Starting phenix.real_space_refine on Thu Mar 5 05:48:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7opl_13020/03_2026/7opl_13020.cif Found real_map, /net/cci-nas-00/data/ceres_data/7opl_13020/03_2026/7opl_13020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7opl_13020/03_2026/7opl_13020.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7opl_13020/03_2026/7opl_13020.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7opl_13020/03_2026/7opl_13020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7opl_13020/03_2026/7opl_13020.map" } resolution = 4.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 Fe 4 7.16 5 Zn 3 6.06 5 S 105 5.16 5 C 12633 2.51 5 N 3352 2.21 5 O 3646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19743 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8641 Classifications: {'peptide': 1070} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1014} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3451 Classifications: {'peptide': 444} Modifications used: {'COO': 1} Link IDs: {'PCIS': 5, 'PTRANS': 26, 'TRANS': 412} Chain: "C" Number of atoms: 3261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3261 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 16, 'TRANS': 372} Chain breaks: 2 Chain: "D" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3562 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 20, 'TRANS': 413} Chain: "E" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain breaks: 1 Chain: "A" 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} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7229 SG CYS A1283 112.373 17.705 58.207 1.00135.57 S ATOM 7249 SG CYS A1286 111.889 15.123 60.842 1.00147.72 S ATOM 7435 SG CYS A1310 113.695 18.494 61.673 1.00149.57 S ATOM 7471 SG CYS A1315 115.418 15.846 59.618 1.00171.25 S ATOM 7749 SG CYS A1348 83.298 50.604 69.806 1.00 90.83 S ATOM 7787 SG CYS A1353 80.639 47.930 70.287 1.00 93.60 S ATOM 7937 SG CYS A1371 80.342 50.706 67.461 1.00 91.47 S ATOM 7955 SG CYS A1374 79.873 51.104 71.398 1.00 94.18 S ATOM 13140 SG CYS C 121 125.948 135.610 55.829 1.00275.08 S ATOM 13146 SG CYS C 122 122.661 136.917 54.444 1.00275.04 S ATOM 13185 SG CYS C 128 125.718 137.241 52.329 1.00274.28 S ATOM 13207 SG CYS C 131 124.419 133.886 52.725 1.00274.93 S ATOM 18208 SG CYS D 367 118.684 61.213 83.318 1.00 94.23 S ATOM 18336 SG CYS D 384 117.254 67.057 87.000 1.00100.01 S ATOM 18652 SG CYS D 424 122.851 64.361 86.683 1.00114.38 S ATOM 17537 SG CYS D 287 117.830 61.835 89.046 1.00111.07 S Time building chain proxies: 4.12, per 1000 atoms: 0.21 Number of scatterers: 19743 At special positions: 0 Unit cell: (160.308, 153.738, 118.26, 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 3 29.99 Fe 4 26.01 S 105 16.00 O 3646 8.00 N 3352 7.00 C 12633 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 904.1 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 D 601 " pdb="FE3 SF4 D 601 " - pdb=" SG CYS D 424 " pdb="FE1 SF4 D 601 " - pdb=" SG CYS D 367 " pdb="FE2 SF4 D 601 " - pdb=" SG CYS D 384 " pdb="FE4 SF4 D 601 " - pdb=" SG CYS D 287 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" SG CYS A1283 " pdb="ZN ZN A1501 " - pdb=" SG CYS A1315 " pdb="ZN ZN A1501 " - pdb=" SG CYS A1286 " pdb="ZN ZN A1501 " - pdb=" SG CYS A1310 " pdb=" ZN A1502 " pdb="ZN ZN A1502 " - pdb=" SG CYS A1353 " pdb="ZN ZN A1502 " - pdb=" SG CYS A1374 " pdb="ZN ZN A1502 " - pdb=" SG CYS A1348 " pdb="ZN ZN A1502 " - pdb=" SG CYS A1371 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 128 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 131 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 122 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 121 " Number of angles added : 18 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4632 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 20 sheets defined 47.5% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 409 through 425 removed outlier: 4.475A pdb=" N ALA A 422 " --> pdb=" O ASP A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 491 Processing helix chain 'A' and resid 522 through 524 No H-bonds generated for 'chain 'A' and resid 522 through 524' Processing helix chain 'A' and resid 597 through 606 Processing helix chain 'A' and resid 614 through 630 Processing helix chain 'A' and resid 642 through 655 Processing helix chain 'A' and resid 658 through 663 removed outlier: 3.559A pdb=" N ILE A 662 " --> pdb=" O TRP A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 701 Processing helix chain 'A' and resid 707 through 715 Processing helix chain 'A' and resid 727 through 732 removed outlier: 3.813A pdb=" N MET A 731 " --> pdb=" O ASN A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 760 Processing helix chain 'A' and resid 760 through 773 Processing helix chain 'A' and resid 775 through 782 Processing helix chain 'A' and resid 783 through 799 removed outlier: 3.676A pdb=" N ARG A 787 " --> pdb=" O GLY A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 873 Processing helix chain 'A' and resid 909 through 931 Processing helix chain 'A' and resid 935 through 961 removed outlier: 4.218A pdb=" N TYR A 957 " --> pdb=" O ALA A 953 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLY A 958 " --> pdb=" O ASN A 954 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 960 " --> pdb=" O MET A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 994 Processing helix chain 'A' and resid 1014 through 1033 Processing helix chain 'A' and resid 1064 through 1066 No H-bonds generated for 'chain 'A' and resid 1064 through 1066' Processing helix chain 'A' and resid 1085 through 1100 Processing helix chain 'A' and resid 1104 through 1125 Processing helix chain 'A' and resid 1129 through 1134 Processing helix chain 'A' and resid 1142 through 1146 removed outlier: 3.533A pdb=" N TYR A1146 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1165 Processing helix chain 'A' and resid 1187 through 1192 removed outlier: 3.632A pdb=" N ALA A1192 " --> pdb=" O SER A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1201 Processing helix chain 'A' and resid 1207 through 1215 Processing helix chain 'A' and resid 1216 through 1225 removed outlier: 4.297A pdb=" N ILE A1223 " --> pdb=" O VAL A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1240 Processing helix chain 'A' and resid 1242 through 1249 Processing helix chain 'A' and resid 1268 through 1273 Processing helix chain 'A' and resid 1299 through 1303 removed outlier: 4.017A pdb=" N ASP A1302 " --> pdb=" O SER A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1305 through 1309 removed outlier: 3.508A pdb=" N ARG A1309 " --> pdb=" O SER A1306 " (cutoff:3.500A) Processing helix chain 'A' and resid 1318 through 1321 Processing helix chain 'A' and resid 1322 through 1343 Processing helix chain 'A' and resid 1384 through 1400 Processing helix chain 'A' and resid 1400 through 1405 Processing helix chain 'A' and resid 1410 through 1421 Processing helix chain 'A' and resid 1423 through 1442 removed outlier: 3.899A pdb=" N ALA A1437 " --> pdb=" O LEU A1433 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N PHE A1440 " --> pdb=" O THR A1436 " (cutoff:3.500A) Processing helix chain 'A' and resid 1451 through 1456 Processing helix chain 'B' and resid 212 through 236 Processing helix chain 'B' and resid 275 through 