Starting phenix.real_space_refine on Sat May 17 05:03:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9c_37364/05_2025/8w9c_37364.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9c_37364/05_2025/8w9c_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_37364/05_2025/8w9c_37364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9c_37364/05_2025/8w9c_37364.map" model { file = "/net/cci-nas-00/data/ceres_data/8w9c_37364/05_2025/8w9c_37364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9c_37364/05_2025/8w9c_37364.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 3 Unusual residues: {' K': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 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: 9.78, per 1000 atoms: 0.64 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: 3.70 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.44 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: 4.59 Time building geometry restraints manager: 4.32 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: 0.000 Normalize map: mean=0, sd=1: 1.740 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: 0.040 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 37.510 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.070 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 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 : 14.24 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.028 0.002 TRP E 492 HIS 0.035 0.001 HIS E 469 PHE 0.027 0.002 PHE C 374 TYR 0.018 0.001 TYR E 356 ARG 0.011 0.000 ARG B 136 Details of bonding type rmsd hydrogen bonds : bond 0.13518 ( 700) hydrogen bonds : angle 5.86930 ( 2022) metal coordination : bond 0.24323 ( 19) metal coordination : angle 19.24830 ( 9) covalent geometry : bond 0.00457 (15615) covalent geometry : angle 0.78867 (21075) *********************** 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 : 1.726 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: 0.6960 (tt) REVERT: A 1337 TYR cc_start: -0.2315 (OUTLIER) cc_final: -0.3761 (t80) REVERT: E 107 LYS cc_start: 0.6088 (OUTLIER) cc_final: 0.5672 (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: 0.6779 (mmtm) REVERT: E 565 LYS cc_start: 0.7619 (ttpt) cc_final: 0.7201 (ttpt) 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: 0.7117 (m-30) REVERT: B 248 ARG cc_start: 0.6650 (ttt180) cc_final: 0.6390 (ttt90) REVERT: D 223 GLN cc_start: 0.7824 (tm-30) cc_final: 0.7514 (tm-30) REVERT: D 228 LEU cc_start: 0.6574 (OUTLIER) cc_final: 0.6334 (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: 0.6526 (tt0) REVERT: D 356 ILE cc_start: 0.7956 (pp) cc_final: 0.7512 (pp) REVERT: F 285 LEU cc_start: 0.7224 (mt) cc_final: 0.6426 (tt) REVERT: F 560 MET cc_start: 0.7887 (tpt) cc_final: 0.7604 (tpt) outliers start: 127 outliers final: 83 residues processed: 417 average time/residue: 0.2942 time to fit residues: 175.2423 Evaluate side-chains 320 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 231 time to evaluate : 1.755 ------------------------------------------------------------------------------- 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 155 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 74 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 87 optimal weight: 0.0970 chunk 107 optimal weight: 0.9980 chunk 167 optimal weight: 9.9990 overall best weight: 1.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 GLN A 961 ASN A1039 ASN A1075 GLN A1216 ASN A1247 GLN A1299 ASN E 352 GLN E 376 ASN E 433 ASN ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 541 GLN E 580 ASN ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 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 302 HIS F 331 ASN F 355 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.215345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.173887 restraints weight = 17705.471| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 2.50 r_work: 0.3880 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 15634 Z= 0.165 Angle : 0.678 10.919 21084 Z= 0.354 Chirality : 0.044 0.237 2277 Planarity : 0.005 0.106 2694 Dihedral : 9.727 67.655 2184 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.09 % Favored : 93.86 % Rotamer: Outliers : 6.25 % Allowed : 21.38 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.18), residues: 1840 helix: -0.18 (0.16), residues: 954 sheet: -1.63 (0.56), residues: 80 loop : -2.31 (0.19), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 428 HIS 0.005 0.001 HIS B 150 PHE 0.027 0.002 PHE E 387 TYR 0.015 0.001 TYR C 326 ARG 0.007 0.001 ARG D 300 Details of bonding type rmsd hydrogen bonds : bond 0.04788 ( 700) hydrogen bonds : angle 4.62689 ( 2022) metal coordination : bond 0.00889 ( 19) metal coordination : angle 5.26597 ( 9) covalent geometry : bond 0.00380 (15615) covalent geometry : angle 0.66931 (21075) *********************** 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 365 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 258 time to evaluate : 1.565 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 912 TRP cc_start: 0.5740 (OUTLIER) cc_final: 0.5008 (t-100) REVERT: A 1256 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6630 (tt) REVERT: A 1294 MET cc_start: 0.5329 (OUTLIER) cc_final: 0.5094 (ptt) REVERT: A 1316 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.7780 (t80) REVERT: A 1337 TYR cc_start: -0.2656 (OUTLIER) cc_final: -0.3584 (t80) REVERT: E 107 LYS cc_start: 0.5754 (OUTLIER) cc_final: 0.5285 (tptp) REVERT: E 345 SER cc_start: 0.8536 (m) cc_final: 0.8150 (t) REVERT: E 490 LYS cc_start: 0.7575 (pttp) cc_final: 0.6436 (mmtm) REVERT: E 565 LYS cc_start: 0.8170 (ttpt) cc_final: 0.7883 (ttpt) REVERT: E 570 GLN cc_start: 0.8273 (pt0) cc_final: 0.7990 (pt0) REVERT: B 72 GLN cc_start: 0.8240 (tt0) cc_final: 0.7417 (mm-40) REVERT: B 114 ASP cc_start: 0.7587 (OUTLIER) cc_final: 0.7095 (m-30) REVERT: B 116 LEU cc_start: 0.8014 (tp) cc_final: 0.7740 (tt) REVERT: B 248 ARG cc_start: 0.7495 (ttt180) cc_final: 0.7150 (ttt90) REVERT: B 259 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7809 (mtp) REVERT: C 358 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.6641 (mt0) REVERT: D 247 ARG cc_start: 0.7355 (ptp90) cc_final: 0.6826 (ptp90) REVERT: D 296 MET cc_start: 0.7550 (ptp) cc_final: 0.7227 (pmm) REVERT: D 315 LYS cc_start: 0.7447 (pttt) cc_final: 0.6889 (tppt) REVERT: F 285 LEU cc_start: 0.7508 (mt) cc_final: 0.6943 (pt) outliers start: 107 outliers final: 59 residues processed: 342 average time/residue: 0.2772 time to fit residues: 139.2217 Evaluate side-chains 292 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 224 time to evaluate : 1.778 ------------------------------------------------------------------------------- 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 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 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 1235 LYS 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 1316 TYR 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 371 GLN 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 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 134 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 226 VAL 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 241 LYS 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 136 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 75 optimal weight: 0.3980 chunk 134 optimal weight: 0.5980 chunk 96 optimal weight: 0.0060 chunk 5 optimal weight: 0.6980 chunk 93 optimal weight: 8.9990 chunk 160 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 66 optimal weight: 0.1980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1283 GLN ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 521 GLN B 317 ASN B 330 ASN C 350 GLN ** F 350 GLN ** 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 = 0.4688 r_free = 0.4688 target = 0.221360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.180143 restraints weight = 17607.473| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 2.35 r_work: 0.3969 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15634 Z= 0.118 Angle : 0.601 9.944 21084 Z= 0.316 Chirality : 0.041 0.222 2277 Planarity : 0.004 0.048 2694 Dihedral : 8.084 60.611 2113 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.16 % Favored : 94.78 % Rotamer: Outliers : 4.38 % Allowed : 23.07 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.19), residues: 1840 helix: 0.63 (0.17), residues: 945 sheet: -1.42 (0.55), residues: 80 loop : -1.91 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 236 HIS 0.005 0.001 HIS A1036 PHE 0.024 0.001 PHE E 387 TYR 0.018 0.001 TYR A1232 ARG 0.008 0.000 ARG A 814 Details of bonding type rmsd hydrogen bonds : bond 0.04031 ( 700) hydrogen bonds : angle 4.21851 ( 2022) metal coordination : bond 0.00549 ( 19) metal coordination : angle 3.54729 ( 9) covalent geometry : bond 0.00253 (15615) covalent geometry : angle 0.59680 (21075) *********************** 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 342 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 267 time to evaluate : 3.231 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: 0.5777 (mmtt) cc_final: 0.5398 (ttpp) REVERT: A 912 TRP cc_start: 0.5528 (OUTLIER) cc_final: 0.4859 (t-100) REVERT: A 1063 MET cc_start: 0.0758 (tmm) cc_final: 0.0500 (tmm) REVERT: A 1235 LYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6690 (pttt) REVERT: A 1287 ARG cc_start: 0.6649 (tmt170) cc_final: 0.6420 (tmt170) REVERT: A 1307 LYS cc_start: 0.8084 (tmmt) cc_final: 0.7595 (ttmt) REVERT: A 1331 GLU cc_start: 0.1472 (OUTLIER) cc_final: 0.0852 (tm-30) REVERT: A 1337 TYR cc_start: -0.2585 (OUTLIER) cc_final: -0.3277 (t80) REVERT: E 107 LYS cc_start: 0.5831 (OUTLIER) cc_final: 0.5379 (tptp) REVERT: E 115 LEU cc_start: 0.5343 (OUTLIER) cc_final: 0.4851 (mp) REVERT: E 342 ASN cc_start: 0.7105 (OUTLIER) cc_final: 0.6704 (m110) REVERT: E 490 LYS cc_start: 0.7471 (pttp) cc_final: 0.6419 (mmtm) REVERT: E 514 TYR cc_start: 0.7560 (OUTLIER) cc_final: 0.6874 (t80) REVERT: E 565 LYS cc_start: 0.8086 (ttpt) cc_final: 0.7861 (ttpt) REVERT: B 72 GLN cc_start: 0.8158 (tt0) cc_final: 0.7366 (mm-40) REVERT: B 114 ASP cc_start: 0.7437 (OUTLIER) cc_final: 0.7020 (m-30) REVERT: B 116 LEU cc_start: 0.7870 (tp) cc_final: 0.7651 (tt) REVERT: B 248 ARG cc_start: 0.7458 (ttt180) cc_final: 0.7221 (ttt90) REVERT: C 296 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.7247 (ptp) REVERT: C 394 TYR cc_start: 0.7801 (t80) cc_final: 0.7554 (t80) REVERT: D 247 ARG cc_start: 0.7500 (ptp90) cc_final: 0.6952 (ptp90) REVERT: D 355 LEU cc_start: 0.6898 (tp) cc_final: 0.6688 (tp) REVERT: F 285 LEU cc_start: 0.7428 (mt) cc_final: 0.6879 (pt) REVERT: F 309 LYS cc_start: 0.8095 (mmmt) cc_final: 0.7782 (mttt) REVERT: F 350 GLN cc_start: 0.7420 (mt0) cc_final: 0.7145 (mt0) outliers start: 75 outliers final: 36 residues processed: 325 average time/residue: 0.2813 time to fit residues: 133.9567 Evaluate side-chains 277 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 231 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 724 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 1134 SER Chi-restraints excluded: chain A residue 1142 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 1249 LEU Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1325 LYS Chi-restraints excluded: chain A residue 1331 GLU 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 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 53 MET 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 308 VAL Chi-restraints excluded: chain B residue 333 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 296 MET 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 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 76 optimal weight: 3.9990 chunk 143 optimal weight: 0.0570 chunk 129 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 chunk 173 optimal weight: 20.0000 chunk 62 optimal weight: 0.0770 chunk 134 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 chunk 181 optimal weight: 0.0370 chunk 9 optimal weight: 4.9990 overall best weight: 0.3134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 519 ASN B 293 ASN B 317 ASN B 330 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.224087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.183236 restraints weight = 17633.851| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 2.50 r_work: 0.3992 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 15634 Z= 0.113 Angle : 0.588 10.362 21084 Z= 0.309 Chirality : 0.041 0.230 2277 Planarity : 0.004 0.061 2694 Dihedral : 6.967 59.334 2084 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.16 % Favored : 94.78 % Rotamer: Outliers : 3.62 % Allowed : 23.71 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.19), residues: 1840 helix: 0.98 (0.17), residues: 948 sheet: -1.10 (0.55), residues: 82 loop : -1.67 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 492 HIS 0.006 0.001 HIS A1036 PHE 0.034 0.001 PHE E 387 TYR 0.024 0.001 TYR A1240 ARG 0.007 0.000 ARG A 814 Details of bonding type rmsd hydrogen bonds : bond 0.03739 ( 700) hydrogen bonds : angle 4.07847 ( 2022) metal coordination : bond 0.00382 ( 19) metal coordination : angle 2.90431 ( 9) covalent geometry : bond 0.00239 (15615) covalent geometry : angle 0.58475 (21075) *********************** 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 319 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 257 time to evaluate : 1.797 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: 0.5704 (mmtt) cc_final: 0.5187 (ptmm) REVERT: A 690 ASN cc_start: 0.7218 (OUTLIER) cc_final: 0.5496 (t0) REVERT: A 694 GLN cc_start: 0.6135 (mp10) cc_final: 0.5897 (mm-40) REVERT: A 912 TRP cc_start: 0.5546 (OUTLIER) cc_final: 0.5149 (m100) REVERT: A 986 TYR cc_start: 0.7611 (m-80) cc_final: 0.7307 (m-80) REVERT: A 1235 LYS cc_start: 0.7155 (OUTLIER) cc_final: 0.6764 (pttp) REVERT: A 1325 LYS cc_start: 0.1401 (OUTLIER) cc_final: 0.0626 (tptt) REVERT: A 1337 TYR cc_start: -0.2252 (OUTLIER) cc_final: -0.2968 (t80) REVERT: E 115 LEU cc_start: 0.5402 (OUTLIER) cc_final: 0.4905 (mp) REVERT: E 387 PHE cc_start: 0.2970 (OUTLIER) cc_final: 0.2745 (p90) REVERT: E 441 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7568 (m-30) REVERT: E 490 LYS cc_start: 0.7480 (pttp) cc_final: 0.6328 (mmtm) REVERT: E 516 ASN cc_start: 0.7070 (OUTLIER) cc_final: 0.6477 (p0) REVERT: B 72 GLN cc_start: 0.8130 (tt0) cc_final: 0.7331 (mm-40) REVERT: B 98 LYS cc_start: 0.8377 (tptt) cc_final: 0.7292 (pttt) REVERT: B 114 ASP cc_start: 0.7361 (m-30) cc_final: 0.7003 (m-30) REVERT: B 248 ARG cc_start: 0.7521 (ttt180) cc_final: 0.7267 (ttt90) REVERT: C 394 TYR cc_start: 0.7763 (t80) cc_final: 0.7451 (t80) REVERT: D 247 ARG cc_start: 0.7418 (ptp90) cc_final: 0.6969 (ptp90) REVERT: D 256 MET cc_start: 0.6350 (ttp) cc_final: 0.4849 (tpt) REVERT: D 290 ASP cc_start: 0.5906 (OUTLIER) cc_final: 0.5637 (p0) REVERT: D 296 MET cc_start: 0.7375 (ptp) cc_final: 0.7070 (pmm) REVERT: D 300 ARG cc_start: 0.5484 (pmt170) cc_final: 0.5103 (pmt170) REVERT: F 285 LEU cc_start: 0.7511 (mt) cc_final: 0.6962 (pt) REVERT: F 309 LYS cc_start: 0.7919 (mmmt) cc_final: 0.7608 (mttt) outliers start: 62 outliers final: 29 residues processed: 301 average time/residue: 0.2589 time to fit residues: 117.5530 Evaluate side-chains 261 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 222 time to evaluate : 1.619 ------------------------------------------------------------------------------- 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 796 ILE Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 912 TRP Chi-restraints excluded: chain A residue 945 THR 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 1325 LYS Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain E residue 115 LEU 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 E residue 516 ASN Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 113 PHE 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 235 ASP Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 253 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 