004 0.060 2694 Dihedral : 7.578 59.395 2090 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.33 % Favored : 94.62 % Rotamer: Outliers : 4.26 % Allowed : 23.89 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.61 (0.19), residues: 1840 helix: 0.76 (0.17), residues: 958 sheet: -1.15 (0.55), residues: 84 loop : -1.81 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 814 TYR 0.030 0.001 TYR A1240 PHE 0.036 0.001 PHE E 387 TRP 0.021 0.001 TRP E 492 HIS 0.005 0.001 HIS A1036 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (15615) covalent geometry : angle 0.60106 / 0.32 (21075) hydrogen bonds : bond 0.04089 / 2.64 ( 700) hydrogen bonds : angle 4.21086 / 3.01 ( 2022) metal coordination : bond 0.00470 / 0.28 ( 19) metal coordination : angle 3.12174 / 2.19 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 249 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 679 LYS cc_start: 0.5877 (mmtt) cc_final: 0.5507 (ttpp) REVERT: A 690 ASN cc_start: 0.7226 (OUTLIER) cc_final: 0.5183 (t0) REVERT: A 912 TRP cc_start: 0.5615 (OUTLIER) cc_final: 0.4923 (t-100) REVERT: A 986 TYR cc_start: 0.7479 (m-80) cc_final: 0.7198 (m-80) REVERT: A 1235 LYS cc_start: 0.7288 (OUTLIER) cc_final: 0.6468 (pttm) REVERT: A 1287 ARG cc_start: 0.6827 (tmt170) cc_final: 0.6500 (tmt170) REVERT: A 1294 MET cc_start: 0.5859 (OUTLIER) cc_final: 0.5654 (ptt) REVERT: A 1337 TYR cc_start: -0.2627 (OUTLIER) cc_final: -0.3326 (t80) REVERT: E 107 LYS cc_start: 0.5559 (OUTLIER) cc_final: 0.5099 (tptp) REVERT: E 115 LEU cc_start: 0.5386 (OUTLIER) cc_final: 0.4819 (mp) REVERT: E 305 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7548 (mm-30) REVERT: E 342 ASN cc_start: 0.7137 (OUTLIER) cc_final: 0.6774 (m110) REVERT: E 387 PHE cc_start: 0.3069 (OUTLIER) cc_final: 0.2773 (p90) REVERT: E 408 ASP cc_start: 0.7330 (t0) cc_final: 0.7023 (t70) REVERT: E 490 LYS cc_start: 0.7605 (pttp) cc_final: 0.6399 (mmtm) REVERT: E 491 VAL cc_start: 0.7306 (OUTLIER) cc_final: 0.6828 (p) REVERT: B 72 GLN cc_start: 0.8169 (tt0) cc_final: 0.7375 (mm-40) REVERT: B 114 ASP cc_start: 0.7335 (OUTLIER) cc_final: 0.6713 (m-30) REVERT: B 116 LEU cc_start: 0.7884 (tp) cc_final: 0.7645 (tt) REVERT: B 248 ARG cc_start: 0.7568 (ttt180) cc_final: 0.7236 (ttt90) REVERT: C 285 LEU cc_start: 0.6184 (OUTLIER) cc_final: 0.5956 (tp) REVERT: C 394 TYR cc_start: 0.7718 (t80) cc_final: 0.7302 (t80) REVERT: D 247 ARG cc_start: 0.7439 (ptp90) cc_final: 0.6863 (ptp90) REVERT: F 285 LEU cc_start: 0.7506 (mt) cc_final: 0.6949 (pt) REVERT: F 309 LYS cc_start: 0.8226 (mmmt) cc_final: 0.7826 (mttt) REVERT: F 350 GLN cc_start: 0.7170 (mt0) cc_final: 0.6948 (mt0) outliers start: 73 outliers final: 41 residues processed: 305 average time/residue: 0.1232 time to fit residues: 56.4073 Evaluate side-chains 274 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 221 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 836 ASN Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1235 LYS Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1325 LYS Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 342 ASN Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 288 TYR Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 353 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 47 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 72 optimal weight: 0.0370 chunk 13 optimal weight: 0.9980 chunk 107 optimal weight: 8.9990 chunk 15 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 132 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1283 GLN ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 519 ASN ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 330 ASN F 295 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.220827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.179632 