Starting phenix.real_space_refine on Sat Jun 6 04:49:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w3g_65600/06_2026/9w3g_65600.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w3g_65600/06_2026/9w3g_65600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w3g_65600/06_2026/9w3g_65600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w3g_65600/06_2026/9w3g_65600.map" model { file = "/net/cci-nas-00/data/ceres_data/9w3g_65600/06_2026/9w3g_65600.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w3g_65600/06_2026/9w3g_65600.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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: 4 Type Number sf(0) Gaussians S 118 5.16 5 C 16000 2.51 5 N 4535 2.21 5 O 4885 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25538 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1759 Classifications: {'peptide': 227} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 217} Chain: "B" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1743 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 215} Chain: "C" Number of atoms: 9670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1228, 9670 Classifications: {'peptide': 1228} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1173} Chain breaks: 1 Chain: "D" Number of atoms: 8994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1149, 8994 Classifications: {'peptide': 1149} Link IDs: {'PCIS': 2, 'PTRANS': 45, 'TRANS': 1101} Chain breaks: 1 Chain: "E" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 534 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "F" Number of atoms: 2320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2320 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain breaks: 1 Chain: "G" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 518 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Time building chain proxies: 5.32, per 1000 atoms: 0.21 Number of scatterers: 25538 At special positions: 0 Unit cell: (130.9, 147.56, 151.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 118 16.00 O 4885 8.00 N 4535 7.00 C 16000 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: 1.95 Conformation dependent library (CDL) restraints added in 1.1 seconds 6448 Ramachandran restraints generated. 3224 Oldfield, 0 Emsley, 3224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6018 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 39 sheets defined 45.5% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.655A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.886A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.546A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N HIS A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.311A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 51 removed outlier: 3.664A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N MET B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 154 through 162 removed outlier: 3.568A pdb=" N HIS B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 230 removed outlier: 4.222A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 10 removed outlier: 3.674A pdb=" N LYS C 9 " --> pdb=" O TYR C 5 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.846A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 57 removed outlier: 3.999A pdb=" N ALA C 51 " --> pdb=" O TYR C 47 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 4.056A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 removed outlier: 3.729A pdb=" N ALA C 362 " --> pdb=" O ASP C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 390 removed outlier: 4.098A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 480 removed outlier: 3.915A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 509 removed outlier: 3.556A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.655A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.549A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 612 removed outlier: 4.011A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 608 through 612' Processing helix chain 'C' and resid 662 through 667 Processing helix chain 'C' and resid 675 through 687 removed outlier: 3.709A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 738 through 741 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 896 through 906 removed outlier: 3.711A pdb=" N PHE C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 982 removed outlier: 3.728A pdb=" N GLY C 970 " --> pdb=" O ILE C 966 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU C 971 " --> pdb=" O LEU C 967 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 992 Processing helix chain 'C' and resid 1004 through 1038 Processing helix chain 'C' and resid 1081 through 1085 removed outlier: 3.776A pdb=" N MET C1085 " --> pdb=" O ILE C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 4.183A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1272 through 1282 Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1297 through 1310 removed outlier: 3.784A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 77 through 81 removed outlier: 3.982A pdb=" N HIS D 80 " --> pdb=" O ARG D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 181 through 192 removed outlier: 3.524A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.890A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 3.538A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 263 through 286 removed outlier: 3.987A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 336 through 343 removed outlier: 4.232A pdb=" N LEU D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 405 through 417 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 515 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 580 Processing helix chain 'D' and resid 581 through 583 No H-bonds generated for 'chain 'D' and resid 581 through 583' Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.671A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 removed outlier: 3.771A pdb=" N SER D 655 " --> pdb=" O HIS D 651 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA D 659 " --> pdb=" O SER D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 702 Processing helix chain 'D' and resid 720 through 728 removed outlier: 3.715A pdb=" N SER D 728 " --> pdb=" O MET D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 