Starting phenix.real_space_refine on Sat Mar 7 01:14:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ubn_26439/03_2026/7ubn_26439.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ubn_26439/03_2026/7ubn_26439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ubn_26439/03_2026/7ubn_26439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ubn_26439/03_2026/7ubn_26439.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ubn_26439/03_2026/7ubn_26439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ubn_26439/03_2026/7ubn_26439.map" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1440 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 115 5.49 5 Mg 1 5.21 5 S 149 5.16 5 C 21597 2.51 5 N 6227 2.21 5 O 6977 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 153 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35069 Number of models: 1 Model: "" Number of chains: 13 Chain: "1" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1096 Classifications: {'DNA': 53} Link IDs: {'rna3p': 52} Chain breaks: 1 Chain: "2" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1052 Classifications: {'DNA': 52} Link IDs: {'rna3p': 51} Chain breaks: 1 Chain: "A" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "B" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2274 Classifications: {'peptide': 294} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 281} Chain breaks: 1 Chain: "C" Number of atoms: 10556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1339, 10556 Classifications: {'peptide': 1339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1282} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 10319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1327, 10319 Classifications: {'peptide': 1327} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1271} Chain breaks: 2 Chain: "E" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "F" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2900 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 5, 'TRANS': 347} Chain breaks: 3 Chain: "N" Number of atoms: 2674 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 340, 2666 Classifications: {'peptide': 340} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 328} Conformer: "B" Number of residues, atoms: 340, 2666 Classifications: {'peptide': 340} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 328} bond proxies already assigned to first conformer: 2688 Chain: "Q" Number of atoms: 1567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1567 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 198} Chain: "R" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 241 Classifications: {'RNA': 11} Modifications used: {'5*END': 1, 'rna3p_pur': 9, 'rna3p_pyr': 2} Link IDs: {'rna3p': 10} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17222 SG CYS D 70 83.986 118.430 82.915 1.00 61.33 S ATOM 17236 SG CYS D 72 85.136 121.740 82.557 1.00 65.83 S ATOM 17344 SG CYS D 85 82.473 120.465 79.850 1.00 64.02 S ATOM 17368 SG CYS D 88 85.964 119.396 79.809 1.00 63.48 S ATOM 23056 SG CYS D 814 82.855 52.032 69.562 1.00 92.32 S ATOM 34134 SG CYS Q 118 70.157 119.268 70.454 1.00 90.41 S ATOM 34159 SG CYS Q 121 72.292 119.930 73.328 1.00 93.32 S ATOM 34337 SG CYS Q 144 70.745 122.970 71.567 1.00112.15 S ATOM 34358 SG CYS Q 147 68.666 120.895 73.735 1.00106.54 S Time building chain proxies: 8.11, per 1000 atoms: 0.23 Number of scatterers: 35069 At special positions: 0 Unit cell: (183.296, 165.888, 169.984, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 149 16.00 P 115 15.00 Mg 1 11.99 O 6977 8.00 N 6227 7.00 C 21597 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.37 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " pdb=" ZN Q1500 " pdb="ZN ZN Q1500 " - pdb=" SG CYS Q 121 " pdb="ZN ZN Q1500 " - pdb=" SG CYS Q 147 " pdb="ZN ZN Q1500 " - pdb=" SG CYS Q 144 " pdb="ZN ZN Q1500 " - pdb=" SG CYS Q 118 " Number of angles added : 12 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7734 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 46 sheets defined 43.1% alpha, 12.9% beta 43 base pairs and 87 stacking pairs defined. Time for finding SS restraints: 4.44 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.787A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.658A pdb=" N ASP A 114 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 115 " --> pdb=" O ALA A 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 111 through 115' Processing helix chain 'A' and resid 154 through 161 Processing helix chain 'A' and resid 212 through 234 removed outlier: 4.711A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'B' and resid 263 through 272 removed outlier: 4.118A pdb=" N ASN B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 292 removed outlier: 3.566A pdb=" N LEU B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 310 removed outlier: 3.914A pdb=" N VAL B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.600A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 55 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 