restraints weight = 17728.704| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 2.50 r_work: 0.3950 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15634 Z= 0.120 Angle : 0.598 10.641 21084 Z= 0.315 Chirality : 0.042 0.231 2277 Planarity : 0.004 0.052 2694 Dihedral : 7.052 59.787 2075 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.05 % Favored : 94.89 % Rotamer: Outliers : 4.38 % Allowed : 24.01 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.28 (0.19), residues: 1840 helix: 1.01 (0.17), residues: 948 sheet: -0.95 (0.56), residues: 84 loop : -1.59 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 814 TYR 0.022 0.001 TYR A1240 PHE 0.034 0.001 PHE E 387 TRP 0.019 0.001 TRP E 492 HIS 0.004 0.001 HIS B 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (15615) covalent geometry : angle 0.59455 / 0.31 (21075) hydrogen bonds : bond 0.03922 / 2.52 ( 700) hydrogen bonds : angle 4.12276 / 2.95 ( 2022) metal coordination : bond 0.00379 / 0.22 ( 19) metal coordination : angle 2.96290 / 2.05 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 240 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 679 LYS cc_start: 0.5837 (mmtt) cc_final: 0.5487 (ttpp) REVERT: A 690 ASN cc_start: 0.7565 (OUTLIER) cc_final: 0.5375 (t0) REVERT: A 912 TRP cc_start: 0.5624 (OUTLIER) cc_final: 0.5002 (t-100) REVERT: A 986 TYR cc_start: 0.7561 (m-80) cc_final: 0.7282 (m-80) REVERT: A 1235 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6751 (pttt) REVERT: A 1287 ARG cc_start: 0.6693 (tmt170) cc_final: 0.6441 (tmt170) REVERT: E 107 LYS cc_start: 0.5435 (OUTLIER) cc_final: 0.4989 (tptp) REVERT: E 187 TRP cc_start: 0.4774 (m-90) cc_final: 0.4555 (m-90) REVERT: E 342 ASN cc_start: 0.7147 (OUTLIER) cc_final: 0.6810 (m110) REVERT: E 408 ASP cc_start: 0.7268 (t0) cc_final: 0.6647 (t0) REVERT: E 490 LYS cc_start: 0.7441 (pttp) cc_final: 0.6289 (mmtm) REVERT: E 514 TYR cc_start: 0.7736 (OUTLIER) cc_final: 0.6975 (t80) REVERT: B 72 GLN cc_start: 0.8165 (tt0) cc_final: 0.7344 (mm-40) REVERT: B 114 ASP cc_start: 0.7333 (OUTLIER) cc_final: 0.6667 (m-30) REVERT: B 116 LEU cc_start: 0.7867 (tp) cc_final: 0.7658 (tt) REVERT: B 248 ARG cc_start: 0.7491 (ttt180) cc_final: 0.7266 (ttt90) REVERT: C 394 TYR cc_start: 0.7759 (t80) cc_final: 0.7393 (t80) REVERT: D 247 ARG cc_start: 0.7405 (ptp90) cc_final: 0.6873 (ptp90) REVERT: D 256 MET cc_start: 0.6434 (ttp) cc_final: 0.4898 (tpt) REVERT: D 290 ASP cc_start: 0.5849 (OUTLIER) cc_final: 0.5586 (p0) REVERT: F 285 LEU cc_start: 0.7482 (mt) cc_final: 0.6951 (pt) REVERT: F 309 LYS cc_start: 0.8090 (mmmt) cc_final: 0.7685 (mttt) REVERT: F 562 GLN cc_start: 0.8303 (tt0) cc_final: 0.8077 (tp-100) outliers start: 75 outliers final: 44 residues processed: 299 average time/residue: 0.1139 time to fit residues: 52.4609 Evaluate side-chains 269 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 217 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1235 LYS Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1325 LYS Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain E residue 342 ASN Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 420 CYS Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 514 TYR Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 288 TYR Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 353 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 5 optimal weight: 0.5980 chunk 18 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 163 optimal weight: 0.9990 chunk 166 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 84 optimal weight: 0.1980 chunk 6 optimal weight: 0.9990 chunk 178 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 884 