280 Processing helix chain 'B' and resid 331 through 336 Processing helix chain 'B' and resid 357 through 371 Processing helix chain 'B' and resid 386 through 391 Processing helix chain 'B' and resid 397 through 413 Processing helix chain 'B' and resid 446 through 452 Processing helix chain 'B' and resid 475 through 484 removed outlier: 4.026A pdb=" N GLU B 483 " --> pdb=" O HIS B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 505 Processing helix chain 'B' and resid 521 through 529 Processing helix chain 'C' and resid 5 through 7 No H-bonds generated for 'chain 'C' and resid 5 through 7' Processing helix chain 'C' and resid 8 through 20 removed outlier: 3.878A pdb=" N LYS C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 32 Processing helix chain 'C' and resid 33 through 35 No H-bonds generated for 'chain 'C' and resid 33 through 35' Processing helix chain 'C' and resid 50 through 52 No H-bonds generated for 'chain 'C' and resid 50 through 52' Processing helix chain 'C' and resid 62 through 74 removed outlier: 3.596A pdb=" N MET C 73 " --> pdb=" O GLU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 94 removed outlier: 5.530A pdb=" N ASN C 92 " --> pdb=" O ASN C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'C' and resid 128 through 131 Processing helix chain 'C' and resid 132 through 149 Processing helix chain 'C' and resid 171 through 176 Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'C' and resid 209 through 227 removed outlier: 4.323A pdb=" N LYS C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TYR C 222 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLU C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLU C 225 " --> pdb=" O LYS C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 247 removed outlier: 3.887A pdb=" N LYS C 242 " --> pdb=" O GLU C 238 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ILE C 243 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU C 246 " --> pdb=" O LYS C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 250 No H-bonds generated for 'chain 'C' and resid 248 through 250' Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 264 through 283 Processing helix chain 'C' and resid 291 through 302 removed outlier: 3.600A pdb=" N MET C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 312 removed outlier: 4.151A pdb=" N SER C 310 " --> pdb=" O ASP C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 359 Processing helix chain 'C' and resid 381 through 386 Processing helix chain 'C' and resid 388 through 412 Processing helix chain 'D' and resid 39 through 63 Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 88 through 111 removed outlier: 3.549A pdb=" N GLU D 92 " --> pdb=" O ASN D 88 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TYR D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU D 94 " --> pdb=" O GLU D 90 " (cutoff:3.500A) Proline residue: D 95 - end of helix Processing helix chain 'D' and resid 113 through 135 Processing helix chain 'D' and resid 136 through 147 removed outlier: 3.511A pdb=" N ILE D 140 " --> pdb=" O PRO D 136 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLN D 141 " --> pdb=" O LYS D 137 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASP D 142 " --> pdb=" O ASP D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 170 removed outlier: 5.053A pdb=" N GLN D 164 " --> pdb=" O THR D 160 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N GLU D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 196 Processing helix chain 'D' and resid 210 through 241 Proline residue: D 238 - end of helix Processing helix chain 'D' and resid 246 through 251 Processing helix chain 'D' and resid 275 through 284 removed outlier: 3.512A pdb=" N PHE D 284 " --> pdb=" O SER D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 299 Processing helix chain 'D' and resid 302 through 316 Processing helix chain 'D' and resid 319 through 333 removed outlier: 3.739A pdb=" N LYS D 333 " --> pdb=" O GLN D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 354 removed outlier: 4.728A pdb=" N TYR D 347 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASN D 348 " --> pdb=" O GLY D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 373 Processing helix chain 'D' and resid 384 through 389 Processing helix chain 'D' and resid 390 through 401 Processing helix chain 'D' and resid 404 through 417 Processing helix chain 'D' and resid 419 through 433 Processing helix chain 'D' and resid 443 through 455 Processing helix chain 'E' and resid 22 through 26 removed outlier: 3.870A pdb=" N VAL E 26 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 49 removed outlier: 3.502A pdb=" N LEU E 39 " --> pdb=" O VAL E 35 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER E 40 " --> pdb=" O GLU E 36 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG E 43 " --> pdb=" O LEU E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 64 Processing sheet with id=AA1, first strand: chain 'A' and resid 519 through 520 removed outlier: 8.786A pdb=" N ALA A 520 " --> pdb=" O CYS A 377 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N MET A 379 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 363 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 380 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 359 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N PHE A 360 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ALA A 348 " --> pdb=" O PHE A 360 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE A 362 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TRP A 366 " --> pdb=" O HIS A 342 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N HIS A 342 " --> pdb=" O TRP A 366 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A 341 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 434 through 436 removed outlier: 3.519A pdb=" N VAL A 435 " --> pdb=" O TYR A 452 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLU A 451 " --> pdb=" O PRO A 391 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS A 475 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 394 through 396 removed outlier: 7.124A pdb=" N LYS A 395 " --> pdb=" O THR A 404 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 581 through 583 removed outlier: 3.867A pdb=" N SER A 581 " --> pdb=" O VAL A 564 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE A 583 " --> pdb=" O ALA A 562 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER A 567 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU A 537 " --> pdb=" O SER A 567 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 585 through 586 removed outlier: 3.697A pdb=" N VAL A 586 " --> pdb=" O GLU A 610 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 850 through 852 removed outlier: 4.030A pdb=" N TYR A1000 " --> pdb=" O MET A1007 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASN A1009 " --> pdb=" O VAL A 998 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL A 998 " --> pdb=" O ASN A1009 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 850 through 852 removed outlier: 5.355A pdb=" N PHE A1044 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL A1060 " --> pdb=" O PHE A1044 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER A1046 " --> pdb=" O LEU A1058 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A1050 " --> pdb=" O LYS A1054 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LYS A1054 " --> pdb=" O LEU A1050 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA A1057 " --> pdb=" O GLU A1073 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU A1073 " --> pdb=" O ALA A1057 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A1061 " --> pdb=" O VAL A1069 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1135 through 1138 Processing sheet with id=AA9, first strand: chain 'A' and resid 1279 through 1282 removed outlier: 3.520A pdb=" N TYR A1292 " --> pdb=" O PHE A1279 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1356 through 1357 Processing sheet with id=AB2, first strand: chain 'A' and resid 1448 through 1450 Processing sheet with id=AB3, first strand: chain 'B' and resid 170 through 174 removed outlier: 5.922A pdb=" N VAL B 170 " --> pdb=" O ARG B 597 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ARG B 597 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B 172 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA B 592 " --> pdb=" O TYR B 575 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N THR B 570 " --> pdb=" O CYS B 346 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N CYS B 346 " --> pdb=" O THR B 570 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA B 572 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 574 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N MET B 341 " --> pdb=" O VAL B 374 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N ILE B 376 " --> pdb=" O MET B 341 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU B 343 " --> pdb=" O ILE B 376 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N PHE B 378 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA B 345 " --> pdb=" O PHE B 378 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU B 420 " --> pdb=" O GLN B 454 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 194 through 195 removed outlier: 6.116A pdb=" N ILE B 468 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ILE B 539 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY B 470 " --> pdb=" O ILE B 539 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE B 547 " --> pdb=" O ASN B 558 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 283 through 285 removed outlier: 3.610A pdb=" N GLY B 255 " --> pdb=" O VAL B 302 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 295 through 296 Processing sheet with id=AB7, first strand: chain 'C' and resid 54 through 58 removed outlier: 4.667A pdb=" N TYR C 57 " --> pdb=" O PHE C 45 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N PHE C 45 " --> pdb=" O TYR C 57 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLU C 44 " --> pdb=" O GLY C 81 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS C 77 " --> pdb=" O THR C 48 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU C 103 " --> pdb=" O VAL C 83 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 54 through 58 removed outlier: 4.667A pdb=" N TYR C 57 " --> pdb=" O PHE C 45 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N PHE C 45 " --> pdb=" O TYR C 57 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLU C 44 " --> pdb=" O GLY C 81 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS C 77 " --> pdb=" O THR C 48 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 317 " --> pdb=" O ILE C 80 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 109 through 111 removed outlier: 4.050A pdb=" N ILE C 110 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 165 " --> pdb=" O ILE C 110 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 152 through 153 removed outlier: 3.708A pdb=" N TYR D 184 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL D 209 " --> pdb=" O TYR D 184 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 14 through 19 removed outlier: 4.169A pdb=" N VAL E 14 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE E 71 " --> pdb=" O GLY E 105 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLY E 105 " --> pdb=" O ILE E 71 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ARG E 73 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N THR E 103 " --> pdb=" O ARG E 73 " (cutoff:3.500A) 899 hydrogen bonds defined for protein. 2574 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: 3.70 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 8369 1.43 - 1.64: 11656 1.64 - 1.86: 146 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 20183 Sorted by residual: bond pdb=" N ILE D 371 " pdb=" CA ILE D 371 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 9.04e+00 bond pdb=" N LEU D 372 " pdb=" CA LEU D 372 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.33e-02 5.65e+03 8.55e+00 bond pdb=" CA SER D 366 " pdb=" CB SER D 366 " ideal model delta sigma weight residual 1.530 1.488 0.042 1.58e-02 4.01e+03 7.23e+00 bond pdb=" N CYS D 367 " pdb=" CA CYS D 367 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.62e+00 bond pdb=" C CYS D 367 " pdb=" O CYS D 367 " ideal model delta sigma weight residual 1.237 1.267 -0.030 1.17e-02 7.31e+03 6.62e+00 ... (remaining 20178 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 26309 1.82 - 3.64: 777 3.64 - 5.46: 151 5.46 - 7.28: 31 7.28 - 9.11: 14 Bond angle restraints: 27282 Sorted by residual: angle pdb=" CA PRO C 333 " pdb=" N PRO C 333 " pdb=" CD PRO C 333 " ideal model delta sigma weight residual 112.00 104.35 7.65 1.40e+00 5.10e-01 2.98e+01 angle pdb=" CA PRO C 22 " pdb=" N PRO C 22 " pdb=" CD PRO C 22 " ideal model delta sigma weight residual 112.00 104.58 7.42 1.40e+00 5.10e-01 2.81e+01 angle pdb=" N PRO C 22 " pdb=" CD PRO C 22 " pdb=" CG PRO C 22 " ideal model delta sigma weight residual 103.20 95.83 7.37 1.50e+00 4.44e-01 2.42e+01 angle pdb=" CA SER D 366 " pdb=" C SER D 366 " pdb=" O SER D 366 " ideal model delta sigma weight residual 121.28 115.94 5.34 1.18e+00 7.18e-01 2.05e+01 angle pdb=" N VAL A 607 " pdb=" CA VAL A 607 " pdb=" C VAL A 607 " ideal model delta sigma weight residual 110.05 105.30 4.75 1.09e+00 8.42e-01 1.90e+01 ... (remaining 27277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 11110 18.00 - 35.99: 967 35.99 - 53.99: 165 53.99 - 71.99: 37 71.99 - 89.98: 26 Dihedral angle restraints: 12305 sinusoidal: 5137 harmonic: 7168 Sorted by residual: dihedral pdb=" CA GLU D 356 " pdb=" C GLU D 356 " pdb=" N GLY D 357 " pdb=" CA GLY D 357 " ideal model delta harmonic sigma weight residual -180.00 -150.07 -29.93 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA SER A1444 " pdb=" C SER A1444 " pdb=" N GLY A1445 " pdb=" CA GLY A1445 " ideal model delta harmonic sigma weight residual 180.00 152.22 27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ASP A1242 " pdb=" C ASP A1242 " pdb=" N PRO A1243 " pdb=" CA PRO A1243 " ideal model delta harmonic sigma weight residual -180.00 -153.24 -26.76 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 12302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2726 0.082 - 0.165: 266 0.165 - 0.247: 7 0.247 - 0.330: 0 0.330 - 0.412: 1 Chirality restraints: 3000 Sorted by residual: chirality pdb=" CA CYS D 367 " pdb=" N CYS D 367 " pdb=" C CYS D 367 " pdb=" CB CYS D 367 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" CB THR A1410 " pdb=" CA THR A1410 " pdb=" OG1 THR A1410 " pdb=" CG2 THR A1410 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA PRO B 199 " pdb=" N PRO B 199 " pdb=" C PRO B 199 " pdb=" CB PRO B 199 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 2997 not shown) Planarity restraints: 3505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 332 " 0.090 5.00e-02 4.00e+02 1.32e-01 2.77e+01 pdb=" N PRO C 333 " -0.227 5.00e-02 4.00e+02 pdb=" CA PRO C 333 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO C 333 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 534 " 0.079 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO A 535 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO A 535 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO A 535 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 588 " -0.077 5.00e-02 4.00e+02 1.15e-01 2.10e+01 pdb=" N PRO B 589 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO B 589 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO B 589 " -0.062 5.00e-02 4.00e+02 ... (remaining 3502 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 415 2.67 - 3.23: 20239 3.23 - 3.79: 32123 3.79 - 4.34: 42041 4.34 - 4.90: 66502 Nonbonded interactions: 161320 Sorted by model distance: nonbonded pdb=" OH TYR A1383 " pdb=" OE1 GLN A1391 " model vdw 2.116 3.040 nonbonded pdb=" OE1 GLU D 57 " pdb=" NE1 TRP D 119 " model vdw 2.155 3.120 nonbonded pdb=" NE2 GLN B 211 " pdb=" OD1 ASP B 521 " model vdw 2.158 3.120 nonbonded pdb=" O ILE D 166 " pdb=" OG SER D 170 " model vdw 2.162 3.040 nonbonded pdb=" NE2 GLN D 425 " pdb=" O PHE D 439 " model vdw 2.167 3.120 ... (remaining 161315 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.460 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 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 : 0.004 0.102 20199 Z= 0.170 Angle : 0.868 41.786 27312 Z= 0.423 Chirality : 0.048 0.412 3000 Planarity : 0.007 0.132 3505 Dihedral : 14.343 89.982 7673 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.46 % Favored : 95.45 % Rotamer: Outliers : 0.05 % Allowed : 0.41 % Favored : 99.55 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 5.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.17), residues: 2420 helix: 0.23 (0.16), residues: 1030 sheet: -0.74 (0.31), residues: 279 loop : -1.19 (0.19), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 28 TYR 0.023 0.001 TYR A1342 PHE 0.029 0.002 PHE A 796 TRP 0.066 0.003 TRP A1238 HIS 0.009 0.001 HIS B 278 Details of bonding type rmsd covalent geometry : bond 0.00360 (20183) covalent geometry : angle 0.77496 (27282) hydrogen bonds : bond 0.14713 ( 889) hydrogen bonds : angle 6.78674 ( 2574) metal coordination : bond 0.00495 ( 16) metal coordination : angle 11.85100 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 220 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 MET cc_start: 0.7369 (tpt) cc_final: 0.6762 (tpp) REVERT: A 731 MET cc_start: 0.9224 (tmm) cc_final: 0.8822 (tmm) REVERT: A 1047 LEU cc_start: 0.8418 (tt) cc_final: 0.8123 (tt) REVERT: B 464 ILE cc_start: 0.9151 (mm) cc_final: 0.8926 (mm) REVERT: B 469 PHE cc_start: 0.7237 (m-80) cc_final: 0.6972 (m-80) REVERT: C 45 PHE cc_start: 0.9105 (m-80) cc_final: 0.8856 (m-80) REVERT: C 70 MET cc_start: 0.8343 (mmm) cc_final: 0.7827 (mmm) REVERT: C 112 MET cc_start: 0.8811 (mmp) cc_final: 0.8437 (mmm) REVERT: C 146 LEU cc_start: 0.9761 (mp) cc_final: 0.9532 (pp) REVERT: C 297 MET cc_start: 0.9015 (ppp) cc_final: 0.8709 (ppp) REVERT: C 300 TYR cc_start: 0.6853 (t80) cc_final: 0.5710 (t80) REVERT: D 74 LEU cc_start: 0.9030 (tp) cc_final: 0.8681 (tp) REVERT: E 70 PHE cc_start: 0.8513 (m-80) cc_final: 0.8277 (m-80) outliers start: 1 outliers final: 0 residues processed: 221 average time/residue: 0.1441 time to fit residues: 47.9426 Evaluate side-chains 130 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 0.5980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 235 optimal weight: 20.0000 overall best weight: 4.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 505 GLN A 713 GLN A 880 GLN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 ASN ** A1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1181 GLN ** A1420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN D 255 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.046699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.031793 restraints weight = 158981.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.032707 restraints weight = 108378.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.033393 restraints weight = 81567.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.033920 restraints weight = 66867.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.034275 restraints weight = 57311.322| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 20199 Z= 0.158 Angle : 0.726 32.818 27312 Z= 0.341 Chirality : 0.045 0.213 3000 Planarity : 0.006 0.104 3505 Dihedral : 5.043 28.556 2657 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.04 % Favored : 94.88 % Rotamer: Outliers : 0.41 % Allowed : 4.71 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.17), residues: 2420 helix: 0.49 (0.16), residues: 1030 sheet: -1.01 (0.29), residues: 302 loop : -1.12 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 28 TYR 0.015 0.001 TYR A 732 PHE 0.016 0.001 PHE A 796 TRP 0.021 0.002 TRP A1238 HIS 0.006 0.001 HIS B 278 Details of bonding type rmsd covalent geometry : bond 0.00353 (20183) covalent geometry : angle 0.65390 (27282) hydrogen bonds : bond 0.04292 ( 889) hydrogen bonds : angle 5.61853 ( 2574) metal coordination : bond 0.00737 ( 16) metal coordination : angle 9.53413 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 MET cc_start: 0.9505 (pmm) cc_final: 0.9285 (pmm) REVERT: A 461 MET cc_start: 0.9077 (mpp) cc_final: 0.8752 (mpp) REVERT: A 544 MET cc_start: 0.6605 (ppp) cc_final: 0.5666 (ppp) REVERT: A 632 ASP cc_start: 0.8112 (m-30) cc_final: 0.7800 (m-30) REVERT: A 731 MET cc_start: 0.9480 (tmm) cc_final: 0.8895 (tmm) REVERT: A 872 PHE cc_start: 0.9470 (m-80) cc_final: 0.9166 (m-80) REVERT: A 956 MET cc_start: 0.9472 (mmp) cc_final: 0.9245 (mmm) REVERT: A 985 MET cc_start: 0.9269 (tmm) cc_final: 0.8869 (tmm) REVERT: A 989 GLU cc_start: 0.9410 (OUTLIER) cc_final: 0.9146 (pm20) REVERT: A 990 MET cc_start: 0.9279 (tmm) cc_final: 0.8903 (tmm) REVERT: A 1007 MET cc_start: 0.9359 (mmp) cc_final: 0.9119 (mmm) REVERT: A 1047 LEU cc_start: 0.9399 (tt) cc_final: 0.9194 (tt) REVERT: A 1052 LYS cc_start: 0.9315 (mmtt) cc_final: 0.8958 (mmtt) REVERT: A 1077 LEU cc_start: 0.8584 (pt) cc_final: 0.8379 (pt) REVERT: A 1333 ASP cc_start: 0.9220 (p0) cc_final: 0.8856 (p0) REVERT: A 1362 LEU cc_start: 0.9253 (mt) cc_final: 0.9032 (mt) REVERT: B 260 ASP cc_start: 0.9631 (t70) cc_final: 0.9237 (m-30) REVERT: B 469 PHE cc_start: 0.9345 (m-80) cc_final: 0.8714 (m-80) REVERT: C 1 MET cc_start: 0.7672 (mmm) cc_final: 0.7247 (tpt) REVERT: C 45 PHE cc_start: 0.9856 (m-80) cc_final: 0.9354 (m-80) REVERT: C 112 MET cc_start: 0.8990 (mmp) cc_final: 0.8418 (mmm) REVERT: C 167 CYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7288 (p) REVERT: C 297 MET cc_start: 0.9216 (ppp) cc_final: 0.8975 (ppp) REVERT: C 300 TYR cc_start: 0.8082 (t80) cc_final: 0.7052 (t80) REVERT: D 288 MET cc_start: 0.8705 (tpp) cc_final: 0.8497 (mmt) REVERT: E 72 LYS cc_start: 0.6089 (mmtm) cc_final: 0.5870 (mmtm) outliers start: 9 outliers final: 2 residues processed: 168 average time/residue: 0.1357 time to fit residues: 35.8873 Evaluate side-chains 122 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 183 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 chunk 152 optimal weight: 30.0000 chunk 162 optimal weight: 10.0000 chunk 154 optimal weight: 30.0000 chunk 201 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 47 optimal weight: 40.0000 overall best weight: 8.