207 through 213 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 318 through 329 removed outlier: 4.085A pdb=" N GLY C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 4.039A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 482 removed outlier: 4.252A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 509 Processing helix chain 'C' and resid 519 through 528 removed outlier: 3.551A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.852A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 removed outlier: 3.507A pdb=" N ASN C 613 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 667 removed outlier: 3.557A pdb=" N LEU C 667 " --> pdb=" O GLY C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 686 removed outlier: 3.733A pdb=" N MET C 681 " --> pdb=" O ASN C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 860 through 864 removed outlier: 3.662A pdb=" N LYS C 864 " --> pdb=" O ALA C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 942 through 983 Processing helix chain 'C' and resid 986 through 991 Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1099 through 1101 No H-bonds generated for 'chain 'C' and resid 1099 through 1101' Processing helix chain 'C' and resid 1102 through 1107 removed outlier: 4.050A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1135 Processing helix chain 'C' and resid 1138 through 1150 Processing helix chain 'C' and resid 1165 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1297 through 1310 Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.636A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.702A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG D 99 " --> pdb=" O LYS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 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 Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.797A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 236 removed outlier: 3.520A pdb=" N TRP D 236 " --> pdb=" O LYS D 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 233 through 236' Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 285 Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 417 removed outlier: 3.536A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) 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 514 Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 573 through 581 removed outlier: 3.922A pdb=" N ALA D 577 " --> pdb=" O THR D 573 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.672A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.955A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 671 Processing helix chain 'D' and resid 674 through 703 Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 4.216A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 876 Processing helix chain 'D' and resid 884 through 888 removed outlier: 3.536A pdb=" N CYS D 888 " --> pdb=" O VAL D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 925 Processing helix chain 'D' and resid 926 through 928 No H-bonds generated for 'chain 'D' and resid 926 through 928' Processing helix chain 'D' and resid 1137 through 1146 Processing helix chain 'D' and resid 1216 through 1225 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 4.043A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 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 1354 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 1375 Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 15 through 32 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 60 through 76 Processing helix chain 'F' and resid 96 through 106 Processing helix chain 'F' and resid 112 through 136 removed outlier: 3.875A pdb=" N GLU F 116 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE F 117 " --> pdb=" O ARG F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 152 removed outlier: 3.704A pdb=" N ILE F 141 " --> pdb=" O TYR F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 234 Processing helix chain 'F' and resid 243 through 256 Processing helix chain 'F' and resid 262 through 294 removed outlier: 3.953A pdb=" N GLN F 294 " --> pdb=" O LEU F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 307 removed outlier: 4.505A pdb=" N PHE F 302 " --> pdb=" O PRO F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 321 Processing helix chain 'F' and resid 326 through 331 Processing helix chain 'F' and resid 333 through 352 Processing helix chain 'F' and resid 354 through 381 removed outlier: 4.087A pdb=" N VAL F 358 " --> pdb=" O THR F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 392 removed outlier: 3.679A pdb=" N VAL F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 418 removed outlier: 3.901A pdb=" N LEU F 404 " --> pdb=" O GLN F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 447 removed outlier: 4.198A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 553 through 561 removed outlier: 3.835A pdb=" N LEU F 559 " --> pdb=" O GLU F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 581 Processing helix chain 'F' and resid 585 through 599 removed