4.193A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.820A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 1139 through 1146 Processing helix chain 'D' and resid 1216 through 1225 removed outlier: 3.616A pdb=" N GLY D1225 " --> pdb=" O LEU D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.649A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.287A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1353 removed outlier: 3.823A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1372 Processing helix chain 'E' and resid 7 through 14 Processing helix chain 'E' and resid 15 through 32 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 72 Processing helix chain 'F' and resid 97 through 107 Processing helix chain 'F' and resid 112 through 132 Processing helix chain 'F' and resid 363 through 383 Processing helix chain 'F' and resid 383 through 392 Processing helix chain 'F' and resid 400 through 418 Processing helix chain 'F' and resid 420 through 424 removed outlier: 3.820A pdb=" N ARG F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY F 424 " --> pdb=" O TYR F 421 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 420 through 424' Processing helix chain 'F' and resid 426 through 447 removed outlier: 3.760A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 475 Processing helix chain 'F' and resid 479 through 488 Processing helix chain 'F' and resid 490 through 501 Processing helix chain 'F' and resid 518 through 523 removed outlier: 3.888A pdb=" N ILE F 523 " --> pdb=" O GLY F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 551 Processing helix chain 'F' and resid 552 through 564 Processing helix chain 'F' and resid 572 through 580 Processing helix chain 'F' and resid 583 through 599 removed outlier: 3.551A pdb=" N ILE F 587 " --> pdb=" O THR F 583 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 21 Processing helix chain 'G' and resid 25 through 43 Processing helix chain 'G' and resid 43 through 66 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 18 removed outlier: 5.721A pdb=" N HIS A 23 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N THR A 207 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LYS A 25 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N MET A 205 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N THR A 27 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE A 203 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU A 29 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU A 201 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N THR A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL A 192 " --> pdb=" O THR A 196 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU A 198 " --> pdb=" O ALA A 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.694A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 13 through 18 removed outlier: 6.440A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR B 196 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ARG B 191 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU B 198 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ALA B 189 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LYS B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL B 187 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B 202 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR B 185 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLU B 204 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE B 183 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLU B 206 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 105 removed outlier: 6.408A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 Processing sheet with id=AB1, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.259A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.095A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.407A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 159 removed outlier: 4.794A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 580 through 581 removed outlier: 7.051A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AB9, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.454A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.793A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 755 through 758 Processing sheet with id=AC3, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC4, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.540A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.821A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AC7, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.635A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 6.380A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1268 through 1271 removed outlier: 3.800A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1335 through 1340 Processing sheet with id=AD2, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.680A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 10.080A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.630A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 159 through 160 removed outlier: 7.401A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 253 through 254 removed outlier: 6.515A pdb=" N PHE D 260 " --> pdb=" O ILE F 505 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AD6, first strand: chain 'D' and resid 703 through 707 Processing sheet with id=AD7, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AD8, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AD9, first strand: chain 'D' and resid 825 through 827 removed outlier: 6.362A pdb=" N GLU D 827 " --> pdb=" O VAL D 831 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N VAL D 831 " --> pdb=" O GLU D 827 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 848 through 849 removed outlier: 6.733A pdb=" N VAL D 848 " --> pdb=" O LEU D 857 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1186 through 1191 Processing sheet with id=AE3, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 4.568A pdb=" N LYS D1263 " --> pdb=" O ASP D1305 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) 1240 hydrogen bonds defined for protein. 