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 33 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 169 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 chunk 42 optimal weight: 0.3980 chunk 77 optimal weight: 0.0030 chunk 31 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 173 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4667 r_free = 0.4667 target = 0.219049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.176809 restraints weight = 17945.105| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 2.83 r_work: 0.3948 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.3142 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= 0.118 Angle : 0.584 8.950 21084 Z= 0.305 Chirality : 0.041 0.202 2277 Planarity : 0.004 0.051 2694 Dihedral : 6.303 56.958 2059 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.95 % Favored : 95.00 % Rotamer: Outliers : 3.21 % Allowed : 24.71 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.19), residues: 1840 helix: 1.23 (0.17), residues: 943 sheet: -0.82 (0.55), residues: 82 loop : -1.57 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 428 HIS 0.004 0.001 HIS B 150 PHE 0.034 0.001 PHE E 387 TYR 0.020 0.001 TYR A1240 ARG 0.005 0.000 ARG A 814 Details of bonding type rmsd hydrogen bonds : bond 0.03705 ( 700) hydrogen bonds : angle 3.98401 ( 2022) metal coordination : bond 0.00361 ( 19) metal coordination : angle 2.76874 ( 9) covalent geometry : bond 0.00261 (15615) covalent geometry : angle 0.58112 (21075) *********************** 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 291 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 236 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 679 LYS cc_start: 0.5705 (mmtt) cc_final: 0.5379 (ttpp) REVERT: A 690 ASN cc_start: 0.7425 (OUTLIER) cc_final: 0.5594 (t0) REVERT: A 912 TRP cc_start: 0.5668 (OUTLIER) cc_final: 0.5061 (t-100) REVERT: A 986 TYR cc_start: 0.7660 (m-80) cc_final: 0.7359 (m-80) REVERT: A 1136 PHE cc_start: 0.7754 (m-80) cc_final: 0.7433 (m-80) REVERT: A 1325 LYS cc_start: 0.1440 (OUTLIER) cc_final: 0.0667 (tptt) REVERT: E 115 LEU cc_start: 0.5630 (OUTLIER) cc_final: 0.5038 (mp) REVERT: E 342 ASN cc_start: 0.7072 (OUTLIER) cc_final: 0.6733 (m110) REVERT: E 490 LYS cc_start: 0.7440 (pttp) cc_final: 0.6301 (mmtm) REVERT: E 516 ASN cc_start: 0.7341 (OUTLIER) cc_final: 0.6873 (p0) REVERT: B 72 GLN cc_start: 0.8160 (tt0) cc_final: 0.7316 (mm-40) REVERT: B 114 ASP cc_start: 0.7464 (m-30) cc_final: 0.7079 (m-30) REVERT: B 248 ARG cc_start: 0.7608 (ttt180) cc_final: 0.7340 (ttt90) REVERT: C 394 TYR cc_start: 0.7838 (t80) cc_final: 0.7534 (t80) REVERT: D 247 ARG cc_start: 0.7376 (ptp90) cc_final: 0.7062 (ptp90) REVERT: D 290 ASP cc_start: 0.5827 (OUTLIER) cc_final: 0.5441 (p0) REVERT: F 285 LEU cc_start: 0.7495 (mt) cc_final: 0.6958 (pt) outliers start: 55 outliers final: 35 residues processed: 281 average time/residue: 0.2504 time to fit residues: 106.1403 Evaluate side-chains 266 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 224 time to evaluate : 1.638 ------------------------------------------------------------------------------- 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 724 VAL Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 781 GLU 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 1152 THR Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1325 LYS Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain E residue 115 LEU 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 491 VAL Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain C residue 221 SER 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 367 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 353 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 153 optimal weight: 0.6980 chunk 127 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 82 optimal weight: 0.3980 chunk 135 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 179 optimal weight: 7.9990 chunk 166 optimal weight: 0.0970 chunk 106 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 ASN ** 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** B 317 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.219300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.176329 restraints weight = 17719.201| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 2.55 r_work: 0.3958 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.3265 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= 0.117 Angle : 0.587 12.538 21084 Z= 0.306 Chirality : 0.041 0.189 2277 Planarity : 0.004 0.047 2694 Dihedral : 6.040 56.809 2051 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.27 % Favored : 94.67 % Rotamer: Outliers : 3.33 % Allowed : 24.71 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.20), residues: 1840 helix: 1.30 (0.17), residues: 951 sheet: -0.59 (0.57), residues: 82 loop : -1.48 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 428 HIS 0.004 0.001 HIS A1036 PHE 0.041 0.001 PHE E 387 TYR 0.016 0.001 TYR E 556 ARG 0.004 0.000 ARG A 814 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 700) hydrogen bonds : angle 3.99031 ( 2022) metal coordination : bond 0.00346 ( 19) metal coordination : angle 2.63241 ( 9) covalent geometry : bond 0.00260 (15615) covalent geometry : angle 0.58447 (21075) *********************** 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 282 