outlier: 3.611A pdb=" N ARG F 599 " --> pdb=" O LEU F 595 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 10 Processing helix chain 'N' and resid 19 through 39 removed outlier: 3.620A pdb=" N ILE N 23 " --> pdb=" O PRO N 19 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR N 39 " --> pdb=" O THR N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 81 Processing helix chain 'N' and resid 82 through 84 No H-bonds generated for 'chain 'N' and resid 82 through 84' Processing helix chain 'N' and resid 103 through 132 Processing helix chain 'N' and resid 201 through 213 removed outlier: 3.660A pdb=" N LEU N 205 " --> pdb=" O LYS N 201 " (cutoff:3.500A) Processing helix chain 'N' and resid 213 through 218 Processing helix chain 'N' and resid 246 through 253 Processing helix chain 'N' and resid 256 through 267 Processing helix chain 'N' and resid 279 through 288 Processing helix chain 'N' and resid 313 through 319 Processing helix chain 'N' and resid 322 through 333 Processing helix chain 'Q' and resid 3 through 10 removed outlier: 3.564A pdb=" N ALA Q 7 " --> pdb=" O LEU Q 3 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 41 Processing helix chain 'Q' and resid 46 through 56 Processing helix chain 'Q' and resid 61 through 78 removed outlier: 3.942A pdb=" N LYS Q 65 " --> pdb=" O ASN Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 81 No H-bonds generated for 'chain 'Q' and resid 79 through 81' Processing helix chain 'Q' and resid 88 through 109 Processing helix chain 'Q' and resid 129 through 137 Processing helix chain 'Q' and resid 157 through 165 removed outlier: 3.635A pdb=" N TYR Q 161 " --> pdb=" O ALA Q 157 " (cutoff:3.500A) Processing helix chain 'Q' and resid 172 through 180 Processing helix chain 'Q' and resid 180 through 206 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 3.659A pdb=" N VAL A 14 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE A 16 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LYS A 25 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 108 removed outlier: 3.593A pdb=" N GLY A 106 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ALA A 138 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N GLY A 108 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 9.633A pdb=" N GLU A 136 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.449A 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 'B' and resid 12 through 16 removed outlier: 3.504A pdb=" N GLU B 29 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR B 27 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 115 through 116 removed outlier: 4.390A pdb=" N THR B 101 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 98 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS B 104 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 180 through 183 Processing sheet with id=AA7, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.278A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 66 through 75 removed outlier: 6.728A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB1, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.661A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AB3, first strand: chain 'C' and resid 184 through 187 Processing sheet with id=AB4, first strand: chain 'C' and resid 284 through 287 removed outlier: 3.773A pdb=" N LEU C 237 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 296 through 297 removed outlier: 4.086A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AB7, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.227A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.527A pdb=" N ASP C 654 " --> pdb=" O ALA C 617 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.384A 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: 6.365A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 757 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: 7.633A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 846 through 847 removed outlier: 3.575A pdb=" N THR C 843 " --> pdb=" O GLY C 846 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 849 through 850 removed outlier: 3.694A pdb=" N GLU C 849 " --> pdb=" O VAL C 887 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 882 through 884 removed outlier: 7.241A 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 Processing sheet with id=AC9, first strand: chain 'C' and resid 1268 through 1270 removed outlier: 3.682A 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 1339 Processing sheet with id=AD2, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.422A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 9.962A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.131A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 83 through 84 removed outlier: 3.572A pdb=" N VAL D 83 " --> pdb=" O VAL D 92 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 159 through 160 removed outlier: 7.149A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.579A pdb=" N GLU D 554 " --> pdb=" O LYS D 566 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AD7, first