3570 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: 6.13 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8653 1.34 - 1.46: 4967 1.46 - 1.58: 12089 1.58 - 1.71: 2 1.71 - 1.83: 208 Bond restraints: 25919 Sorted by residual: bond pdb=" N VAL C1103 " pdb=" CA VAL C1103 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.23e-02 6.61e+03 7.74e+00 bond pdb=" CB PRO B 109 " pdb=" CG PRO B 109 " ideal model delta sigma weight residual 1.492 1.625 -0.133 5.00e-02 4.00e+02 7.06e+00 bond pdb=" N MET C 488 " pdb=" CA MET C 488 " ideal model delta sigma weight residual 1.453 1.482 -0.030 1.18e-02 7.18e+03 6.30e+00 bond pdb=" CA MET C 488 " pdb=" C MET C 488 " ideal model delta sigma weight residual 1.520 1.545 -0.024 9.90e-03 1.02e+04 5.96e+00 bond pdb=" C ILE D1190 " pdb=" N PRO D1191 " ideal model delta sigma weight residual 1.332 1.363 -0.031 1.32e-02 5.74e+03 5.65e+00 ... (remaining 25914 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 34663 2.91 - 5.82: 275 5.82 - 8.74: 31 8.74 - 11.65: 3 11.65 - 14.56: 5 Bond angle restraints: 34977 Sorted by residual: angle pdb=" CA PRO B 109 " pdb=" N PRO B 109 " pdb=" CD PRO B 109 " ideal model delta sigma weight residual 112.00 105.53 6.47 1.40e+00 5.10e-01 2.13e+01 angle pdb=" CA GLU F 481 " pdb=" CB GLU F 481 " pdb=" CG GLU F 481 " ideal model delta sigma weight residual 114.10 123.31 -9.21 2.00e+00 2.50e-01 2.12e+01 angle pdb=" C ILE A 211 " pdb=" N ASP A 212 " pdb=" CA ASP A 212 " ideal model delta sigma weight residual 121.61 127.90 -6.29 1.39e+00 5.18e-01 2.05e+01 angle pdb=" CB MET C 370 " pdb=" CG MET C 370 " pdb=" SD MET C 370 " ideal model delta sigma weight residual 112.70 125.52 -12.82 3.00e+00 1.11e-01 1.82e+01 angle pdb=" CA LEU F 498 " pdb=" CB LEU F 498 " pdb=" CG LEU F 498 " ideal model delta sigma weight residual 116.30 130.86 -14.56 3.50e+00 8.16e-02 1.73e+01 ... (remaining 34972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 13914 17.84 - 35.68: 1616 35.68 - 53.52: 404 53.52 - 71.36: 68 71.36 - 89.21: 26 Dihedral angle restraints: 16028 sinusoidal: 6689 harmonic: 9339 Sorted by residual: dihedral pdb=" CA GLY C 907 " pdb=" C GLY C 907 " pdb=" N GLU C 908 " pdb=" CA GLU C 908 " ideal model delta harmonic sigma weight residual 180.00 -156.52 -23.48 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA ILE C 905 " pdb=" C ILE C 905 " pdb=" N PHE C 906 " pdb=" CA PHE C 906 " ideal model delta harmonic sigma weight residual -180.00 -158.74 -21.26 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA ARG C 368 " pdb=" C ARG C 368 " pdb=" N MET C 369 " pdb=" CA MET C 369 " ideal model delta harmonic sigma weight residual 180.00 159.36 20.64 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 16025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3398 0.066 - 0.132: 524 0.132 - 0.198: 36 0.198 - 0.264: 7 0.264 - 0.331: 1 Chirality restraints: 3966 Sorted by residual: chirality pdb=" CB THR D 218 " pdb=" CA THR D 218 " pdb=" OG1 THR D 218 " pdb=" CG2 THR D 218 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA MET C 488 " pdb=" N MET C 488 " pdb=" C MET C 488 " pdb=" CB MET C 488 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CG LEU D 120 " pdb=" CB LEU D 120 " pdb=" CD1 LEU D 120 " pdb=" CD2 LEU D 120 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 3963 not shown) Planarity restraints: 4592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 723 " 0.017 2.00e-02 2.50e+03 2.70e-02 1.46e+01 pdb=" CG TYR D 723 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR D 723 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR D 723 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR D 723 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR D 723 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR D 723 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 723 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 357 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.94e+00 pdb=" C VAL D 357 " -0.052 2.00e-02 2.50e+03 pdb=" O VAL D 357 " 0.020 2.00e-02 2.50e+03 pdb=" N GLY D 358 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 129 " 0.015 2.00e-02 2.50e+03 2.93e-02 8.57e+00 pdb=" C ASP D 129 " -0.051 2.00e-02 2.50e+03 pdb=" O ASP D 129 " 0.019 2.00e-02 2.50e+03 pdb=" N MET D 130 " 0.017 2.00e-02 2.50e+03 ... (remaining 4589 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5786 2.79 - 3.32: 21935 3.32 - 3.85: 42491 3.85 - 4.37: 49344 4.37 - 4.90: 86046 Nonbonded interactions: 205602 Sorted by model distance: nonbonded pdb=" O GLY D 613 " pdb=" OG1 THR D 617 " model vdw 2.265 3.040 nonbonded pdb=" O TYR C 346 " pdb=" OG1 THR C 350 " model vdw 2.286 3.040 nonbonded pdb=" OG SER C1322 " pdb=" OD1 ASN D 341 " model vdw 2.314 3.040 nonbonded pdb=" O ILE D1309 " pdb=" OG SER D1313 " model vdw 2.320 3.040 nonbonded pdb=" O SER D1271 " pdb=" OG SER D1271 " model vdw 2.330 3.040 ... (remaining 205597 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 8 through 232) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 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: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 24.880 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 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 0.133 25919 Z= 0.194 Angle : 0.733 14.559 34977 Z= 0.398 Chirality : 0.047 0.331 3966 Planarity : 0.006 0.074 4592 Dihedral : 16.156 89.205 10010 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.32 % Allowed : 16.37 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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: -0.73 (0.13), residues: 3224 helix: -0.71 (0.12), residues: 1359 sheet: 0.11 (0.25), residues: 403 loop : -0.22 (0.15), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 394 TYR 0.064 0.002 TYR D 723 PHE 0.024 0.002 PHE C 224 TRP 0.014 0.001 TRP D 868 HIS 0.008 0.001 HIS C1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (25919) covalent geometry : angle 0.73277 / 0.40 (34977) hydrogen bonds : bond 0.13575 / 9.50 ( 1238) hydrogen bonds : angle 6.26713 / 4.36 ( 3570) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6448 Ramachandran restraints generated. 3224 Oldfield, 0 Emsley, 3224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6448 Ramachandran restraints generated. 