HIS A1127 GLN E 430 HIS ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.219846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.178762 restraints weight = 17723.898| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 2.47 r_work: 0.3937 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15634 Z= 0.127 Angle : 0.598 9.282 21084 Z= 0.316 Chirality : 0.041 0.212 2277 Planarity : 0.004 0.048 2694 Dihedral : 6.382 56.578 2060 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.65 % Favored : 94.29 % Rotamer: Outliers : 4.15 % Allowed : 24.82 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.20), residues: 1840 helix: 1.17 (0.17), residues: 948 sheet: -0.57 (0.58), residues: 82 loop : -1.52 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 814 TYR 0.030 0.001 TYR A1016 PHE 0.039 0.002 PHE E 387 TRP 0.019 0.001 TRP E 492 HIS 0.005 0.001 HIS B 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (15615) covalent geometry : angle 0.59567 / 0.32 (21075) hydrogen bonds : bond 0.03955 / 2.56 ( 700) hydrogen bonds : angle 4.10561 / 2.95 ( 2022) metal coordination : bond 0.00361 / 0.20 ( 19) metal coordination : angle 2.72850 / 1.94 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 233 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 679 LYS cc_start: 0.5832 (mmtt) cc_final: 0.5494 (ttpp) REVERT: A 690 ASN cc_start: 0.7661 (OUTLIER) cc_final: 0.5729 (t0) REVERT: A 912 TRP cc_start: 0.5678 (OUTLIER) cc_final: 0.4992 (t-100) REVERT: A 986 TYR cc_start: 0.7629 (m-80) cc_final: 0.7373 (m-80) REVERT: A 1016 TYR cc_start: 0.8171 (m-80) cc_final: 0.7717 (m-80) REVERT: A 1228 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6871 (tp) REVERT: A 1235 LYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6788 (pttt) REVERT: A 1287 ARG cc_start: 0.6675 (tmt170) cc_final: 0.6373 (tmt170) REVERT: A 1316 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.7759 (t80) REVERT: A 1325 LYS cc_start: 0.1151 (OUTLIER) cc_final: 0.0493 (tptt) REVERT: E 305 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7574 (mm-30) REVERT: E 316 MET cc_start: 0.6935 (ttt) cc_final: 0.5805 (tpp) REVERT: E 334 LYS cc_start: 0.7659 (tptp) cc_final: 0.7320 (tppp) REVERT: E 342 ASN cc_start: 0.7118 (OUTLIER) cc_final: 0.6772 (m110) REVERT: E 408 ASP cc_start: 0.7276 (t0) cc_final: 0.6683 (t0) REVERT: E 490 LYS cc_start: 0.7355 (pttp) cc_final: 0.6246 (mmtm) REVERT: E 514 TYR cc_start: 0.7717 (OUTLIER) cc_final: 0.6872 (t80) REVERT: B 53 MET cc_start: 0.7712 (tpp) cc_final: 0.7415 (mmp) REVERT: B 72 GLN cc_start: 0.8146 (tt0) cc_final: 0.7342 (mm-40) REVERT: B 114 ASP cc_start: 0.7322 (OUTLIER) cc_final: 0.6789 (m-30) REVERT: B 248 ARG cc_start: 0.7536 (ttt180) cc_final: 0.7258 (ttt90) REVERT: C 394 TYR cc_start: 0.7782 (t80) cc_final: 0.7434 (t80) REVERT: D 247 ARG cc_start: 0.7474 (ptp90) cc_final: 0.6931 (ptp90) REVERT: D 290 ASP cc_start: 0.5818 (OUTLIER) cc_final: 0.5481 (p0) REVERT: F 285 LEU cc_start: 0.7587 (mt) cc_final: 0.7017 (pt) REVERT: F 350 GLN cc_start: 0.7092 (mt0) cc_final: 0.6803 (mt0) REVERT: F 562 GLN cc_start: 0.8289 (tt0) cc_final: 0.8047 (tp-100) outliers start: 71 outliers final: 45 residues processed: 285 average time/residue: 0.1194 time to fit residues: 51.7556 Evaluate side-chains 268 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 213 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1235 LYS Chi-restraints excluded: chain A residue 1316 TYR Chi-restraints excluded: chain A residue 1325 LYS Chi-restraints excluded: chain E residue 342 ASN Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 514 TYR Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 288 TYR Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain F residue 304 ASN