strand: chain 'D' and resid 958 through 961 removed outlier: 3.593A pdb=" N SER D 961 " --> pdb=" O GLU D 981 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AD9, first strand: chain 'D' and resid 1025 through 1026 Processing sheet with id=AE1, first strand: chain 'D' and resid 1033 through 1034 Processing sheet with id=AE2, first strand: chain 'D' and resid 1047 through 1048 removed outlier: 4.453A pdb=" N VAL D1060 " --> pdb=" O THR D1047 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1077 through 1079 removed outlier: 3.541A pdb=" N TYR D1099 " --> pdb=" O LEU D1078 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1189 through 1190 removed outlier: 3.540A pdb=" N VAL D1176 " --> pdb=" O SER D1164 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 4.420A pdb=" N LYS D1263 " --> pdb=" O ASP D1305 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 63 through 64 removed outlier: 5.769A pdb=" N LEU N 63 " --> pdb=" O ILE N 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'N' and resid 136 through 141 removed outlier: 3.811A pdb=" N GLU N 136 " --> pdb=" O LEU N 183 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU N 183 " --> pdb=" O GLU N 136 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL N 182 " --> pdb=" O THR N 198 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N VAL N 161 " --> pdb=" O VAL N 197 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS N 144 " --> pdb=" O SER N 151 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 222 through 229 removed outlier: 5.055A pdb=" N ILE N 223 " --> pdb=" O LYS N 239 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LYS N 239 " --> pdb=" O ILE N 223 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA N 225 " --> pdb=" O ALA N 237 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA N 234 " --> pdb=" O ASP N 272 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N VAL N 274 " --> pdb=" O ALA N 234 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ILE N 236 " --> pdb=" O VAL N 274 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 295 through 299 removed outlier: 3.831A pdb=" N SER N 295 " --> pdb=" O ALA N 308 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR N 304 " --> pdb=" O ASP N 299 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N MET N 339 " --> pdb=" O MET N 305 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE N 307 " --> pdb=" O MET N 339 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Q' and resid 126 through 127 1444 hydrogen bonds defined for protein. 4166 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 101 hydrogen bonds 198 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 87 stacking parallelities Total time for adding SS restraints: 8.48 Time building geometry restraints manager: 4.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10111 1.33 - 1.45: 6323 1.45 - 1.58: 18904 1.58 - 1.70: 226 1.70 - 1.82: 258 Bond restraints: 35822 Sorted by residual: bond pdb=" N LEU Q 87 " pdb=" CA LEU Q 87 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.31e-02 5.83e+03 7.59e+00 bond pdb=" N LEU Q 58 " pdb=" CA LEU Q 58 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.21e-02 6.83e+03 6.56e+00 bond pdb=" N LEU N 266 " pdb=" CA LEU N 266 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.35e-02 5.49e+03 6.20e+00 bond pdb=" N ASP F 445 " pdb=" CA ASP F 445 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.23e-02 6.61e+03 5.91e+00 bond pdb=" N LEU D 78 " pdb=" CA LEU D 78 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.31e-02 5.83e+03 5.50e+00 ... (remaining 35817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 47901 2.51 - 5.02: 833 5.02 - 7.53: 89 7.53 - 10.05: 30 10.05 - 12.56: 4 Bond angle restraints: 48857 Sorted by residual: angle pdb=" C GLU N 83 " pdb=" N ASP N 84 " pdb=" CA ASP N 84 " ideal model delta sigma weight residual 122.82 131.77 -8.95 1.42e+00 4.96e-01 3.98e+01 angle pdb=" C ARG D 709 " pdb=" N ASP D 710 " pdb=" CA ASP D 710 " ideal model delta sigma weight residual 121.54 132.71 -11.17 1.91e+00 2.74e-01 3.42e+01 angle pdb=" C4' U R 1 " pdb=" C3' U R 1 " pdb=" O3' U R 1 " ideal model delta sigma weight residual 113.00 104.69 8.31 1.50e+00 4.44e-01 3.07e+01 angle pdb=" C MET F 322 " pdb=" N ASN F 323 " pdb=" CA ASN F 323 " ideal model delta sigma weight residual 122.46 130.04 -7.58 1.41e+00 5.03e-01 2.89e+01 angle pdb=" C VAL D1027 " pdb=" N ILE D1028 " pdb=" CA ILE D1028 " ideal model delta sigma weight residual 120.69 128.24 -7.55 1.46e+00 4.69e-01 2.68e+01 ... (remaining 48852 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 20674 36.00 - 71.99: 1126 71.99 - 107.99: 29 107.99 - 143.98: 3 143.98 - 179.98: 1 Dihedral angle restraints: 21833 sinusoidal: 9839 harmonic: 11994 Sorted by residual: dihedral pdb=" CD BARG N 326 " pdb=" NE BARG N 326 " pdb=" CZ BARG N 326 " pdb=" NH1BARG N 326 " ideal model delta sinusoidal sigma weight residual 0.00 -179.98 179.98 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CA PRO D 121 " pdb=" C PRO D 121 " pdb=" N SER D 122 " pdb=" CA SER D 122 " ideal model delta harmonic sigma weight residual -180.00 -152.14 -27.86 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA ASP D 710 " pdb=" C ASP D 710 " pdb=" N GLY D 711 " pdb=" CA GLY D 711 " ideal model delta harmonic sigma weight residual 180.00 152.75 27.25 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 21830 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 4634 0.069 - 0.139: 852 0.139 - 0.208: 72 0.208 - 0.277: 10 0.277 - 0.346: 3 Chirality restraints: 5571 Sorted by residual: chirality pdb=" CB ILE C 30 " pdb=" CA ILE C 30 " pdb=" CG1 ILE C 30 " pdb=" CG2 ILE C 30 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CB VAL F 333 " pdb=" CA VAL F 333 " pdb=" CG1 VAL F 333 " pdb=" CG2 VAL F 333 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CB THR C 164 " pdb=" CA THR C 164 " pdb=" OG1 THR C 164 " pdb=" CG2 THR C 164 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 5568 not shown) Planarity restraints: 5984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 504 " -0.022 2.00e-02 2.50e+03 4.44e-02 1.98e+01 pdb=" C GLN D 504 " 0.077 2.00e-02 2.50e+03 pdb=" O GLN D 504 " -0.028 2.00e-02 2.50e+03 pdb=" N ASP D 505 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 519 " 0.056 5.00e-02 4.00e+02 8.43e-02 1.14e+01 pdb=" N PRO C 520 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO C 520 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 520 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 324 " -0.047 5.00e-02 4.00e+02 7.17e-02 8.23e+00 pdb=" N PRO F 325 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO F 325 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO F 325 " -0.040 5.00e-02 4.00e+02 ... (remaining 5981 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 721 2.65 - 3.21: 30041 3.21 - 3.78: 58623 3.78 - 4.34: 75563 4.34 - 4.90: 122567 Nonbonded interactions: 287515 Sorted by model distance: nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1503 " model vdw 2.088 2.170 nonbonded pdb=" OD2 ASP D 464 " pdb="MG MG D1503 " model vdw 2.101 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1503 " model vdw 2.116 2.170 nonbonded pdb=" O3' A R 11 " pdb="MG MG D1503 " model vdw 2.174 2.170 nonbonded pdb=" O ARG C1033 " pdb=" OG1 THR C1037 " model vdw 2.233 3.040 ... (remaining 287510 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.37 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 42.450 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 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 : 0.007 0.247 35831 Z= 0.284 Angle : 0.862 12.557 48869 Z= 0.482 Chirality : 0.053 0.346 5571 Planarity : 0.007 0.084 5984 Dihedral : 18.994 179.979 14099 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 5.70 % Allowed : 18.52 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -3.81 (0.10), residues: 4138 helix: -2.49 (0.09), residues: 1689 sheet: -2.10 (0.22), residues: 420 loop : -2.62 (0.11), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 417 TYR 0.019 0.002 TYR Q 184 PHE 0.021 0.002 PHE C1323 TRP 0.009 0.002 TRP D 580 HIS 0.010 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00637 (35822) covalent geometry : angle 0.85691 (48857) hydrogen bonds : bond 0.13077 ( 1543) hydrogen bonds : angle 6.79061 ( 4364) metal coordination : bond 0.08277 ( 9) metal coordination : angle 6.22471 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 284 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.9113 (ptmt) cc_final: 0.8870 (ptmm) REVERT: C 325 LEU cc_start: 0.9404 (mm) cc_final: 0.9144 (mm) REVERT: C 903 ARG cc_start: 0.8873 (ptm160) cc_final: 0.8571 (ptp90) REVERT: C 1025 PHE cc_start: 0.8073 (t80) cc_final: 0.7697 (t80) REVERT: C 1085 MET cc_start: 0.9221 (mmm) cc_final: 0.8878 (mmt) REVERT: D 15 GLU cc_start: 0.5853 (OUTLIER) cc_final: 0.4515 (tm-30) REVERT: D 162 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7812 (pm20) REVERT: D 166 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9260 (mm) REVERT: D 837 ASP cc_start: 0.8805 (OUTLIER) cc_final: 0.8589 (t0) REVERT: D 979 ASN cc_start: 0.9072 (p0) cc_final: 0.8491 (p0) REVERT: E 15 ASN cc_start: 0.7122 (t0) cc_final: 0.6306 (t0) REVERT: E 56 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8096 (tm-30) REVERT: E 61 ASN cc_start: 0.7624 (t0) cc_final: 0.7359 (t0) REVERT: F 147 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8204 (pp30) REVERT: F 297 MET cc_start: 0.6137 (ppp) cc_final: 0.4511 (ptp) REVERT: F 298 PRO cc_start: 0.8594 (Cg_exo) cc_final: 0.8322 (Cg_endo) REVERT: F 561 MET cc_start: 0.7357 (ptp) cc_final: 0.6794 (ptp) REVERT: F 579 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7869 (pp30) REVERT: N 24 PHE cc_start: 0.8890 (m-10) cc_final: 0.8491 (m-80) REVERT: N 125 MET cc_start: 0.9340 (tmm) cc_final: 0.9129 (tmm) REVERT: N 209 PHE cc_start: 0.9320 (m-80) cc_final: 0.8816 (m-80) REVERT: Q 58 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8005 (pp) REVERT: Q 155 MET cc_start: 0.8706 (tpp) cc_final: 0.8349 (ttt) outliers start: 202 outliers