3224 Oldfield, 0 Emsley, 3224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 270 time to evaluate : 0.668 Fit side-chains REVERT: D 1244 GLN cc_start: 0.8006 (mp10) cc_final: 0.7612 (mp10) REVERT: D 1325 PHE cc_start: 0.6762 (t80) cc_final: 0.6525 (t80) REVERT: E 30 MET cc_start: 0.7579 (mtp) cc_final: 0.7347 (mtm) REVERT: F 105 MET cc_start: 0.6712 (ppp) cc_final: 0.6505 (ppp) REVERT: G 6 LYS cc_start: 0.7233 (mmmt) cc_final: 0.6154 (tttp) outliers start: 9 outliers final: 6 residues processed: 275 average time/residue: 0.1636 time to fit residues: 70.9844 Evaluate side-chains 259 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 253 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 867 GLU Chi-restraints excluded: chain D residue 724 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 7.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS B 84 ASN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C1038 GLN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.145101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.110463 restraints weight = 35390.997| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.95 r_work: 0.3049 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25919 Z= 0.163 Angle : 0.505 8.797 34977 Z= 0.266 Chirality : 0.041 0.146 3966 Planarity : 0.005 0.047 4592 Dihedral : 4.338 46.063 3580 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.05 % Allowed : 15.83 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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: 0.63 (0.14), residues: 3224 helix: 0.92 (0.13), residues: 1380 sheet: 0.22 (0.25), residues: 376 loop : 0.14 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 170 TYR 0.011 0.001 TYR D 511 PHE 0.015 0.001 PHE C 405 TRP 0.010 0.001 TRP G 47 HIS 0.006 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (25919) covalent geometry : angle 0.50484 / 0.27 (34977) hydrogen bonds : bond 0.04111 / 2.79 ( 1238) hydrogen bonds : angle 4.54509 / 3.18 ( 3570) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6448 Ramachandran restraints generated. 3224 Oldfield, 0 Emsley, 3224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6448 Ramachandran restraints generated. 3224 Oldfield, 0 Emsley, 3224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 255 time to evaluate : 0.860 Fit side-chains REVERT: B 86 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7420 (ttpp) REVERT: C 492 MET cc_start: 0.8375 (mtp) cc_final: 0.7852 (mtp) REVERT: C 541 GLU cc_start: 0.5065 (mp0) cc_final: 0.4751 (pp20) REVERT: C 951 MET cc_start: 0.8614 (mtm) cc_final: 0.8383 (mtm) REVERT: D 430 HIS cc_start: 0.8616 (OUTLIER) cc_final: 0.7578 (p90) REVERT: D 723 TYR cc_start: 0.7667 (t80) cc_final: 0.7387 (t80) REVERT: F 598 LEU cc_start: 0.6326 (tp) cc_final: 0.5958 (mt) outliers start: 57 outliers final: 33 residues processed: 296 average time/residue: 0.1642 time to fit residues: 76.8208 Evaluate side-chains 273 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 238 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 1109 ILE Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 1138 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 426 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 307 optimal weight: 6.9990 chunk 172 optimal weight: 0.8980 chunk 260 optimal weight: 0.0970 chunk 17 optimal weight: 0.8980 chunk 118 optimal weight: 6.9990 chunk 149 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 221 optimal weight: 8.9990 chunk 191 optimal weight: 5.9990 chunk 279 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 856 ASN D 341 ASN ** D 875 ASN ** 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 = 0.3770 r_free = 0.3770 target = 0.147945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.113108 restraints weight = 35171.104| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.86 r_work: 0.3089 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25919 Z= 0.087 Angle : 0.417 8.921 34977 Z= 0.220 Chirality : 0.039 0.139 3966 Planarity : 0.004 0.047 4592 Dihedral : 3.699 31.673 3569 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.30 % Allowed : 16.80 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.15), residues: 3224 helix: 1.72 (0.14), residues: 1377 sheet: 0.16 (0.26), residues: 370 loop : 0.40 (0.16), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 293 TYR 0.012 0.001 TYR B 152 PHE 0.010 0.001 PHE B 231 TRP 0.007 0.001 TRP G 47 HIS 0.009 0.001 HIS C1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00187 / 0.09 (25919) covalent geometry : angle 0.41677 / 0.22 (34977) hydrogen bonds : bond 0.03286 / 2.23 ( 1238) hydrogen bonds : angle 4.16048 / 2.92 ( 3570) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6448 Ramachandran restraints generated. 3224 Oldfield, 0 Emsley, 3224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6448 Ramachandran restraints generated. 3224 Oldfield, 0 Emsley, 3224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 270 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: B 86 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.7238 (ttpp) REVERT: B 183 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8738 (tt) REVERT: C 47 TYR cc_start: 0.8240 (OUTLIER) cc_final: 0.8022 (m-80) REVERT: C 492 MET cc_start: 0.8214 (mtp) cc_final: 0.7688 (mtp) REVERT: C 541 GLU cc_start: 0.5062 (mp0) cc_final: 0.4794 (pp20) REVERT: C 731 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7613 (ptt180) REVERT: C 1315 MET cc_start: 0.7567 (ptp) cc_final: 0.7290 (ptp) REVERT: F 598 LEU cc_start: 0.6454 (tp) cc_final: 0.6125 (mt) outliers start: 36 outliers final: 22 residues processed: 297 average time/residue: 0.1633 time to fit residues: 77.2553 Evaluate side-chains 271 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 245 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 867 GLU Chi-restraints excluded: chain C residue 963 GLU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 1138 LEU Chi-restraints excluded: chain D residue 1349 GLU Chi-restraints excluded: chain E residue 58 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 280 optimal weight: 0.3980 chunk 249 optimal weight: 0.6980 chunk 171 optimal weight: 0.0670 chunk 89 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 56 optimal weight: 0.2980 chunk 254 optimal weight: 9.9990 chunk 319 optimal weight: 4.9990 chunk 313 optimal weight: 1.