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 946 GLN A 954 ASN ** A1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1391 GLN ** A1420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 GLN ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 HIS D 421 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.044055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.029538 restraints weight = 166883.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.030426 restraints weight = 115073.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.030991 restraints weight = 85997.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.031401 restraints weight = 70504.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.031758 restraints weight = 62578.504| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.124 20199 Z= 0.255 Angle : 0.771 31.664 27312 Z= 0.369 Chirality : 0.045 0.208 3000 Planarity : 0.006 0.110 3505 Dihedral : 5.203 27.940 2657 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 21.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.70 % Favored : 94.21 % Rotamer: Outliers : 0.05 % Allowed : 6.29 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.17), residues: 2420 helix: 0.36 (0.16), residues: 1032 sheet: -1.09 (0.29), residues: 293 loop : -1.17 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 28 TYR 0.013 0.002 TYR A1292 PHE 0.019 0.002 PHE A1246 TRP 0.023 0.002 TRP C 29 HIS 0.008 0.001 HIS B 419 Details of bonding type rmsd covalent geometry : bond 0.00528 (20183) covalent geometry : angle 0.69788 (27282) hydrogen bonds : bond 0.04222 ( 889) hydrogen bonds : angle 5.64158 ( 2574) metal coordination : bond 0.01374 ( 16) metal coordination : angle 9.88000 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.624 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 428 MET cc_start: 0.9508 (pmm) cc_final: 0.9152 (pmm) REVERT: A 461 MET cc_start: 0.9025 (mpp) cc_final: 0.8678 (mpp) REVERT: A 519 MET cc_start: 0.9002 (ttp) cc_final: 0.8424 (ttp) REVERT: A 544 MET cc_start: 0.7045 (ppp) cc_final: 0.5762 (ppp) REVERT: A 632 ASP cc_start: 0.8106 (m-30) cc_final: 0.7734 (m-30) REVERT: A 731 MET cc_start: 0.9483 (tmm) cc_final: 0.9091 (tmm) REVERT: A 956 MET cc_start: 0.9421 (mmp) cc_final: 0.9185 (mmm) REVERT: A 990 MET cc_start: 0.9199 (tmm) cc_final: 0.8849 (tmm) REVERT: A 1007 MET cc_start: 0.9414 (mmp) cc_final: 0.9134 (mmm) REVERT: A 1333 ASP cc_start: 0.9356 (p0) cc_final: 0.8953 (p0) REVERT: A 1446 TYR cc_start: 0.8501 (m-80) cc_final: 0.8291 (m-80) REVERT: B 260 ASP cc_start: 0.9722 (t70) cc_final: 0.9227 (m-30) REVERT: B 469 PHE cc_start: 0.9345 (m-80) cc_final: 0.8638 (m-80) REVERT: C 1 MET cc_start: 0.7954 (mmm) cc_final: 0.7512 (tpt) REVERT: C 45 PHE cc_start: 0.9827 (m-80) cc_final: 0.9357 (m-80) REVERT: C 73 MET cc_start: 0.9763 (mmp) cc_final: 0.9531 (mpp) REVERT: C 112 MET cc_start: 0.9052 (mmp) cc_final: 0.8579 (mmm) REVERT: C 297 MET cc_start: 0.9246 (ppp) cc_final: 0.9011 (ppp) REVERT: C 300 TYR cc_start: 0.8178 (t80) cc_final: 0.7173 (t80) REVERT: D 74 LEU cc_start: 0.9415 (tp) cc_final: 0.9186 (tp) REVERT: D 307 MET cc_start: 0.9425 (ptm) cc_final: 0.9137 (ptm) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.1331 time to fit residues: 29.3245 Evaluate side-chains 113 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 200 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 65 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 160 optimal weight: 1.9990 chunk 147 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN ** A 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 ASN ** A1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1380 GLN ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.045298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.031006 restraints weight = 161588.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.031778 restraints weight = 107831.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.032434 restraints weight = 81505.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.032883 restraints weight = 66851.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.033225 restraints weight = 58258.738| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 20199 Z= 0.145 Angle : 0.714 33.365 27312 Z= 0.327 Chirality : 0.045 0.217 3000 Planarity : 0.005 0.108 3505 Dihedral : 5.015 26.753 2657 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.75 % Favored : 95.17 % Rotamer: Outliers : 0.05 % Allowed : 3.58 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.17), residues: 2420 helix: 0.57 (0.16), residues: 1028 sheet: -1.05 (0.29), residues: 286 loop : -1.07 (0.19), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1115 TYR 0.011 0.001 TYR A 957 PHE 0.014 0.001 PHE D 447 TRP 0.016 0.002 TRP C 29 HIS 0.007 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00328 (20183) covalent geometry : angle 0.62904 (27282) hydrogen bonds : bond 0.03809 ( 889) hydrogen bonds : angle 5.36555 ( 2574) metal coordination : bond 0.00680 ( 16) metal coordination : angle 10.21758 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 0.756 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 428 MET cc_start: 0.9470 (pmm) cc_final: 0.9099 (pmm) REVERT: A 461 MET cc_start: 0.9011 (mpp) cc_final: 0.8663 (mpp) REVERT: A 519 MET cc_start: 0.9104 (ttp) cc_final: 0.8504 (ttp) REVERT: A 632 ASP cc_start: 0.7959 (m-30) cc_final: 0.7596 (m-30) REVERT: A 731 MET cc_start: 0.9471 (tmm) cc_final: 0.9024 (tmm) REVERT: A 872 PHE cc_start: 0.9456 (m-80) cc_final: 0.9142 (m-80) REVERT: A 956 MET cc_start: 0.9410 (mmp) cc_final: 0.9145 (mmm) REVERT: A 990 MET cc_start: 0.9155 (tmm) cc_final: 0.8796 (tmm) REVERT: A 1007 MET cc_start: 0.9378 (mmp) cc_final: 0.9158 (mmm) REVERT: A 1047 LEU cc_start: 0.9477 (tt) cc_final: 0.9175 (tt) REVERT: A 1333 ASP cc_start: 0.9293 (p0) cc_final: 0.8918 (p0) REVERT: A 1446 TYR cc_start: 0.8526 (m-80) cc_final: 0.8275 (m-80) REVERT: B 260 ASP cc_start: 0.9723 (t70) cc_final: 0.9115 (m-30) REVERT: B 469 PHE cc_start: 0.9263 (m-80) cc_final: 0.8522 (m-80) REVERT: C 1 MET cc_start: 0.7843 (mmm) cc_final: 0.7398 (tpt) REVERT: C 45 PHE cc_start: 0.9823 (m-80) cc_final: 0.9282 (m-80) REVERT: C 73 MET cc_start: 0.9764 (mmp) cc_final: 0.9511 (mpp) REVERT: C 112 MET cc_start: 0.9085 (mmp) cc_final: 0.8568 (mmm) REVERT: C 212 ILE cc_start: 0.8990 (mp) cc_final: 0.8679 (mp) REVERT: C 297 MET cc_start: 0.9357 (ppp) cc_final: 0.9111 (ppp) REVERT: C 300 TYR cc_start: 0.8112 (t80) cc_final: 0.7136 (t80) REVERT: D 74 LEU cc_start: 0.9373 (tp) cc_final: 0.9137 (tp) REVERT: D 260 GLN cc_start: 0.8812 (tm-30) cc_final: 0.8471 (tm-30) REVERT: D 307 MET cc_start: 0.9412 (ptm) cc_final: 0.9117 (ptm) outliers start: 1 outliers final: 1 residues processed: 148 average time/residue: 0.1277 time to fit residues: 30.2305 Evaluate side-chains 117 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 197 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 7 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 231 optimal weight: 20.0000 chunk 78 optimal weight: 0.0770 chunk 188 optimal weight: 40.0000 chunk 1 optimal weight: 7.9990 chunk 92 optimal weight: 20.0000 overall best weight: 6.