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 225 time to evaluate : 1.599 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: 0.5663 (mmtt) cc_final: 0.5398 (ttpp) REVERT: A 690 ASN cc_start: 0.7429 (OUTLIER) cc_final: 0.5620 (t0) REVERT: A 912 TRP cc_start: 0.5437 (OUTLIER) cc_final: 0.4930 (t-100) REVERT: A 986 TYR cc_start: 0.7692 (m-80) cc_final: 0.7420 (m-80) REVERT: A 1136 PHE cc_start: 0.7630 (m-80) cc_final: 0.7272 (m-80) REVERT: A 1300 MET cc_start: 0.5690 (tpp) cc_final: 0.5015 (tpt) REVERT: A 1325 LYS cc_start: 0.1254 (OUTLIER) cc_final: 0.0539 (tptt) REVERT: E 342 ASN cc_start: 0.7073 (OUTLIER) cc_final: 0.6734 (m110) REVERT: E 459 ASN cc_start: 0.7586 (t0) cc_final: 0.7305 (t0) REVERT: E 490 LYS cc_start: 0.7316 (pttp) cc_final: 0.6217 (mmtm) REVERT: E 516 ASN cc_start: 0.7290 (OUTLIER) cc_final: 0.6796 (p0) REVERT: B 53 MET cc_start: 0.7656 (tpp) cc_final: 0.7357 (mpp) REVERT: B 72 GLN cc_start: 0.8073 (tt0) cc_final: 0.7216 (mm-40) REVERT: B 114 ASP cc_start: 0.7528 (m-30) cc_final: 0.7242 (m-30) REVERT: B 248 ARG cc_start: 0.7509 (ttt180) cc_final: 0.7272 (ttt90) REVERT: C 394 TYR cc_start: 0.7836 (t80) cc_final: 0.7548 (t80) REVERT: D 247 ARG cc_start: 0.7399 (ptp90) cc_final: 0.7076 (ptp90) REVERT: D 290 ASP cc_start: 0.5614 (OUTLIER) cc_final: 0.5247 (p0) REVERT: F 285 LEU cc_start: 0.7493 (mt) cc_final: 0.6902 (pt) REVERT: F 309 LYS cc_start: 0.8139 (mmmt) cc_final: 0.7765 (mttt) REVERT: F 350 GLN cc_start: 0.7027 (mt0) cc_final: 0.6720 (mt0) REVERT: F 562 GLN cc_start: 0.8324 (tt0) cc_final: 0.8033 (tp-100) outliers start: 57 outliers final: 38 residues processed: 270 average time/residue: 0.2701 time to fit residues: 112.2722 Evaluate side-chains 254 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 210 time to evaluate : 1.626 ------------------------------------------------------------------------------- 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 779 ASN Chi-restraints excluded: chain A residue 781 GLU 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 1152 THR Chi-restraints excluded: chain A residue 1191 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 452 VAL Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 113 PHE 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 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 355 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 386 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 353 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 176 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 143 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 166 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 ASN A 884 HIS ** 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 D 305 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.219625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.178735 restraints weight = 17831.751| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 2.61 r_work: 0.3922 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15634 Z= 0.136 Angle : 0.605 11.347 21084 Z= 0.316 Chirality : 0.042 0.191 2277 Planarity : 0.004 0.048 2694 Dihedral : 5.783 55.662 2042 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.82 % Favored : 94.13 % Rotamer: Outliers : 3.86 % Allowed : 24.77 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.20), residues: 1840 helix: 1.27 (0.17), residues: 957 sheet: -0.51 (0.57), residues: 82 loop : -1.44 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 428 HIS 0.005 0.001 HIS B 150 PHE 0.032 0.002 PHE E 387 TYR 0.016 0.001 TYR B 176 ARG 0.004 0.000 ARG A 814 Details of bonding type rmsd hydrogen bonds : bond 0.03945 ( 700) hydrogen bonds : angle 4.03304 ( 2022) metal coordination : bond 0.00382 ( 19) metal coordination : angle 2.80383 ( 9) covalent geometry : bond 0.00312 (15615) covalent geometry : angle 0.60214 (21075) *********************** 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 284 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 218 time to evaluate : 1.628 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: 0.5776 (mmtt) cc_final: 0.5560 (ttpp) REVERT: A 690 ASN cc_start: 0.7739 (OUTLIER) cc_final: 0.5618 (t0) REVERT: A 912 TRP cc_start: 0.5736 (OUTLIER) cc_final: 0.5153 (t-100) REVERT: A 986 TYR cc_start: 0.7577 (m-80) cc_final: 0.7354 (m-80) REVERT: A 1136 PHE cc_start: 0.7779 (m-80) cc_final: 0.7514 (m-80) REVERT: A 1235 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6904 (pttp) REVERT: A 1300 MET cc_start: 0.6156 (tpp) cc_final: 0.5874 (mmm) REVERT: A 1316 TYR cc_start: 0.8373 (OUTLIER) cc_final: 0.7813 (t80) REVERT: A 1325 LYS cc_start: 0.1321 (OUTLIER) cc_final: 0.0575 (tptt) REVERT: E 316 MET cc_start: 0.6720 (ttt) cc_final: 0.5635 (tpp) REVERT: E 334 LYS cc_start: 0.7603 (tptp) cc_final: 0.7297 (tppp) REVERT: E 342 ASN cc_start: 0.7118 (OUTLIER) cc_final: 0.6755 (m110) REVERT: E 490 LYS cc_start: 0.7456 (pttp) cc_final: 0.6479 (mmtm) REVERT: E 507 GLU cc_start: 0.7548 (tt0) cc_final: 0.6659 (pm20) REVERT: B 72 GLN cc_start: 0.8122 (tt0) cc_final: 0.7378 (mm-40) REVERT: B 114 ASP cc_start: 0.7578 (m-30) cc_final: 0.7352 (m-30) REVERT: B 248 ARG cc_start: 0.7657 (ttt180) cc_final: 0.7343 (ttt90) REVERT: C 394 TYR cc_start: 0.7870 (t80) cc_final: 0.7621 (t80) REVERT: D 247 ARG cc_start: 0.7517 (ptp90) cc_final: 0.6956 (ptp90) REVERT: D 290 ASP cc_start: 0.6102 (OUTLIER) cc_final: 0.5840 (p0) REVERT: D 291 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7214 (mmmt) REVERT: F 309 LYS cc_start: 0.8202 (mmmt) cc_final: 0.7861 (mttt) REVERT: F 562 GLN cc_start: 0.8266 (tt0) cc_final: 0.7904 (tp-100) REVERT: F 571 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7687 (mt-10) outliers start: 66 outliers final: 46 residues processed: 268 average time/residue: 0.2526 time to fit residues: 102.2747 Evaluate side-chains 257 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 203 time to evaluate : 1.596 ------------------------------------------------------------------------------- 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 781 GLU 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 859 SER 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 1152 THR Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1235 LYS Chi-restraints excluded: chain A residue 1241 THR Chi-restraints excluded: chain A residue 1257 MET 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 516 ASN Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 249 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 355 LEU Chi-restraints excluded: chain C residue 367 LEU 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 291 LYS Chi-restraints excluded: chain D residue 325 ILE 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 63 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 159 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 84 optimal weight: 0.0980 chunk 59 optimal weight: 8.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 ASN E 430 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.217993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.175499 restraints weight = 17667.946| |-----------------------------------------------------------------------------| r_work (start): 0.4213 rms_B_bonded: 2.63 r_work: 0.3933 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 15634 Z= 0.156 Angle : 0.634 10.901 21084 Z= 0.331 Chirality : 0.043 0.215 2277 Planarity : 0.004 0.048 2694 Dihedral : 5.917 57.703 2042 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.09 % Favored : 93.86 % Rotamer: Outliers : 3.80 % Allowed : 24.94 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.20), residues: 1840 helix: 1.13 (0.17), residues: 963 sheet: -0.53 (0.57), residues: 82 loop : -1.52 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 236 HIS 0.006 0.001 HIS B 150 PHE 0.036 0.002 PHE E 567 TYR 0.033 0.002 TYR A1240 ARG 0.004 0.000 ARG B 248 Details of bonding type rmsd hydrogen bonds : bond 0.04141 ( 700) hydrogen bonds : angle 4.13990 ( 2022) metal coordination : bond 0.00452 ( 19) metal coordination : angle 2.85624 ( 9) covalent geometry : bond 0.00366 (15615) covalent geometry : angle 0.63159 (21075) *********************** 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 282 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 217 time to evaluate : 1.650 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: 0.5994 (mmtt) cc_final: 0.5679 (ttpp) REVERT: A 690 ASN cc_start: 0.7747 (OUTLIER) cc_final: 0.6480 (t0) REVERT: A 912 TRP cc_start: 0.5677 (OUTLIER) cc_final: 0.5007 (t-100) REVERT: A 986 TYR cc_start: 0.7679 (m-80) cc_final: 0.7456 (m-80) REVERT: A 1136 PHE cc_start: 0.7728 (m-80) cc_final: 0.7456 (m-80) REVERT: A 1228 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6924 (tp) REVERT: A 1235 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.6868 (pttp) REVERT: A 1300 MET cc_start: 0.6081 (tpp) cc_final: 0.5807 (mmm) REVERT: A 1316 TYR cc_start: 0.8273 (OUTLIER) cc_final: 0.7707 (t80) REVERT: A 1325 LYS cc_start: 0.1216 (OUTLIER) cc_final: 0.0550 (tptt) REVERT: E 316 MET cc_start: 0.6698 (ttt) cc_final: 0.5746 (tpp) REVERT: E 334 LYS cc_start: 0.7647 (tptp) cc_final: 0.7289 (tppp) REVERT: E 342 ASN cc_start: 0.7217 (OUTLIER) cc_final: 0.6825 (m110) REVERT: E 490 LYS cc_start: 0.7215 (pttp) cc_final: 0.6145 (mmtm) REVERT: E 507 GLU cc_start: 0.7526 (tt0) cc_final: 0.6500 (pm20) REVERT: E 514 TYR cc_start: 0.7701 (OUTLIER) cc_final: 0.7124 (t80) REVERT: E 516 ASN cc_start: 0.7825 (OUTLIER) cc_final: 0.7340 (p0) REVERT: B 72 GLN cc_start: 0.8124 (tt0) cc_final: 0.7289 (mm-40) REVERT: B 114 ASP cc_start: 0.7638 (m-30) cc_final: 0.7242 (m-30) REVERT: B 248 ARG cc_start: 0.7491 (ttt180) cc_final: 0.7170 (ttt90) REVERT: C 315 LYS cc_start: 0.8027 (tppt) cc_final: 0.7695 (ttmm) REVERT: D 247 ARG cc_start: 0.7512 (ptp90) cc_final: 0.6946 (ptp90) REVERT: D 290 ASP cc_start: 0.5812 (OUTLIER) cc_final: 0.5471 (p0) REVERT: F 309 LYS cc_start: 0.8126 (mmmt) cc_final: 0.7821 (mttt) REVERT: F 350 GLN cc_start: 0.7076 (mt0) cc_final: 0.6853 (mt0) REVERT: F 365 LYS cc_start: 0.6585 (mmmt) cc_final: 0.5709 (mtpt) REVERT: F 555 ILE cc_start: 0.6576 (pp) cc_final: 0.6194 (mt) REVERT: F 562 GLN cc_start: 0.8312 (tt0) cc_final: 0.7834 (tp-100) outliers start: 65 outliers final: 46 residues processed: 270 average time/residue: 0.2510 time to fit residues: 102.7687 Evaluate side-chains 264 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 208 time to evaluate : 1.640 ------------------------------------------------------------------------------- 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 779 ASN Chi-restraints excluded: chain A residue 781 GLU 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 1152 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 