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN C 856 ASN D 465 GLN D 875 ASN F 545 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.148508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.113709 restraints weight = 34954.287| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.93 r_work: 0.3097 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25919 Z= 0.083 Angle : 0.413 8.633 34977 Z= 0.216 Chirality : 0.039 0.179 3966 Planarity : 0.003 0.047 4592 Dihedral : 3.488 21.739 3567 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.66 % Allowed : 16.98 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.15), residues: 3224 helix: 2.12 (0.14), residues: 1370 sheet: 0.29 (0.26), residues: 368 loop : 0.52 (0.16), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 562 TYR 0.011 0.001 TYR B 152 PHE 0.010 0.001 PHE F 427 TRP 0.007 0.001 TRP G 47 HIS 0.008 0.001 HIS C1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00182 / 0.08 (25919) covalent geometry : angle 0.41256 / 0.22 (34977) hydrogen bonds : bond 0.03100 / 2.10 ( 1238) hydrogen bonds : angle 4.00591 / 2.81 ( 3570) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6448 Ramachandran restraints generated. 3224 Oldfield, 0 Emsley, 3224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6448 Ramachandran restraints generated. 3224 Oldfield, 0 Emsley, 3224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 261 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: B 86 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7381 (ttpp) REVERT: B 181 GLU cc_start: 0.7469 (tt0) cc_final: 0.7196 (tp30) REVERT: C 492 MET cc_start: 0.8237 (mtp) cc_final: 0.7865 (mtp) REVERT: C 541 GLU cc_start: 0.5080 (mp0) cc_final: 0.4720 (pp20) REVERT: C 731 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7634 (ptt180) REVERT: C 1315 MET cc_start: 0.7503 (ptp) cc_final: 0.7228 (ptp) REVERT: D 430 HIS cc_start: 0.8315 (OUTLIER) cc_final: 0.7188 (p90) REVERT: D 870 ASP cc_start: 0.6249 (m-30) cc_final: 0.5737 (m-30) REVERT: D 1244 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7319 (mt0) REVERT: F 598 LEU cc_start: 0.6673 (tp) cc_final: 0.6260 (mt) REVERT: G 46 MET cc_start: 0.7207 (mmp) cc_final: 0.6954 (mmm) outliers start: 46 outliers final: 27 residues processed: 296 average time/residue: 0.1693 time to fit residues: 79.1917 Evaluate side-chains 275 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 244 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 867 GLU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 1138 LEU Chi-restraints excluded: chain D residue 1244 GLN Chi-restraints excluded: chain D residue 1349 GLU Chi-restraints excluded: chain E residue 58 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 48 optimal weight: 10.0000 chunk 290 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 39 optimal weight: 0.3980 chunk 141 optimal weight: 4.9990 chunk 317 optimal weight: 10.0000 chunk 148 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN E 29 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.142793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.109481 restraints weight = 35459.422| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.00 r_work: 0.3003 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 25919 Z= 0.257 Angle : 0.585 7.952 34977 Z= 0.303 Chirality : 0.045 0.208 3966 Planarity : 0.005 0.047 4592 Dihedral : 4.182 21.164 3567 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.78 % Allowed : 16.40 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.14), residues: 3224 helix: 1.62 (0.14), residues: 1385 sheet: 0.04 (0.25), residues: 377 loop : 0.28 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 170 TYR 0.015 0.002 TYR C1229 PHE 0.019 0.002 PHE B 231 TRP 0.013 0.002 TRP D 686 HIS 0.007 0.001 HIS C 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.26 (25919) covalent geometry : angle 0.58518 / 0.30 (34977) hydrogen bonds : bond 0.04497 / 3.02 ( 1238) hydrogen bonds : angle 4.45812 / 3.12 ( 3570) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6448 Ramachandran restraints generated. 3224 Oldfield, 0 Emsley, 3224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6448 Ramachandran restraints generated. 3224 Oldfield, 0 Emsley, 3224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 248 time to evaluate : 0.926 Fit side-chains REVERT: B 28 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8291 (tt) REVERT: B 181 GLU cc_start: 0.7748 (tt0) cc_final: 0.7533 (tp30) REVERT: C 492 MET cc_start: 0.8291 (mtp) cc_final: 0.7957 (mtp) REVERT: C 504 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8281 (tt0) REVERT: C 541 GLU cc_start: 0.5315 (mp0) cc_final: 0.4936 (pp20) REVERT: C 728 ASP cc_start: 0.8455 (t0) cc_final: 0.8251 (t0) REVERT: C 731 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7691 (ptt180) REVERT: C 773 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8841 (mp) REVERT: C 951 MET cc_start: 0.8606 (mtm) cc_final: 0.8397 (mtm) REVERT: D 430 HIS cc_start: 0.8603 (OUTLIER) cc_final: 0.7722 (p-80) REVERT: D 1244 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7313 (mt0) REVERT: F 385 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7775 (mtp85) outliers start: 77 outliers final: 53 residues processed: 307 average time/residue: 0.1619 time to fit residues: 78.9196 Evaluate side-chains 300 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 240 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 867 GLU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 892 PHE Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 1138 LEU Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1244 GLN Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1349 GLU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 385 ARG Chi-restraints excluded: chain F residue 524 GLU Chi-restraints excluded: chain F residue 537 THR Chi-restraints excluded: chain F residue 607 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 143 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 208 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 283 optimal weight: 6.9990 chunk 299 optimal weight: 1.9990 chunk 296 optimal weight: 6.9990 chunk 260 optimal weight: 5.9990 chunk 231 optimal weight: 20.0000 chunk 102 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN B 132 HIS ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1244 HIS D 910 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.145235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.112482 