final: 136 residues processed: 478 average time/residue: 0.2097 time to fit residues: 164.0866 Evaluate side-chains 372 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 229 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 255 ARG Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 596 ASP Chi-restraints excluded: chain C residue 613 ASN Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 920 VAL Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1241 ASP Chi-restraints excluded: chain C residue 1250 SER Chi-restraints excluded: chain C residue 1322 SER Chi-restraints excluded: chain C residue 1341 ASP Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 802 ASP Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 837 ASP Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1047 THR Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1093 THR Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1271 SER Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1280 VAL Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain D residue 1321 SER Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 232 ARG Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 568 ASN Chi-restraints excluded: chain F residue 579 GLN Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain N residue 35 THR Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain N residue 186 VAL Chi-restraints excluded: chain N residue 238 VAL Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 309 VAL Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 43 SER Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 202 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 40.0000 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS B 268 ASN C 120 GLN C 238 GLN C 343 HIS C 447 HIS C 518 ASN C 620 ASN C 622 ASN C 673 HIS C 799 ASN ** C1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1111 GLN D 45 ASN D 94 GLN D 294 ASN D 341 ASN D 450 HIS D 545 HIS D 651 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1084 GLN D1108 GLN D1114 GLN D1197 ASN D1227 HIS D1249 ASN D1259 GLN F 265 GLN F 283 GLN F 309 ASN F 331 HIS F 383 ASN F 406 GLN F 409 ASN ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 241 ASN ** N 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 97 GLN Q 190 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.109513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.068217 restraints weight = 109639.734| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.23 r_work: 0.2812 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 35831 Z= 0.169 Angle : 0.598 8.582 48869 Z= 0.319 Chirality : 0.042 0.291 5571 Planarity : 0.005 0.064 5984 Dihedral : 16.680 178.785 6121 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.55 % Allowed : 19.90 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -2.11 (0.12), residues: 4138 helix: -0.49 (0.12), residues: 1711 sheet: -1.84 (0.24), residues: 383 loop : -2.12 (0.12), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1033 TYR 0.023 0.001 TYR D 995 PHE 0.049 0.001 PHE N 283 TRP 0.021 0.002 TRP N 276 HIS 0.010 0.001 HIS N 133 Details of bonding type rmsd covalent geometry : bond 0.00381 (35822) covalent geometry : angle 0.59477 (48857) hydrogen bonds : bond 0.04322 ( 1543) hydrogen bonds : angle 5.09015 ( 4364) metal coordination : bond 0.00621 ( 9) metal coordination : angle 4.16618 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 248 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.9080 (ptmt) cc_final: 0.8843 (ptmm) REVERT: B 186 ASN cc_start: 0.8661 (OUTLIER) cc_final: 0.8448 (p0) REVERT: C 315 MET cc_start: 0.8235 (ptp) cc_final: 0.7964 (ptp) REVERT: C 325 LEU cc_start: 0.9696 (mm) cc_final: 0.9487 (mm) REVERT: C 903 ARG cc_start: 0.9330 (ptm160) cc_final: 0.8963 (ptp90) REVERT: C 1017 GLN cc_start: 0.9295 (OUTLIER) cc_final: 0.8939 (mt0) REVERT: C 1023 HIS cc_start: 0.9100 (m90) cc_final: 0.8760 (m-70) REVERT: C 1025 PHE cc_start: 0.8231 (t80) cc_final: 0.7904 (t80) REVERT: C 1085 MET cc_start: 0.9326 (mmm) cc_final: 0.9117 (mmt) REVERT: D 166 LEU cc_start: 0.9566 (OUTLIER) cc_final: 0.9330 (mm) REVERT: D 789 LYS cc_start: 0.5902 (mmtt) cc_final: 0.5489 (mmtp) REVERT: D 979 ASN cc_start: 0.9044 (p0) cc_final: 0.8632 (p0) REVERT: D 1040 MET cc_start: 0.9052 (ttp) cc_final: 0.8766 (tmm) REVERT: D 1084 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7716 (pm20) REVERT: D 1156 LEU cc_start: 0.9041 (tp) cc_final: 0.8776 (tp) REVERT: D 1189 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8530 (mmm) REVERT: D 1355 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8561 (mtp85) REVERT: E 15 ASN cc_start: 0.6710 (t0) cc_final: 0.5864 (t0) REVERT: E 56 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8076 (tm-30) REVERT: F 102 MET cc_start: 0.8618 (mmm) cc_final: 0.8358 (mtm) REVERT: F 147 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8454 (pp30) REVERT: F 276 MET cc_start: 0.8760 (mpp) cc_final: 0.8543 (mpp) REVERT: F 297 MET cc_start: 0.8051 (ppp) cc_final: 0.7314 (ppp) REVERT: F 322 MET cc_start: 