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN ** A 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 ASN ** A1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.044279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.029809 restraints weight = 164652.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.030577 restraints weight = 112153.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.031204 restraints weight = 85002.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.031644 restraints weight = 69985.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.031942 restraints weight = 60955.012| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 20199 Z= 0.192 Angle : 0.736 32.700 27312 Z= 0.339 Chirality : 0.044 0.215 3000 Planarity : 0.005 0.109 3505 Dihedral : 5.056 26.750 2657 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.54 % Favored : 94.38 % Rotamer: Outliers : 0.18 % Allowed : 4.12 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.17), residues: 2420 helix: 0.56 (0.16), residues: 1029 sheet: -1.00 (0.29), residues: 291 loop : -1.11 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 24 TYR 0.014 0.001 TYR B 509 PHE 0.023 0.002 PHE C 47 TRP 0.019 0.002 TRP C 29 HIS 0.007 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00419 (20183) covalent geometry : angle 0.64995 (27282) hydrogen bonds : bond 0.03782 ( 889) hydrogen bonds : angle 5.40275 ( 2574) metal coordination : bond 0.01103 ( 16) metal coordination : angle 10.44209 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 143 time to evaluate : 0.561 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 519 MET cc_start: 0.9029 (ttp) cc_final: 0.8748 (ttm) REVERT: A 632 ASP cc_start: 0.8067 (m-30) cc_final: 0.7718 (m-30) REVERT: A 731 MET cc_start: 0.9485 (tmm) cc_final: 0.9029 (tmm) REVERT: A 872 PHE cc_start: 0.9470 (m-80) cc_final: 0.9142 (m-80) REVERT: A 956 MET cc_start: 0.9452 (mmp) cc_final: 0.9207 (mmm) REVERT: A 990 MET cc_start: 0.9111 (tmm) cc_final: 0.8789 (tmm) REVERT: A 1052 LYS cc_start: 0.9461 (mmtt) cc_final: 0.9040 (mptt) REVERT: A 1228 ASP cc_start: 0.9063 (m-30) cc_final: 0.8345 (p0) REVERT: A 1333 ASP cc_start: 0.9363 (p0) cc_final: 0.8969 (p0) REVERT: A 1446 TYR cc_start: 0.8416 (m-80) cc_final: 0.8059 (m-80) REVERT: B 260 ASP cc_start: 0.9753 (t70) cc_final: 0.9132 (m-30) REVERT: B 469 PHE cc_start: 0.9315 (m-80) cc_final: 0.8623 (m-80) REVERT: C 1 MET cc_start: 0.8104 (mmm) cc_final: 0.7688 (tpt) REVERT: C 45 PHE cc_start: 0.9806 (m-80) cc_final: 0.9332 (m-80) REVERT: C 73 MET cc_start: 0.9759 (mmp) cc_final: 0.9516 (mpp) REVERT: C 112 MET cc_start: 0.9052 (mmp) cc_final: 0.8606 (mmm) REVERT: C 300 TYR cc_start: 0.8191 (t80) cc_final: 0.7243 (t80) REVERT: D 74 LEU cc_start: 0.9347 (tp) cc_final: 0.9103 (tp) REVERT: D 247 GLN cc_start: 0.9022 (pp30) cc_final: 0.8643 (pp30) REVERT: D 260 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8416 (tm-30) REVERT: D 307 MET cc_start: 0.9458 (ptm) cc_final: 0.9137 (ptm) outliers start: 4 outliers final: 1 residues processed: 147 average time/residue: 0.1196 time to fit residues: 27.8264 Evaluate side-chains 116 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 137 optimal weight: 3.9990 chunk 228 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 197 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 119 optimal weight: 30.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN A 548 GLN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 ASN ** A1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN D 141 GLN ** D 410 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 = 0.3306 r_free = 0.3306 target = 0.044237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.029794 restraints weight = 165519.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.030573 restraints weight = 112129.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.031189 restraints weight = 84995.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.031631 restraints weight = 70289.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.031923 restraints weight = 61215.559| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 20199 Z= 0.180 Angle : 0.739 34.175 27312 Z= 0.338 Chirality : 0.044 0.226 3000 Planarity : 0.005 0.110 3505 Dihedral : 5.051 26.426 2657 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.21 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.17), residues: 2420 helix: 0.52 (0.16), residues: 1044 sheet: -1.04 (0.29), residues: 291 loop : -1.13 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A1081 TYR 0.012 0.001 TYR A 964 PHE 0.017 0.002 PHE C 47 TRP 0.019 0.002 TRP C 29 HIS 0.007 0.001 HIS B 278 Details of bonding type rmsd covalent geometry : bond 0.00397 (20183) covalent geometry : angle 0.64800 (27282) hydrogen bonds : bond 0.03802 ( 889) hydrogen bonds : angle 5.39463 ( 2574) metal coordination : bond 0.01254 ( 16) metal coordination : angle 10.74916 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 MET cc_start: 0.9029 (ttp) cc_final: 0.8731 (ttm) REVERT: A 632 ASP cc_start: 0.8028 (m-30) cc_final: 0.7676 (m-30) REVERT: A 731 MET cc_start: 0.9495 (tmm) cc_final: 0.9015 (tmm) REVERT: A 872 PHE cc_start: 0.9469 (m-80) cc_final: 0.9159 (m-80) REVERT: A 956 MET cc_start: 0.9456 (mmp) cc_final: 0.9172 (mmm) REVERT: A 1047 LEU cc_start: 0.9235 (tt) cc_final: 0.9025 (tt) REVERT: A 1333 ASP cc_start: 0.9238 (p0) cc_final: 0.8826 (p0) REVERT: A 1446 TYR cc_start: 0.8387 (m-80) cc_final: 0.8045 (m-80) REVERT: B 260 ASP cc_start: 0.9756 (t70) cc_final: 0.9152 (m-30) REVERT: B 469 PHE cc_start: 0.9307 (m-80) cc_final: 0.8630 (m-80) REVERT: C 1 MET cc_start: 0.8170 (mmm) cc_final: 0.7742 (tpt) REVERT: C 45 PHE cc_start: 0.9810 (m-80) cc_final: 0.9333 (m-80) REVERT: C 73 MET cc_start: 0.9746 (mmp) cc_final: 0.9479 (mpp) REVERT: C 112 MET cc_start: 0.9055 (mmp) cc_final: 0.8619 (mmm) REVERT: C 300 TYR cc_start: 0.8286 (t80) cc_final: 0.7344 (t80) REVERT: D 74 LEU cc_start: 0.9342 (tp) cc_final: 0.9099 (tp) REVERT: D 260 GLN cc_start: 0.8768 (tm-30) cc_final: 0.8393 (tm-30) REVERT: D 307 MET cc_start: 0.9461 (ptm) cc_final: 0.9217 (ptm) REVERT: E 22 GLN cc_start: 0.6822 (tm-30) cc_final: 0.6620 (tm-30) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.1264 time to fit residues: 29.2150 Evaluate side-chains 116 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 17 optimal weight: 30.0000 chunk 191 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 157 optimal weight: 30.0000 chunk 100 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 238 optimal weight: 50.0000 chunk 26 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 GLN ** A1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1391 GLN ** A1420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 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 = 0.3292 r_free = 0.3292 target = 0.043620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.029358 restraints weight = 166609.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.030199 restraints weight = 114138.