restraints weight = 35222.840| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.94 r_work: 0.3055 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25919 Z= 0.115 Angle : 0.451 8.803 34977 Z= 0.235 Chirality : 0.040 0.168 3966 Planarity : 0.004 0.048 4592 Dihedral : 3.776 20.927 3567 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.34 % Allowed : 16.91 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.15), residues: 3224 helix: 2.04 (0.14), residues: 1372 sheet: 0.14 (0.26), residues: 374 loop : 0.41 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 974 TYR 0.014 0.001 TYR D 723 PHE 0.010 0.001 PHE B 231 TRP 0.008 0.001 TRP G 47 HIS 0.006 0.001 HIS C1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 (25919) covalent geometry : angle 0.45101 / 0.24 (34977) hydrogen bonds : bond 0.03512 / 2.37 ( 1238) hydrogen bonds : angle 4.15031 / 2.92 ( 3570) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6448 Ramachandran restraints generated. 3224 Oldfield, 0 Emsley, 3224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6448 Ramachandran restraints generated. 3224 Oldfield, 0 Emsley, 3224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 249 time to evaluate : 0.725 Fit side-chains REVERT: B 28 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8255 (tt) REVERT: B 86 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7430 (ttpp) REVERT: C 492 MET cc_start: 0.8255 (mtp) cc_final: 0.7932 (mtp) REVERT: C 541 GLU cc_start: 0.5167 (mp0) cc_final: 0.4880 (pp20) REVERT: C 731 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7768 (ptt180) REVERT: C 773 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8780 (mp) REVERT: D 135 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.8089 (tt) REVERT: D 430 HIS cc_start: 0.8595 (OUTLIER) cc_final: 0.7529 (p90) REVERT: D 870 ASP cc_start: 0.6245 (m-30) cc_final: 0.5704 (m-30) REVERT: D 1244 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7247 (mt0) REVERT: F 385 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7813 (mtp85) REVERT: F 561 MET cc_start: 0.5036 (mpp) cc_final: 0.4757 (mtp) REVERT: F 580 PHE cc_start: 0.1366 (OUTLIER) cc_final: 0.0336 (t80) REVERT: F 598 LEU cc_start: 0.6651 (tp) cc_final: 0.6339 (mt) outliers start: 65 outliers final: 48 residues processed: 299 average time/residue: 0.1657 time to fit residues: 78.7498 Evaluate side-chains 296 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 239 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 867 GLU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 1109 ILE Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 892 PHE Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 1138 LEU Chi-restraints excluded: chain D residue 1244 GLN Chi-restraints excluded: chain D residue 1280 VAL Chi-restraints excluded: chain D residue 1349 GLU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 385 ARG Chi-restraints excluded: chain F residue 426 LYS Chi-restraints excluded: chain F residue 524 GLU Chi-restraints excluded: chain F residue 580 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 56 optimal weight: 0.0070 chunk 67 optimal weight: 5.9990 chunk 164 optimal weight: 0.0670 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 27 optimal weight: 0.0570 chunk 205 optimal weight: 0.0970 chunk 213 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 276 optimal weight: 7.9990 overall best weight: 0.2052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN C 554 HIS C 856 ASN C1244 HIS D 777 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.149563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.115354 restraints weight = 35011.891| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.88 r_work: 0.3127 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25919 Z= 0.076 Angle : 0.409 8.791 34977 Z= 0.213 Chirality : 0.039 0.168 3966 Planarity : 0.003 0.048 4592 Dihedral : 3.371 20.235 3567 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.62 % Allowed : 17.45 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.15), residues: 3224 helix: 2.39 (0.14), residues: 1380 sheet: 0.28 (0.26), residues: 376 loop : 0.55 (0.17), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 562 TYR 0.012 0.001 TYR D 723 PHE 0.011 0.001 PHE C 405 TRP 0.011 0.001 TRP D 33 HIS 0.008 0.001 HIS C1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00157 / 0.08 (25919) covalent geometry : angle 0.40900 / 0.21 (34977) hydrogen bonds : bond 0.02841 / 1.92 ( 1238) hydrogen bonds : angle 3.85997 / 2.72 ( 3570) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6448 Ramachandran restraints generated. 3224 Oldfield, 0 Emsley, 3224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6448 Ramachandran restraints generated. 3224 Oldfield, 0 Emsley, 3224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 274 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: C 158 ASP cc_start: 0.7306 (t0) cc_final: 0.7028 (t0) REVERT: C 492 MET cc_start: 0.8274 (mtp) cc_final: 0.7943 (mtp) REVERT: C 541 GLU cc_start: 0.5131 (mp0) cc_final: 0.4857 (pp20) REVERT: C 731 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7503 (ptt180) REVERT: D 29 MET cc_start: 0.7563 (tpt) cc_final: 0.7359 (tpt) REVERT: D 102 MET cc_start: 0.8866 (mtp) cc_final: 0.8520 (ttm) REVERT: D 135 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7923 (tt) REVERT: D 180 MET cc_start: 0.8145 (ttm) cc_final: 0.7825 (ttm) REVERT: D 743 MET cc_start: 0.5758 (ptm) cc_final: 0.5217 (ptp) REVERT: D 870 ASP cc_start: 0.6135 (m-30) cc_final: 0.5576 (m-30) REVERT: D 1244 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7207 (mt0) REVERT: F 385 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7852 (mtp85) REVERT: F 580 PHE cc_start: 0.1472 (OUTLIER) cc_final: 0.0522 (t80) REVERT: F 598 LEU cc_start: 0.6464 (tp) cc_final: 0.5971 (mt) outliers start: 45 outliers final: 27 residues processed: 308 average time/residue: 0.1661 time to fit residues: 81.2625 Evaluate side-chains 284 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 252 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 867 GLU Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 1138 LEU Chi-restraints excluded: chain D residue 1244 GLN Chi-restraints excluded: chain D residue 1280 VAL Chi-restraints excluded: chain D residue 1349 