1257 MET 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 514 TYR Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 113 PHE 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 241 LYS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 367 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 D residue 331 LEU 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 113 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 82 optimal weight: 0.0070 chunk 151 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 41 optimal weight: 0.0770 chunk 170 optimal weight: 9.9990 chunk 140 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.218995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.177461 restraints weight = 17613.496| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 2.40 r_work: 0.3928 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15634 Z= 0.139 Angle : 0.616 10.614 21084 Z= 0.322 Chirality : 0.042 0.187 2277 Planarity : 0.004 0.053 2694 Dihedral : 5.871 57.853 2042 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.97 % Allowed : 24.88 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.20), residues: 1840 helix: 1.17 (0.17), residues: 964 sheet: -0.48 (0.57), residues: 82 loop : -1.46 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 236 HIS 0.005 0.001 HIS B 150 PHE 0.033 0.002 PHE E 567 TYR 0.026 0.001 TYR A1240 ARG 0.007 0.000 ARG A1009 Details of bonding type rmsd hydrogen bonds : bond 0.03998 ( 700) hydrogen bonds : angle 4.10869 ( 2022) metal coordination : bond 0.00419 ( 19) metal coordination : angle 2.73876 ( 9) covalent geometry : bond 0.00321 (15615) covalent geometry : angle 0.61348 (21075) *********************** 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 280 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 212 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 679 LYS cc_start: 0.5961 (mmtt) cc_final: 0.5665 (ttpp) REVERT: A 690 ASN cc_start: 0.7670 (OUTLIER) cc_final: 0.5527 (t0) REVERT: A 841 MET cc_start: 0.5278 (OUTLIER) cc_final: 0.4913 (mpp) REVERT: A 912 TRP cc_start: 0.5700 (OUTLIER) cc_final: 0.5076 (t-100) REVERT: A 986 TYR cc_start: 0.7670 (m-80) cc_final: 0.7399 (m-80) REVERT: A 1136 PHE cc_start: 0.7696 (m-80) cc_final: 0.7435 (m-80) REVERT: A 1228 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6869 (tp) REVERT: A 1235 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.6932 (pttp) REVERT: A 1300 MET cc_start: 0.6046 (tpp) cc_final: 0.5809 (mmm) REVERT: A 1325 LYS cc_start: 0.1172 (OUTLIER) cc_final: 0.0501 (tptt) REVERT: E 316 MET cc_start: 0.6635 (ttt) cc_final: 0.5686 (tpp) REVERT: E 334 LYS cc_start: 0.7647 (tptp) cc_final: 0.7313 (tppp) REVERT: E 342 ASN cc_start: 0.7343 (OUTLIER) cc_final: 0.6931 (m110) REVERT: E 490 LYS cc_start: 0.7232 (pttp) cc_final: 0.6223 (mmtm) REVERT: E 507 GLU cc_start: 0.7523 (tt0) cc_final: 0.6504 (pm20) REVERT: E 514 TYR cc_start: 0.7678 (OUTLIER) cc_final: 0.7131 (t80) REVERT: E 516 ASN cc_start: 0.7698 (OUTLIER) cc_final: 0.7171 (p0) REVERT: B 72 GLN cc_start: 0.8089 (tt0) cc_final: 0.7274 (mm-40) REVERT: B 114 ASP cc_start: 0.7593 (m-30) cc_final: 0.7265 (m-30) REVERT: B 248 ARG cc_start: 0.7485 (ttt180) cc_final: 0.7164 (ttt90) REVERT: C 368 MET cc_start: 0.5279 (mpp) cc_final: 0.4665 (mmt) REVERT: C 394 TYR cc_start: 0.7860 (t80) cc_final: 0.7611 (t80) REVERT: D 226 ILE cc_start: 0.6203 (mt) cc_final: 0.5984 (tt) REVERT: D 247 ARG cc_start: 0.7632 (ptp90) cc_final: 0.7106 (ptp90) REVERT: D 290 ASP cc_start: 0.5862 (OUTLIER) cc_final: 0.5505 (p0) REVERT: F 285 LEU cc_start: 0.7516 (mt) cc_final: 0.6953 (pt) REVERT: F 365 LYS cc_start: 0.6807 (mmmt) cc_final: 0.5951 (mtpt) REVERT: F 555 ILE cc_start: 0.6563 (pp) cc_final: 0.6193 (mt) REVERT: F 562 GLN cc_start: 0.8288 (tt0) cc_final: 0.7845 (tp40) outliers start: 68 outliers final: 43 residues processed: 265 average time/residue: 0.2547 time to fit residues: 103.6572 Evaluate side-chains 257 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 204 time to evaluate : 1.738 ------------------------------------------------------------------------------- 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 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 841 MET 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 1152 THR Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1207 VAL 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 1325 LYS Chi-restraints excluded: chain A residue 1331 GLU 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 514 TYR Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 113 PHE 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 253 THR Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 367 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 353 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 152 optimal weight: 0.9980 chunk 156 optimal weight: 0.0070 chunk 119 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 63 optimal weight: 0.0870 chunk 145 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 chunk 154 optimal weight: 5.