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.030799 restraints weight = 86046.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.031177 restraints weight = 70402.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.031438 restraints weight = 61997.062| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 20199 Z= 0.197 Angle : 0.747 34.694 27312 Z= 0.345 Chirality : 0.045 0.214 3000 Planarity : 0.005 0.111 3505 Dihedral : 5.100 26.374 2657 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.70 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.17), residues: 2420 helix: 0.46 (0.16), residues: 1051 sheet: -1.15 (0.30), residues: 281 loop : -1.14 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 28 TYR 0.012 0.001 TYR A 801 PHE 0.016 0.002 PHE C 47 TRP 0.021 0.002 TRP C 29 HIS 0.008 0.001 HIS B 278 Details of bonding type rmsd covalent geometry : bond 0.00430 (20183) covalent geometry : angle 0.65761 (27282) hydrogen bonds : bond 0.03848 ( 889) hydrogen bonds : angle 5.44262 ( 2574) metal coordination : bond 0.01212 ( 16) metal coordination : angle 10.71288 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.721 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 519 MET cc_start: 0.9022 (ttp) cc_final: 0.8707 (ttm) REVERT: A 544 MET cc_start: 0.7369 (ppp) cc_final: 0.5947 (ppp) REVERT: A 632 ASP cc_start: 0.7931 (m-30) cc_final: 0.7638 (m-30) REVERT: A 731 MET cc_start: 0.9489 (tmm) cc_final: 0.8976 (tmm) REVERT: A 872 PHE cc_start: 0.9479 (m-80) cc_final: 0.9157 (m-80) REVERT: A 956 MET cc_start: 0.9457 (mmp) cc_final: 0.9172 (mmm) REVERT: A 985 MET cc_start: 0.9149 (tmm) cc_final: 0.8903 (tmm) REVERT: A 1047 LEU cc_start: 0.9238 (tt) cc_final: 0.9022 (tt) REVERT: A 1228 ASP cc_start: 0.9109 (m-30) cc_final: 0.8408 (p0) REVERT: A 1333 ASP cc_start: 0.9172 (p0) cc_final: 0.8719 (p0) REVERT: A 1446 TYR cc_start: 0.8438 (m-80) cc_final: 0.8095 (m-80) REVERT: B 260 ASP cc_start: 0.9729 (t70) cc_final: 0.9138 (m-30) REVERT: B 469 PHE cc_start: 0.9328 (m-80) cc_final: 0.8666 (m-80) REVERT: C 1 MET cc_start: 0.8318 (mmm) cc_final: 0.7916 (tpt) REVERT: C 45 PHE cc_start: 0.9804 (m-80) cc_final: 0.9375 (m-80) REVERT: C 73 MET cc_start: 0.9738 (mmp) cc_final: 0.9464 (mpp) REVERT: C 112 MET cc_start: 0.9066 (mmp) cc_final: 0.8646 (mmm) REVERT: C 300 TYR cc_start: 0.8348 (t80) cc_final: 0.7436 (t80) REVERT: D 74 LEU cc_start: 0.9351 (tp) cc_final: 0.9106 (tp) REVERT: D 260 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8404 (tm-30) REVERT: D 307 MET cc_start: 0.9469 (ptm) cc_final: 0.9145 (ptm) REVERT: D 347 TYR cc_start: 0.9263 (m-10) cc_final: 0.8972 (m-10) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1242 time to fit residues: 27.1067 Evaluate side-chains 112 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 9 optimal weight: 30.0000 chunk 233 optimal weight: 30.0000 chunk 149 optimal weight: 30.0000 chunk 175 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 148 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 122 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 870 GLN ** A1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.043064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.028984 restraints weight = 167427.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.029854 restraints weight = 115122.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.030436 restraints weight = 85987.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.030907 restraints weight = 70263.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.031134 restraints weight = 60881.511| |-----------------------------------------------------------------------------| r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 20199 Z= 0.213 Angle : 0.771 35.254 27312 Z= 0.353 Chirality : 0.045 0.212 3000 Planarity : 0.005 0.112 3505 Dihedral : 5.192 26.465 2657 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.99 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.17), residues: 2420 helix: 0.40 (0.16), residues: 1053 sheet: -1.39 (0.29), residues: 286 loop : -1.12 (0.19), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1081 TYR 0.030 0.002 TYR A 344 PHE 0.018 0.002 PHE D 386 TRP 0.024 0.002 TRP C 29 HIS 0.007 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00460 (20183) covalent geometry : angle 0.67698 (27282) hydrogen bonds : bond 0.03887 ( 889) hydrogen bonds : angle 5.47524 ( 2574) metal coordination : bond 0.01412 ( 16) metal coordination : angle 11.13238 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 MET cc_start: 0.9036 (ttp) cc_final: 0.8698 (ttp) REVERT: A 632 ASP cc_start: 0.8026 (m-30) cc_final: 0.7736 (m-30) REVERT: A 731 MET cc_start: 0.9545 (tmm) cc_final: 0.9032 (tmm) REVERT: A 956 MET cc_start: 0.9480 (mmp) cc_final: 0.9185 (mmm) REVERT: A 985 MET cc_start: 0.9097 (tmm) cc_final: 0.8757 (tmm) REVERT: A 1047 LEU cc_start: 0.9241 (tt) cc_final: 0.9031 (tt) REVERT: A 1228 ASP cc_start: 0.9096 (m-30) cc_final: 0.8592 (p0) REVERT: A 1333 ASP cc_start: 0.9207 (p0) cc_final: 0.8743 (p0) REVERT: A 1446 TYR cc_start: 0.8277 (m-80) cc_final: 0.7958 (m-80) REVERT: B 260 ASP cc_start: 0.9730 (t70) cc_final: 0.9121 (m-30) REVERT: C 1 MET cc_start: 0.8313 (mmm) cc_final: 0.7764 (tpt) REVERT: C 45 PHE cc_start: 0.9717 (m-80) cc_final: 0.9201 (m-80) REVERT: C 73 MET cc_start: 0.9770 (mmp) cc_final: 0.9443 (mpp) REVERT: C 112 MET cc_start: 0.9044 (mmp) cc_final: 0.8615 (mmm) REVERT: C 212 ILE cc_start: 0.8784 (mp) cc_final: 0.8391 (mp) REVERT: C 297 MET cc_start: 0.9409 (ppp) cc_final: 0.9159 (ppp) REVERT: C 300 TYR cc_start: 0.8412 (t80) cc_final: 0.7501 (t80) REVERT: D 74 LEU cc_start: 0.9362 (tp) cc_final: 0.9112 (tp) REVERT: D 307 MET cc_start: 0.9470 (ptm) cc_final: 0.9093 (ptm) REVERT: D 347 TYR cc_start: 0.9232 (m-10) cc_final: 0.8935 (m-10) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1297 time to fit residues: 27.9556 Evaluate side-chains 105 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 5 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 195 optimal weight: 0.4980 chunk 96 optimal weight: 20.0000 chunk 148 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 160 optimal weight: 0.1980 chunk 59 optimal weight: 5.9990 chunk 233 optimal weight: 7.9990 chunk 138 optimal weight: 8.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN A 870 GLN A1164 GLN ** A1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1391 GLN ** A1420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 GLN C 90 GLN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.044318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.029982 restraints weight = 164337.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.030878 restraints weight = 111392.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.031510 restraints weight = 83198.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.031974 restraints weight = 68430.