Chi-restraints excluded: chain F residue 353 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 122 optimal weight: 0.0970 chunk 136 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 154 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 chunk 176 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 overall best weight: 1.1180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 330 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.217848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.176407 restraints weight = 17424.075| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 2.37 r_work: 0.3921 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 15634 Z= 0.148 Angle : 0.633 11.569 21084 Z= 0.330 Chirality : 0.042 0.193 2277 Planarity : 0.004 0.048 2694 Dihedral : 6.217 55.671 2051 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.98 % Favored : 93.97 % Rotamer: Outliers : 4.21 % Allowed : 24.94 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.15 (0.20), residues: 1840 helix: 1.08 (0.17), residues: 954 sheet: -0.48 (0.58), residues: 82 loop : -1.56 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 814 TYR 0.018 0.001 TYR A1016 PHE 0.034 0.002 PHE E 387 TRP 0.019 0.001 TRP E 492 HIS 0.006 0.001 HIS B 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (15615) covalent geometry : angle 0.62994 / 0.33 (21075) hydrogen bonds : bond 0.04100 / 2.64 ( 700) hydrogen bonds : angle 4.21239 / 3.02 ( 2022) metal coordination : bond 0.00422 / 0.24 ( 19) metal coordination : angle 2.86684 / 2.01 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 215 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 679 LYS cc_start: 0.5976 (mmtt) cc_final: 0.5648 (ttpp) REVERT: A 690 ASN cc_start: 0.7696 (OUTLIER) cc_final: 0.5581 (t0) REVERT: A 912 TRP cc_start: 0.5791 (OUTLIER) cc_final: 0.5079 (t-100) REVERT: A 986 TYR cc_start: 0.7613 (m-80) cc_final: 0.7380 (m-80) REVERT: A 1007 LYS cc_start: 0.8525 (mttt) cc_final: 0.8130 (ttpt) REVERT: A 1016 TYR cc_start: 0.8114 (m-80) cc_final: 0.7669 (m-80) REVERT: A 1228 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6866 (tp) REVERT: A 1235 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6830 (pttp) REVERT: A 1316 TYR cc_start: 0.8253 (OUTLIER) cc_final: 0.7694 (t80) REVERT: A 1325 LYS cc_start: 0.0903 (OUTLIER) cc_final: 0.0599 (tppt) REVERT: E 316 MET cc_start: 0.6912 (ttt) cc_final: 0.5683 (tpp) REVERT: E 334 LYS cc_start: 0.7676 (tptp) cc_final: 0.7348 (tppp) REVERT: E 342 ASN cc_start: 0.7204 (OUTLIER) cc_final: 0.6805 (m110) REVERT: E 408 ASP cc_start: 0.7296 (t0) cc_final: 0.6720 (t0) REVERT: E 490 LYS cc_start: 0.7347 (pttp) cc_final: 0.6264 (mmtm) REVERT: E 514 TYR cc_start: 0.7673 (OUTLIER) cc_final: 0.6953 (t80) REVERT: B 72 GLN cc_start: 0.8149 (tt0) cc_final: 0.7347 (mm-40) REVERT: B 114 ASP cc_start: 0.7469 (OUTLIER) cc_final: 0.6945 (m-30) REVERT: B 128 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7433 (mpp) REVERT: B 248 ARG cc_start: 0.7549 (ttt180) cc_final: 0.7204 (ttt90) REVERT: C 315 LYS cc_start: 0.7985 (tppt) cc_final: 0.7634 (ttmm) REVERT: C 394 TYR cc_start: 0.7856 (t80) cc_final: 0.7576 (t80) REVERT: D 247 ARG cc_start: 0.7714 (ptp90) cc_final: 0.7155 (ptp90) REVERT: D 290 ASP cc_start: 0.6006 (OUTLIER) cc_final: 0.5687 (p0) REVERT: F 285 LEU cc_start: 0.7529 (mt) cc_final: 0.6957 (pt) REVERT: F 571 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7793 (mt-10) outliers start: 72 outliers final: 50 residues processed: 271 average time/residue: 0.1171 time to fit residues: 48.9364 Evaluate side-chains 263 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 202 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1134 SER Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1235 