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 ASN ** 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 = 0.4668 r_free = 0.4668 target = 0.219117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.177401 restraints weight = 17791.406| |-----------------------------------------------------------------------------| r_work (start): 0.4321 rms_B_bonded: 2.49 r_work: 0.4044 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.3720 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= 0.116 Angle : 0.602 13.316 21084 Z= 0.312 Chirality : 0.041 0.174 2277 Planarity : 0.004 0.052 2694 Dihedral : 5.691 58.675 2042 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.57 % Allowed : 26.23 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.20), residues: 1840 helix: 1.32 (0.17), residues: 964 sheet: -0.34 (0.57), residues: 82 loop : -1.36 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 428 HIS 0.005 0.001 HIS B 49 PHE 0.026 0.001 PHE E 567 TYR 0.016 0.001 TYR B 176 ARG 0.006 0.000 ARG A1009 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 700) hydrogen bonds : angle 4.01589 ( 2022) metal coordination : bond 0.00350 ( 19) metal coordination : angle 2.44591 ( 9) covalent geometry : bond 0.00255 (15615) covalent geometry : angle 0.60020 (21075) ********************** 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 263 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 219 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 690 ASN cc_start: 0.7726 (OUTLIER) cc_final: 0.5847 (t0) REVERT: A 841 MET cc_start: 0.5259 (OUTLIER) cc_final: 0.4889 (mpp) REVERT: A 912 TRP cc_start: 0.5714 (OUTLIER) cc_final: 0.5244 (t-100) REVERT: A 986 TYR cc_start: 0.7531 (m-80) cc_final: 0.7241 (m-80) REVERT: A 1136 PHE cc_start: 0.7741 (m-80) cc_final: 0.7504 (m-80) REVERT: A 1235 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.6997 (pttp) REVERT: A 1300 MET cc_start: 0.5923 (tpp) cc_final: 0.5706 (mmm) REVERT: A 1325 LYS cc_start: 0.1506 (OUTLIER) cc_final: 0.0664 (tptt) REVERT: E 334 LYS cc_start: 0.7573 (tptp) cc_final: 0.7288 (tppp) REVERT: E 342 ASN cc_start: 0.7192 (OUTLIER) cc_final: 0.6845 (m110) REVERT: E 413 LYS cc_start: 0.8204 (mttt) cc_final: 0.7125 (ptmm) REVERT: E 490 LYS cc_start: 0.7419 (pttp) cc_final: 0.6503 (mmtm) REVERT: E 516 ASN cc_start: 0.7592 (OUTLIER) cc_final: 0.7053 (p0) REVERT: B 72 GLN cc_start: 0.8060 (tt0) cc_final: 0.7366 (mm-40) REVERT: B 114 ASP cc_start: 0.7516 (m-30) cc_final: 0.7313 (m-30) REVERT: B 248 ARG cc_start: 0.7591 (ttt180) cc_final: 0.7389 (ttt90) REVERT: C 368 MET cc_start: 0.5229 (mpp) cc_final: 0.4887 (mmt) REVERT: C 394 TYR cc_start: 0.7691 (t80) cc_final: 0.7355 (t80) REVERT: D 247 ARG cc_start: 0.7697 (ptp90) cc_final: 0.7191 (ptp90) REVERT: D 290 ASP cc_start: 0.5905 (OUTLIER) cc_final: 0.5503 (p0) REVERT: F 285 LEU cc_start: 0.7594 (mt) cc_final: 0.7033 (pt) REVERT: F 365 LYS cc_start: 0.6856 (mmmt) cc_final: 0.6074 (mtpt) REVERT: F 555 ILE cc_start: 0.6304 (pp) cc_final: 0.5955 (mt) REVERT: F 562 GLN cc_start: 0.8272 (tt0) cc_final: 0.7897 (tp40) outliers start: 44 outliers final: 35 residues processed: 250 average time/residue: 0.2690 time to fit residues: 101.9626 Evaluate side-chains 250 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 207 time to evaluate : 1.626 ------------------------------------------------------------------------------- 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 815 HIS Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 841 MET 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 1191 LEU Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1235 LYS Chi-restraints excluded: chain A residue 1325 LYS Chi-restraints excluded: chain A residue 1331 GLU 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 420 CYS Chi-restraints excluded: chain E residue 441 ASP Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 113 PHE 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 367 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 353 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 96 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 159 optimal weight: 0.0980 chunk 163 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 143 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 chunk 149 optimal weight: 0.2980 chunk 68 optimal weight: 0.0570 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 295 ASN F 347 ASN ** F 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.220503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.178971 restraints weight = 17768.553| |-----------------------------------------------------------------------------| r_work (start): 0.4337 rms_B_bonded: 2.58 r_work: 0.4030 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15634 Z= 0.116 Angle : 0.602 12.884 21084 Z= 0.313 Chirality : 0.041 0.222 2277 Planarity : 0.004 0.051 2694 Dihedral : 5.572 58.427 2040 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.86 % Allowed : 26.17 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.20), residues: 1840 helix: 1.40 (0.17), residues: 964 sheet: -0.15 (0.58), residues: 82 loop : -1.29 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 428 HIS 0.003 0.001 HIS A1036 PHE 0.035 0.001 PHE D 289 TYR 0.022 0.001 TYR D 238 ARG 0.007 0.000 ARG F 564 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 700) hydrogen bonds : angle 4.03305 ( 2022) metal coordination : bond 0.00451 ( 19) metal coordination : angle 2.73026 ( 9) covalent geometry : bond 0.00255 (15615) covalent geometry : angle 0.59941 (21075) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8503.88 seconds wall clock time: 148 minutes 8.36 seconds (8888.36 seconds total)