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.032256 restraints weight = 58746.658| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 20199 Z= 0.144 Angle : 0.751 36.060 27312 Z= 0.342 Chirality : 0.045 0.261 3000 Planarity : 0.005 0.111 3505 Dihedral : 5.084 25.377 2657 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.12 % Favored : 94.79 % Rotamer: Outliers : 0.09 % Allowed : 1.09 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.17), residues: 2420 helix: 0.55 (0.16), residues: 1042 sheet: -1.20 (0.30), residues: 280 loop : -1.11 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1081 TYR 0.021 0.001 TYR B 508 PHE 0.015 0.001 PHE A 341 TRP 0.023 0.002 TRP A 498 HIS 0.006 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00330 (20183) covalent geometry : angle 0.66145 (27282) hydrogen bonds : bond 0.03681 ( 889) hydrogen bonds : angle 5.36158 ( 2574) metal coordination : bond 0.00805 ( 16) metal coordination : angle 10.74095 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 142 time to evaluate : 0.752 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 519 MET cc_start: 0.9069 (ttp) cc_final: 0.8728 (ttm) REVERT: A 540 MET cc_start: 0.8671 (tmm) cc_final: 0.8464 (tmm) REVERT: A 632 ASP cc_start: 0.7741 (m-30) cc_final: 0.7444 (m-30) REVERT: A 731 MET cc_start: 0.9535 (tmm) cc_final: 0.8984 (tmm) REVERT: A 872 PHE cc_start: 0.9498 (m-80) cc_final: 0.9162 (m-10) REVERT: A 956 MET cc_start: 0.9467 (mmp) cc_final: 0.9167 (mmm) REVERT: A 1228 ASP cc_start: 0.9070 (m-30) cc_final: 0.8545 (p0) REVERT: A 1333 ASP cc_start: 0.9137 (p0) cc_final: 0.8686 (p0) REVERT: A 1446 TYR cc_start: 0.8339 (m-80) cc_final: 0.7963 (m-80) REVERT: B 260 ASP cc_start: 0.9740 (t70) cc_final: 0.9150 (m-30) REVERT: C 1 MET cc_start: 0.8382 (mmm) cc_final: 0.7858 (tpt) REVERT: C 45 PHE cc_start: 0.9702 (m-80) cc_final: 0.9128 (m-80) REVERT: C 73 MET cc_start: 0.9736 (mmp) cc_final: 0.9415 (mpp) REVERT: C 112 MET cc_start: 0.9036 (mmp) cc_final: 0.8612 (mmm) REVERT: C 300 TYR cc_start: 0.8304 (t80) cc_final: 0.7439 (t80) REVERT: D 74 LEU cc_start: 0.9289 (tp) cc_final: 0.9043 (tp) REVERT: D 307 MET cc_start: 0.9451 (ptm) cc_final: 0.9079 (ptm) REVERT: D 347 TYR cc_start: 0.9249 (m-10) cc_final: 0.8949 (m-10) outliers start: 2 outliers final: 0 residues processed: 144 average time/residue: 0.1260 time to fit residues: 29.5015 Evaluate side-chains 114 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 96 optimal weight: 5.9990 chunk 206 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 157 optimal weight: 40.0000 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 chunk 168 optimal weight: 20.0000 chunk 209 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN ** A1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 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 = 0.3328 r_free = 0.3328 target = 0.044470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.030105 restraints weight = 164975.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.031002 restraints weight = 111449.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.031622 restraints weight = 83379.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.032008 restraints weight = 68112.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.032394 restraints weight = 58961.852| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 20199 Z= 0.140 Angle : 0.754 34.888 27312 Z= 0.343 Chirality : 0.045 0.253 3000 Planarity : 0.005 0.112 3505 Dihedral : 5.008 25.035 2657 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.00 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.17), residues: 2420 helix: 0.63 (0.16), residues: 1041 sheet: -1.20 (0.30), residues: 280 loop : -1.07 (0.19), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 28 TYR 0.017 0.001 TYR B 508 PHE 0.015 0.001 PHE A 341 TRP 0.027 0.002 TRP C 294 HIS 0.006 0.001 HIS B 278 Details of bonding type rmsd covalent geometry : bond 0.00324 (20183) covalent geometry : angle 0.67000 (27282) hydrogen bonds : bond 0.03652 ( 889) hydrogen bonds : angle 5.32863 ( 2574) metal coordination : bond 0.00768 ( 16) metal coordination : angle 10.46248 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.651 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 519 MET cc_start: 0.9008 (ttp) cc_final: 0.8691 (ttm) REVERT: A 632 ASP cc_start: 0.7661 (m-30) cc_final: 0.7362 (m-30) REVERT: A 683 ASN cc_start: 0.8531 (m110) cc_final: 0.7454 (t0) REVERT: A 731 MET cc_start: 0.9540 (tmm) cc_final: 0.8977 (tmm) REVERT: A 872 PHE cc_start: 0.9496 (m-80) cc_final: 0.9153 (m-10) REVERT: A 956 MET cc_start: 0.9487 (mmp) cc_final: 0.9198 (mmm) REVERT: A 985 MET cc_start: 0.9167 (tmm) cc_final: 0.8812 (tmm) REVERT: A 1047 LEU cc_start: 0.9238 (tt) cc_final: 0.9027 (tt) REVERT: A 1228 ASP cc_start: 0.9116 (m-30) cc_final: 0.8388 (p0) REVERT: A 1333 ASP cc_start: 0.9145 (p0) cc_final: 0.8687 (p0) REVERT: A 1446 TYR cc_start: 0.8306 (m-80) cc_final: 0.7987 (m-80) REVERT: B 260 ASP cc_start: 0.9741 (t70) cc_final: 0.9159 (m-30) REVERT: B 469 PHE cc_start: 0.9305 (m-80) cc_final: 0.8639 (m-80) REVERT: C 1 MET cc_start: 0.8434 (mmm) cc_final: 0.7954 (tpt) REVERT: C 45 PHE cc_start: 0.9707 (m-80) cc_final: 0.9124 (m-80) REVERT: C 73 MET cc_start: 0.9769 (mmp) cc_final: 0.9433 (mpp) REVERT: C 112 MET cc_start: 0.9077 (mmp) cc_final: 0.8650 (mmm) REVERT: C 300 TYR cc_start: 0.8281 (t80) cc_final: 0.7391 (t80) REVERT: D 74 LEU cc_start: 0.9287 (tp) cc_final: 0.9049 (tp) REVERT: D 260 GLN cc_start: 0.8513 (tm-30) cc_final: 0.8044 (tm-30) REVERT: D 307 MET cc_start: 0.9462 (ptm) cc_final: 0.9122 (ptm) REVERT: D 347 TYR cc_start: 0.9248 (m-10) cc_final: 0.8941 (m-10) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1277 time to fit residues: 30.2351 Evaluate side-chains 118 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 188 optimal weight: 7.9990 chunk 93 optimal weight: 0.1980 chunk 197 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 177 optimal weight: 20.0000 chunk 147 optimal weight: 8.9990 chunk 11 optimal weight: 20.0000 chunk 162 optimal weight: 7.9990 chunk 239 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 overall best weight: 6.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN ** A1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1391 GLN ** A1420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.043408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.029316 restraints weight = 168406.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.030127 restraints weight = 113197.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.030744 restraints weight = 85548.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.031153 restraints weight = 70115.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.031408 restraints weight = 61236.037| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 20199 Z= 0.196 Angle : 0.779 34.250 27312 Z= 0.358 Chirality : 0.045 0.247 3000 Planarity : 0.005 0.115 3505 Dihedral : 5.075 25.264 2657 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.66 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.17), residues: 2420 helix: 0.53 (0.16), residues: 1056 sheet: -1.23 (0.29), residues: 286 loop : -1.09 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 24 TYR 0.030 0.002 TYR D 257 PHE 0.018 0.002 PHE A 861 TRP 0.031 0.002 TRP C 29 HIS 0.007 0.001 HIS B 278 Details of bonding type rmsd covalent geometry : bond 0.00433 (20183) covalent geometry : angle 0.69278 (27282) hydrogen bonds : bond 0.03731 ( 889) hydrogen bonds : angle 5.42202 ( 2574) metal coordination : bond 0.01252 ( 16) metal coordination : angle 10.78689 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3247.56 seconds wall clock time: 57 minutes 56.02 seconds (3476.02 seconds total)