GLU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 385 ARG Chi-restraints excluded: chain F residue 580 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 246 optimal weight: 0.4980 chunk 171 optimal weight: 20.0000 chunk 160 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 186 optimal weight: 9.9990 chunk 139 optimal weight: 9.9990 chunk 157 optimal weight: 7.9990 chunk 128 optimal weight: 4.9990 chunk 229 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 243 optimal weight: 20.0000 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN C 856 ASN C1244 HIS D 519 ASN F 545 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.142586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.107178 restraints weight = 35409.330| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.99 r_work: 0.2986 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 25919 Z= 0.223 Angle : 0.544 8.191 34977 Z= 0.281 Chirality : 0.044 0.234 3966 Planarity : 0.004 0.049 4592 Dihedral : 3.959 20.107 3567 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.24 % Allowed : 17.16 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.15), residues: 3224 helix: 1.94 (0.14), residues: 1386 sheet: 0.09 (0.26), residues: 381 loop : 0.35 (0.16), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 170 TYR 0.017 0.002 TYR C1229 PHE 0.018 0.002 PHE B 231 TRP 0.013 0.002 TRP D 686 HIS 0.007 0.001 HIS C1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.22 (25919) covalent geometry : angle 0.54450 / 0.28 (34977) hydrogen bonds : bond 0.04114 / 2.76 ( 1238) hydrogen bonds : angle 4.23633 / 2.97 ( 3570) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6448 Ramachandran restraints generated. 3224 Oldfield, 0 Emsley, 3224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6448 Ramachandran restraints generated. 3224 Oldfield, 0 Emsley, 3224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 251 time to evaluate : 0.897 Fit side-chains REVERT: B 116 THR cc_start: 0.6111 (OUTLIER) cc_final: 0.5566 (p) REVERT: C 492 MET cc_start: 0.8206 (mtp) cc_final: 0.7890 (mtp) REVERT: C 504 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7981 (tt0) REVERT: C 541 GLU cc_start: 0.5345 (mp0) cc_final: 0.5082 (pp20) REVERT: C 731 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7721 (ptt180) REVERT: D 135 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.8002 (tt) REVERT: D 430 HIS cc_start: 0.8388 (OUTLIER) cc_final: 0.7280 (p90) REVERT: D 519 ASN cc_start: 0.7318 (OUTLIER) cc_final: 0.7108 (m110) REVERT: D 1244 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7205 (mt0) REVERT: F 385 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7551 (mtp85) REVERT: F 538 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6919 (mt-10) REVERT: F 580 PHE cc_start: 0.1752 (OUTLIER) cc_final: 0.0767 (t80) REVERT: F 598 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.6393 (mt) outliers start: 62 outliers final: 43 residues processed: 300 average time/residue: 0.1611 time to fit residues: 76.7764 Evaluate side-chains 299 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 245 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 867 GLU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1109 ILE Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 519 ASN Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 892 PHE Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 1138 LEU Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1244 GLN Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1280 VAL Chi-restraints excluded: chain D residue 1349 GLU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 385 ARG Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 538 GLU Chi-restraints excluded: chain F residue 580 PHE Chi-restraints excluded: chain F residue 598 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 164 optimal weight: 3.9990 chunk 294 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 230 optimal weight: 20.0000 chunk 241 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 226 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 273 optimal weight: 20.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN C 856 ASN ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1244 HIS D 488 ASN D 519 ASN D 777 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.144403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.108829 restraints weight = 35322.831| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.95 r_work: 0.3016 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25919 Z= 0.125 Angle : 0.467 8.413 34977 Z= 0.242 Chirality : 0.041 0.144 3966 Planarity : 0.004 0.049 4592 Dihedral : 3.770 20.575 3567 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.91 % Allowed : 17.59 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.15), residues: 3224 helix: 2.12 (0.14), residues: 1380 sheet: 0.09 (0.26), residues: 379 loop : 0.46 (0.16), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 170 TYR 0.016 0.001 TYR D 723 PHE 0.013 0.001 PHE D 116 TRP 0.009 0.001 TRP G 47 HIS 0.006 0.001 HIS C1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (25919) covalent geometry : angle 0.46663 / 0.24 (34977) hydrogen bonds : bond 0.03545 / 2.39 ( 1238) hydrogen bonds : angle 4.09796 / 2.88 ( 3570) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6448 Ramachandran restraints generated. 3224 Oldfield, 0 Emsley, 3224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6448 Ramachandran restraints generated. 