LYS Chi-restraints excluded: chain A residue 1241 THR Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1316 TYR Chi-restraints excluded: chain A residue 1325 LYS Chi-restraints excluded: chain E residue 342 ASN Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 420 CYS Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 514 TYR Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 288 TYR Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain F residue 304 ASN Chi-restraints excluded: chain F residue 353 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 36 optimal weight: 5.9990 chunk 60 optimal weight: 0.0040 chunk 64 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 160 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.215608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.173183 restraints weight = 17811.885| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 2.62 r_work: 0.3875 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 15634 Z= 0.181 Angle : 0.665 12.476 21084 Z= 0.349 Chirality : 0.044 0.191 2277 Planarity : 0.004 0.051 2694 Dihedral : 6.191 54.776 2046 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.52 % Favored : 93.42 % Rotamer: Outliers : 3.97 % Allowed : 25.18 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.36 (0.19), residues: 1840 helix: 0.89 (0.17), residues: 962 sheet: -0.44 (0.58), residues: 82 loop : -1.66 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1009 TYR 0.033 0.002 TYR A1240 PHE 0.036 0.002 PHE E 567 TRP 0.027 0.002 TRP D 236 HIS 0.007 0.001 HIS B 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (15615) covalent geometry : angle 0.66180 / 0.35 (21075) hydrogen bonds : bond 0.04385 / 2.80 ( 700) hydrogen bonds : angle 4.33411 / 3.10 ( 2022) metal coordination : bond 0.00554 / 0.32 ( 19) metal coordination : angle 3.17898 / 2.20 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 222 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 679 LYS cc_start: 0.6079 (mmtt) cc_final: 0.5718 (ttpp) REVERT: A 690 ASN cc_start: 0.7782 (OUTLIER) cc_final: 0.6214 (t0) REVERT: A 912 TRP cc_start: 0.5907 (OUTLIER) cc_final: 0.5160 (t-100) REVERT: A 986 TYR cc_start: 0.7652 (m-80) cc_final: 0.7431 (m-80) REVERT: A 1007 LYS cc_start: 0.8543 (mttt) cc_final: 0.8166 (ttpt) REVERT: A 1016 TYR cc_start: 0.8121 (m-80) cc_final: 0.7577 (m-80) REVERT: A 1228 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6673 (tp) REVERT: A 1235 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.6818 (pttt) REVERT: A 1316 TYR cc_start: 0.8297 (OUTLIER) cc_final: 0.7726 (t80) REVERT: E 168 LYS cc_start: 0.6887 (mttm) cc_final: 0.6524 (mtmt) REVERT: E 305 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7523 (mm-30) REVERT: E 316 MET cc_start: 0.6692 (ttt) cc_final: 0.5671 (tpp) REVERT: E 334 LYS cc_start: 0.7919 (tptp) cc_final: 0.7612 (tppp) REVERT: E 342 ASN cc_start: 0.7483 (OUTLIER) cc_final: 0.6968 (m110) REVERT: E 408 ASP cc_start: 0.7330 (t0) cc_final: 0.7015 (t70) REVERT: E 490 LYS cc_start: 0.7417 (pttp) cc_final: 0.6293 (mmtm) REVERT: E 507 GLU cc_start: 0.7504 (tt0) cc_final: 0.6540 (pm20) REVERT: E 514 TYR cc_start: 0.7804 (OUTLIER) cc_final: 0.7176 (t80) REVERT: B 72 GLN cc_start: 0.8198 (tt0) cc_final: 0.7387 (mm-40) REVERT: B 114 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7043 (m-30) REVERT: B 128 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7433 (mpp) REVERT: B 248 ARG cc_start: 0.7550 (ttt180) cc_final: 0.7212 (ttt90) REVERT: B 344 TYR cc_start: 0.6066 (t80) cc_final: 0.5618 (p90) REVERT: D 226 ILE cc_start: 0.6258 (mt) cc_final: 0.6044 (tt) REVERT: D 247 ARG cc_start: 0.7699 (ptp90) cc_final: 0.6709 (ptp90) REVERT: D 290 ASP cc_start: 0.6073 (OUTLIER) cc_final: 0.5592 (p0) REVERT: F 309 LYS cc_start: 0.8209 (mmmt) cc_final: 0.7846 (mttt) REVERT: F 571 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7940 (mt-10) outliers start: 68 outliers final: 51 residues processed: 278 average time/residue: 0.1179 time to fit residues: 49.9960 Evaluate side-chains 269 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 208 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1134 SER Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1235 LYS Chi-restraints excluded: chain A residue 1241 THR Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1314 ILE Chi-restraints excluded: chain A residue 1316 TYR Chi-restraints excluded: chain A residue 1325 LYS Chi-restraints excluded: chain E residue 342 ASN Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 420 CYS Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 466 CYS Chi-restraints excluded: chain E residue 514 TYR Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain F residue 304 ASN Chi-restraints excluded: chain F residue 353 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 144 optimal weight: 0.9990 chunk 171 optimal weight: 10.0000 chunk 169 optimal weight: 0.0000 chunk 120 optimal weight: 1.9990 chunk 118 optimal weight: 0.0980 chunk 31 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 110 optimal weight: 0.4980 chunk 4 optimal weight: 0.9980 chunk 159 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.221390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.180778 restraints weight = 17634.996| |-----------------------------------------------------------------------------| r_work (start): 0.4227 rms_B_bonded: 2.54 r_work: 0.3955 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15634 Z= 0.120 Angle : 0.610 11.988 21084 Z= 0.319 Chirality : 0.041 0.180 2277 Planarity : 0.004 0.052 2694 Dihedral : 5.972 56.611 2046 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.56 % Allowed : 25.88 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.01 (0.20), residues: 1840 helix: 1.15 (0.17), residues: 963 sheet: -0.27 (0.57), residues: 82 loop : -1.45 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1009 TYR 0.019 0.001 TYR A1240 PHE 0.031 0.001 PHE E 567 TRP 0.021 0.002 TRP E 428 HIS 0.004 0.001 HIS B 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (15615) covalent geometry : angle 0.60832 / 0.32 (21075) hydrogen bonds : bond 0.03734 / 2.40 ( 700) hydrogen bonds : angle 4.14390 / 2.98 ( 2022) metal coordination : bond 0.00381 / 0.22 ( 19) metal coordination : angle 2.50750 / 1.78 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 224 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 679 LYS cc_start: 0.5823 (mmtt) cc_final: 0.5494 (ttpp) REVERT: A 690 ASN cc_start: 0.7632 (OUTLIER) cc_final: 0.6170 (t0) REVERT: A 912 TRP cc_start: 0.5675 (OUTLIER) cc_final: 0.5039 (t-100) REVERT: A 986 TYR cc_start: 0.7588 (m-80) cc_final: 0.7356 (m-80) REVERT: A 1007 LYS cc_start: 0.8481 (mttt) cc_final: 0.7970 (ttpt) REVERT: A 1016 TYR cc_start: 0.8104 (m-80) cc_final: 0.7525 (m-80) REVERT: A 1235 LYS cc_start: 0.7200 (OUTLIER) cc_final: 0.6823 (pttp) REVERT: A 1261 LYS cc_start: 0.4928 (mmtm) cc_final: 0.4716 (tppt) REVERT: A 1325 LYS cc_start: 0.0924 (OUTLIER) cc_final: 0.0340 (tptt) REVERT: E 316 MET cc_start: 0.6661 (ttt) cc_final: 0.5824 (tpp) REVERT: E 334 LYS cc_start: 0.7625 (tptp) cc_final: 0.7290 (tppp) REVERT: E 342 ASN cc_start: 0.7352 (OUTLIER) cc_final: 0.6935 (m110) REVERT: E 408 ASP cc_start: 0.7252 (t0) cc_final: 0.6837 (t0) REVERT: E 490 LYS cc_start: 0.7310 (pttp) cc_final: 0.6235 (mmtm) REVERT: E 514 TYR cc_start: 0.7655 (OUTLIER) cc_final: 0.6924 (t80) REVERT: E 556 TYR cc_start: 0.7926 (m-80) cc_final: 0.7066 (m-80) REVERT: B 72 GLN cc_start: 0.8139 (tt0) cc_final: 0.7271 (mm-40) REVERT: B 114 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.6784 (m-30) REVERT: B 128 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7435 (mpp) REVERT: B 248 ARG cc_start: 0.7538 (ttt180) cc_final: 0.7256 (ttt90) REVERT: C 394 TYR cc_start: 0.7738 (t80) cc_final: 0.7394 (t80) REVERT: D 226 ILE cc_start: 0.6263 (mt) cc_final: 0.6045 (tt) REVERT: D 247 ARG cc_start: 0.7784 (ptp90) cc_final: 0.6814 (ptp90) REVERT: D 290 ASP cc_start: 0.5897 (OUTLIER) cc_final: 0.5474 (p0) REVERT: F 285 LEU cc_start: 0.7546 (mt) cc_final: 0.6979 (pt) REVERT: F 309 LYS cc_start: 0.8125 (mmmt) cc_final: 0.7778 (mttt) REVERT: F 346 HIS cc_start: 0.7234 (OUTLIER) cc_final: 0.6600 (t-170) REVERT: F 555 ILE cc_start: 0.6606 (pp) cc_final: 0.6272 (mt) REVERT: F 562 GLN cc_start: 0.8272 (tt0) cc_final: 0.7929 (tp40) outliers start: 61 outliers final: 42 residues processed: 272 average time/residue: 0.1155 time to fit residues: 48.2108 Evaluate side-chains 267 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 215 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1235 LYS Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1325 LYS Chi-restraints excluded: chain E residue 342 ASN Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 420 CYS Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 514 TYR Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 288 TYR Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain F residue 346 HIS Chi-restraints excluded: chain F residue 353 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 158 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 154 optimal weight: 9.9990 chunk 171 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 153 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 173 optimal weight: 0.0670 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 430 HIS ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.217801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.178164 restraints weight = 17915.147| |-----------------------------------------------------------------------------| r_work (start): 0.4334 rms_B_bonded: 2.59 r_work: 0.4039 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15634 Z= 0.122 Angle : 0.623 12.214 21084 Z= 0.323 Chirality : 0.042 0.221 2277 Planarity : 0.004 0.052 2694 Dihedral : 5.867 55.685 2046 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.50 % Allowed : 26.46 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.14 (0.20), residues: 1840 helix: 1.24 (0.17), residues: 965 sheet: -0.14 (0.57), residues: 82 loop : -1.36 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 814 TYR 0.016 0.001 TYR B 176 PHE 0.032 0.002 PHE A1017 TRP 0.019 0.001 TRP E 428 HIS 0.005 0.001 HIS B 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (15615) covalent geometry : angle 0.62057 / 0.32 (21075) hydrogen bonds : bond 0.03728 / 2.39 ( 700) hydrogen bonds : angle 4.15584 / 2.99 ( 2022) metal coordination : bond 0.00321 / 0.18 ( 19) metal coordination : angle 2.45611 / 1.76 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 219 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 679 LYS cc_start: 0.5794 (mmtt) cc_final: 0.5341 (ptmm) REVERT: A 690 ASN cc_start: 0.7572 (OUTLIER) cc_final: 0.6086 (t0) REVERT: A 912 TRP cc_start: 0.5786 (OUTLIER) cc_final: 0.5241 (t-100) REVERT: A 986 TYR cc_start: 0.7522 (m-80) cc_final: 0.7249 (m-80) REVERT: A 1007 LYS cc_start: 0.8492 (mttt) cc_final: 0.8032 (ttpt) REVERT: A 1016 TYR cc_start: 0.7966 (m-80) cc_final: 0.7437 (m-80) REVERT: A 1228 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6845 (tp) REVERT: A 1235 LYS cc_start: 0.7283 (OUTLIER) cc_final: 0.6912 (pttp) REVERT: A 1325 LYS cc_start: 0.1202 (OUTLIER) cc_final: 0.0514 (tptt) REVERT: E 305 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7501 (mm-30) REVERT: E 316 MET cc_start: 0.6601 (ttt) cc_final: 0.5876 (tpp) REVERT: E 334 LYS cc_start: 0.7592 (tptp) cc_final: 0.7288 (tppp) REVERT: E 342 ASN cc_start: 0.7341 (OUTLIER) cc_final: 0.6928 (m110) REVERT: E 490 LYS cc_start: 0.7367 (pttp) cc_final: 0.6445 (mmtm) REVERT: E 514 TYR cc_start: 0.7824 (OUTLIER) cc_final: 0.7176 (t80) REVERT: E 556 TYR cc_start: 0.7960 (m-80) cc_final: 0.7056 (m-80) REVERT: B 72 GLN cc_start: 0.8135 (tt0) cc_final: 0.7378 (mm-40) REVERT: B 105 ASN cc_start: 0.8698 (t0) cc_final: 0.8330 (t0) REVERT: B 114 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.6817 (m-30) REVERT: B 207 SER cc_start: 0.7952 (OUTLIER) cc_final: 0.7386 (m) REVERT: B 248 ARG cc_start: 0.7580 (ttt180) cc_final: 0.7285 (ttt90) REVERT: C 394 TYR cc_start: 0.7729 (t80) cc_final: 0.7432 (t80) REVERT: D 226 ILE cc_start: 0.6289 (mt) cc_final: 0.6059 (tt) REVERT: D 247 ARG cc_start: 0.7862 (ptp90) cc_final: 0.6899 (ptp90) REVERT: D 290 ASP cc_start: 0.5939 (OUTLIER) cc_final: 0.5510 (p0) REVERT: F 285 LEU cc_start: 0.7627 (mt) cc_final: 0.7057 (pt) REVERT: F 309 LYS cc_start: 0.8129 (mmmt) cc_final: 0.7752 (mttt) REVERT: F 346 HIS cc_start: 0.7146 (OUTLIER) cc_final: 0.6504 (t-170) REVERT: F 365 LYS cc_start: 0.6168 (mmmt) cc_final: 0.5187 (ptpp) REVERT: F 555 ILE cc_start: 0.6443 (pp) cc_final: 0.6107 (mt) outliers start: 60 outliers final: 44 residues processed: 265 average time/residue: 0.1153 time to fit residues: 46.9879 Evaluate side-chains 268 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 213 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1070 HIS Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1235 LYS Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1325 LYS Chi-restraints excluded: chain E residue 342 ASN Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 420 CYS Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 514 TYR Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 288 TYR Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain F residue 346 HIS Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 567 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 178 optimal weight: 0.0060 chunk 135 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 30.0000 chunk 74 optimal weight: 0.5980 chunk 90 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.217398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.176800 restraints weight = 17762.110| |-----------------------------------------------------------------------------| r_work (start): 0.4314 rms_B_bonded: 2.70 r_work: 0.4002 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15634 Z= 0.130 Angle : 0.631 13.090 21084 Z= 0.330 Chirality : 0.042 0.197 2277 Planarity : 0.004 0.051 2694 Dihedral : 5.856 55.221 2046 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.33 % Allowed : 26.58 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.17 (0.20), residues: 1840 helix: 1.25 (0.17), residues: 965 sheet: -0.08 (0.57), residues: 82 loop : -1.31 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 814 TYR 0.017 0.001 TYR B 176 PHE 0.057 0.002 PHE E 567 TRP 0.018 0.001 TRP E 492 HIS 0.005 0.001 HIS B 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (15615) covalent geometry : angle 0.62929 / 0.33 (21075) hydrogen bonds : bond 0.03830 / 2.46 ( 700) hydrogen bonds : angle 4.23568 / 3.04 ( 2022) metal coordination : bond 0.00339 / 0.18 ( 19) metal coordination : angle 2.48404 / 1.79 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4088.90 seconds wall clock time: 71 minutes 5.91 seconds (4265.91 seconds total)