3224 Oldfield, 0 Emsley, 3224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 247 time to evaluate : 0.985 Fit side-chains REVERT: B 116 THR cc_start: 0.6216 (OUTLIER) cc_final: 0.5673 (p) REVERT: C 492 MET cc_start: 0.8246 (mtp) cc_final: 0.7907 (mtp) REVERT: C 504 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7996 (tt0) REVERT: C 541 GLU cc_start: 0.5173 (mp0) cc_final: 0.4970 (pp20) REVERT: C 731 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7696 (ptt180) REVERT: C 773 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8798 (mp) REVERT: C 1216 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8047 (mtm180) REVERT: D 135 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7972 (tt) REVERT: D 430 HIS cc_start: 0.8330 (OUTLIER) cc_final: 0.7219 (p90) REVERT: D 1244 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7121 (mt0) REVERT: F 96 ASP cc_start: 0.5800 (t70) cc_final: 0.5590 (t0) REVERT: F 385 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7591 (mtp85) REVERT: F 580 PHE cc_start: 0.1912 (OUTLIER) cc_final: 0.0643 (t80) REVERT: F 598 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6440 (mt) outliers start: 53 outliers final: 36 residues processed: 290 average time/residue: 0.1661 time to fit residues: 76.4234 Evaluate side-chains 290 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 243 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 867 GLU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1216 ARG Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 1138 LEU Chi-restraints excluded: chain D residue 1244 GLN Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1280 VAL Chi-restraints excluded: chain D residue 1349 GLU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 385 ARG Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 524 GLU Chi-restraints excluded: chain F residue 580 PHE Chi-restraints excluded: chain F residue 598 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 15 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 317 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 234 optimal weight: 20.0000 chunk 74 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 221 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN C 856 ASN C1111 GLN C1244 HIS ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.140532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.104819 restraints weight = 35598.553| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.01 r_work: 0.2960 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 25919 Z= 0.287 Angle : 0.624 8.113 34977 Z= 0.322 Chirality : 0.046 0.267 3966 Planarity : 0.005 0.047 4592 Dihedral : 4.335 20.290 3567 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.27 % Allowed : 17.38 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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: 0.93 (0.14), residues: 3224 helix: 1.52 (0.14), residues: 1388 sheet: -0.25 (0.25), residues: 375 loop : 0.10 (0.16), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 170 TYR 0.021 0.002 TYR D 723 PHE 0.025 0.002 PHE B 231 TRP 0.016 0.002 TRP D 686 HIS 0.008 0.001 HIS C1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00700 / 0.29 (25919) covalent geometry : angle 0.62377 / 0.32 (34977) hydrogen bonds : bond 0.04664 / 3.13 ( 1238) hydrogen bonds : angle 4.51573 / 3.17 ( 3570) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6448 Ramachandran restraints generated. 3224 Oldfield, 0 Emsley, 3224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6448 Ramachandran restraints generated. 3224 Oldfield, 0 Emsley, 3224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 243 time to evaluate : 0.976 Fit side-chains REVERT: B 116 THR cc_start: 0.6308 (OUTLIER) cc_final: 0.5773 (p) REVERT: C 492 MET cc_start: 0.8283 (mtp) cc_final: 0.7979 (mtp) REVERT: C 504 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8003 (tt0) REVERT: C 541 GLU cc_start: 0.5426 (mp0) cc_final: 0.5047 (pp20) REVERT: C 731 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7648 (ptt180) REVERT: C 773 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8837 (mp) REVERT: C 1216 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.7818 (mtm180) REVERT: D 135 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7988 (tt) REVERT: D 430 HIS cc_start: 0.8553 (OUTLIER) cc_final: 0.7513 (p90) REVERT: D 1138 LEU cc_start: 0.5863 (OUTLIER) cc_final: 0.5617 (tp) REVERT: D 1244 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7074 (mt0) REVERT: F 385 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7572 (mtp85) REVERT: F 580 PHE cc_start: 0.2116 (OUTLIER) cc_final: 0.0801 (t80) REVERT: F 598 LEU cc_start: 0.6416 (OUTLIER) cc_final: 0.6144 (mt) outliers start: 63 outliers final: 46 residues processed: 295 average time/residue: 0.1749 time to fit residues: 82.8337 Evaluate side-chains 296 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 238 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 867 GLU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1109 ILE Chi-restraints excluded: chain C residue 1216 ARG Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 892 PHE Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 1138 LEU Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1244 GLN Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1280 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 385 ARG Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 524 GLU Chi-restraints excluded: chain F residue 580 PHE Chi-restraints excluded: chain F residue 598 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 276 optimal weight: 0.9990 chunk 30 optimal weight: 20.0000 chunk 142 optimal weight: 0.9980 chunk 244 optimal weight: 5.9990 chunk 262 optimal weight: 5.9990 chunk 239 optimal weight: 0.0010 chunk 236 optimal weight: 9.9990 chunk 166 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 241 optimal weight: 1.9990 chunk 270 optimal weight: 0.0020 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN C 856 ASN C1244 HIS D 777 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.145052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.110317 restraints weight = 34830.206| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.86 r_work: 0.3054 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25919 Z= 0.091 Angle : 0.450 8.933 34977 Z= 0.233 Chirality : 0.040 0.196 3966 Planarity : 0.004 0.048 4592 Dihedral : 3.679 19.594 3567 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.51 % Allowed : 18.24 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.15), residues: 3224 helix: 2.16 (0.14), residues: 1381 sheet: -0.06 (0.25), residues: 392 loop : 0.41 (0.17), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1369 TYR 0.015 0.001 TYR B 152 PHE 0.011 0.001 PHE D 116 TRP 0.009 0.001 TRP F 433 HIS 0.004 0.001 HIS A 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 (25919) covalent geometry : angle 0.44968 / 0.23 (34977) hydrogen bonds : bond 0.03238 / 2.19 ( 1238) hydrogen bonds : angle 4.05123 / 2.86 ( 3570) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5580.25 seconds wall clock time: 96 minutes 24.01 seconds (5784.01 seconds total)