0.7391 (ppp) cc_final: 0.7128 (ppp) REVERT: F 567 MET cc_start: 0.4089 (OUTLIER) cc_final: 0.3493 (ptt) REVERT: F 579 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7988 (pp30) REVERT: N 20 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7717 (tpp-160) REVERT: N 209 PHE cc_start: 0.9635 (m-80) cc_final: 0.9306 (m-80) REVERT: N 283 PHE cc_start: 0.9174 (t80) cc_final: 0.8886 (t80) REVERT: Q 16 MET cc_start: 0.7765 (pmm) cc_final: 0.7468 (pmm) REVERT: Q 60 GLN cc_start: 0.7892 (pp30) cc_final: 0.7678 (pp30) REVERT: Q 155 MET cc_start: 0.9026 (tpp) cc_final: 0.8554 (ttt) outliers start: 161 outliers final: 93 residues processed: 396 average time/residue: 0.2169 time to fit residues: 141.1841 Evaluate side-chains 327 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 224 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 255 ARG Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 876 GLU Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 920 VAL Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1047 THR Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1084 GLN Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1186 TYR Chi-restraints excluded: chain D residue 1189 MET Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1210 ILE Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1240 VAL Chi-restraints excluded: chain D residue 1268 ASN Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1280 VAL Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain D residue 1355 ARG Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 567 MET Chi-restraints excluded: chain F residue 579 GLN Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain N residue 186 VAL Chi-restraints excluded: chain N residue 238 VAL Chi-restraints excluded: chain Q residue 6 VAL Chi-restraints excluded: chain Q residue 33 ASP Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 202 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 57 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 264 optimal weight: 3.9990 chunk 223 optimal weight: 0.6980 chunk 161 optimal weight: 8.9990 chunk 43 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 110 optimal weight: 20.0000 chunk 369 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 238 GLN C 620 ASN C1017 GLN D1249 ASN ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 133 HIS ** N 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.109706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.067389 restraints weight = 92223.369| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.85 r_work: 0.2840 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 35831 Z= 0.158 Angle : 0.577 9.900 48869 Z= 0.305 Chirality : 0.042 0.286 5571 Planarity : 0.004 0.058 5984 Dihedral : 16.376 179.605 6008 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.90 % Allowed : 21.01 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -1.40 (0.12), residues: 4138 helix: 0.28 (0.12), residues: 1705 sheet: -1.53 (0.24), residues: 395 loop : -1.88 (0.13), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 275 TYR 0.016 0.001 TYR N 92 PHE 0.026 0.001 PHE N 283 TRP 0.019 0.001 TRP N 276 HIS 0.004 0.001 HIS Q 10 Details of bonding type rmsd covalent geometry : bond 0.00360 (35822) covalent geometry : angle 0.57325 (48857) hydrogen bonds : bond 0.04057 ( 1543) hydrogen bonds : angle 4.77334 ( 4364) metal coordination : bond 0.00571 ( 9) metal coordination : angle 3.96028 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 230 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.9111 (ptmt) cc_final: 0.8865 (ptmm) REVERT: B 186 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8571 (p0) REVERT: C 275 ARG cc_start: 0.9444 (mmp80) cc_final: 0.9197 (mmp80) REVERT: C 315 MET cc_start: 0.8606 (ptp) cc_final: 0.8363 (ptp) REVERT: C 325 LEU cc_start: 0.9676 (mm) cc_final: 0.9470 (mm) REVERT: C 342 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7096 (p0) REVERT: C 483 ASP cc_start: 0.6698 (OUTLIER) cc_final: 0.6484 (p0) REVERT: C 493 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8311 (tp) REVERT: C 903 ARG cc_start: 0.9342 (ptm160) cc_final: 0.8949 (ptp90) REVERT: C 1017 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8657 (mt0) REVERT: C 1023 HIS cc_start: 0.9155 (m90) cc_final: 0.8712 (m-70) REVERT: C 1027 LYS cc_start: 0.9267 (mttt) cc_final: 0.9031 (mttt) REVERT: C 1085 MET cc_start: 0.9342 (mmm) cc_final: 0.9113 (mmt) REVERT: D 15 GLU cc_start: 0.5898 (OUTLIER) cc_final: 0.4224 (tm-30) REVERT: D 702 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8619 (tm-30) REVERT: D 704 GLU cc_start: 0.6482 (OUTLIER) cc_final: 0.6056 (pp20) REVERT: D 821 MET cc_start: 0.8896 (tpt) cc_final: 0.8450 (tpt) REVERT: D 979 ASN cc_start: 0.9010 (p0) cc_final: 0.8575 (p0) REVERT: D 1355 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8589 (mtp85) REVERT: E 15 ASN cc_start: 0.6802 (t0) cc_final: 0.5890 (t0) REVERT: E 29 GLN cc_start: 0.8609 (mt0) cc_final: 0.7843 (mt0) REVERT: E 56 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8005 (tm-30) REVERT: F 102 MET cc_start: 0.8787 (mmm) cc_final: 0.8573 (mtp) REVERT: F 147 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8553 (pp30) REVERT: F 276 MET cc_start: 0.8856 (mpp) cc_final: 0.8651 (mpp) REVERT: F 297 MET cc_start: 0.8199 (ppp) cc_final: 0.7571 (ppp) REVERT: F 322 MET cc_start: 0.7498 (ppp) cc_final: 0.7022 (ppp) REVERT: F 567 MET cc_start: 0.4585 (ptt) cc_final: 0.4028 (ptt) REVERT: N 20 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7718 (tpp-160) REVERT: N 209 PHE cc_start: 0.9640 (m-80) cc_final: 0.9320 (m-80) REVERT: N 283 PHE cc_start: 0.9277 (t80) cc_final: 0.9045 (t80) REVERT: Q 60 GLN cc_start: 0.8025 (pp30) cc_final: 0.7716 (pp30) REVERT: Q 92 LYS cc_start: 0.9451 (OUTLIER) cc_final: 0.9179 (ttmm) REVERT: Q 155 MET cc_start: 0.9064 (tpp) cc_final: 0.8578 (ttt) REVERT: Q 195 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8722 (tm-30) outliers start: 138 outliers final: 94 residues processed: 358 average time/residue: 0.2217 time to fit residues: 130.6341 Evaluate side-chains 321 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 215 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 920 VAL Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1341 ASP Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 802 ASP Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1047 THR Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1186 TYR Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1210 ILE Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1240 VAL Chi-restraints excluded: chain D residue 1268 ASN Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1280 VAL Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain D residue 1355 ARG Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain N residue 186 VAL Chi-restraints excluded: chain Q residue 6 VAL Chi-restraints excluded: chain Q residue 33 ASP Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 92 LYS Chi-restraints excluded: chain Q residue 128 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 338 optimal weight: 30.0000 chunk 7 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 355 optimal weight: 30.0000 chunk 168 optimal weight: 6.9990 chunk 129 optimal weight: 0.8980 chunk 232 optimal weight: 0.0020 chunk 30 optimal weight: 3.9990 chunk 288 optimal weight: 40.0000 chunk 176 optimal weight: 5.9990 overall best weight: 2.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN C1008 GLN C1017 GLN D 669 GLN ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.109496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.066892 restraints weight = 110396.343| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.05 r_work: 0.2813 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 35831 Z= 0.177 Angle : 0.573 8.991 48869 Z= 0.302 Chirality : 0.043 0.290 5571 Planarity : 0.004 0.058 5984 Dihedral : 16.274 179.611 5986 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.04 % Allowed : 21.77 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -1.07 (0.13), residues: 4138 helix: 0.56 (0.13), residues: 1708 sheet: -1.32 (0.24), residues: 401 loop : -1.72 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 744 TYR 0.024 0.001 TYR N 92 PHE 0.020 0.001 PHE N 283 TRP 0.014 0.001 TRP N 334 HIS 0.006 0.001 HIS Q 10 Details of bonding type rmsd covalent geometry : bond 0.00406 (35822) covalent geometry : angle 0.56997 (48857) hydrogen bonds : bond 0.03995 ( 1543) hydrogen bonds : angle 4.65728 ( 4364) metal coordination : bond 0.00667 ( 9) metal coordination : angle 3.99451 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 218 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8403 (p0) REVERT: C 239 MET cc_start: 0.9218 (tmm) cc_final: 0.8862 (ppp) REVERT: C 275 ARG cc_start: 0.9487 (mmp80) cc_final: 0.9252 (mmp80) REVERT: C 315 MET cc_start: 0.8621 (ptp) cc_final: 0.8392 (ptp) REVERT: C 342 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7174 (p0) REVERT: C 484 LEU cc_start: 0.8532 (mm) cc_final: 0.8259 (mm) REVERT: C 653 MET cc_start: 0.8990 (tpt) cc_final: 0.8608 (tpt) REVERT: C 903 ARG cc_start: 0.9359 (ptm160) cc_final: 0.9009 (ptp90) REVERT: C 1023 HIS cc_start: 0.9101 (m90) cc_final: 0.8664 (m-70) REVERT: C 1027 LYS cc_start: 0.9234 (mttt) cc_final: 0.8999 (mttt) REVERT: C 1085 MET cc_start: 0.9274 (mmm) cc_final: 0.9018 (mmt) REVERT: D 15 GLU cc_start: 0.5816 (OUTLIER) cc_final: 0.4196 (tm-30) REVERT: D 504 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7668 (pt0) REVERT: D 704 GLU cc_start: 0.6350 (OUTLIER) cc_final: 0.5815 (pp20) REVERT: D 821 MET cc_start: 0.8668 (tpt) cc_final: 0.8277 (tpt) REVERT: D 979 ASN cc_start: 0.8970 (p0) cc_final: 0.8609 (p0) REVERT: D 1189 MET cc_start: 0.8628 (mmp) cc_final: 0.8372 (mmp) REVERT: D 1355 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8494 (mtp85) REVERT: E 15 ASN cc_start: 0.6955 (t0) cc_final: 0.6101 (t0) REVERT: E 56 GLU cc_start: 0.8504 (tm-30) cc_final: 0.7962 (tm-30) REVERT: F 147 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8570 (pp30) REVERT: F 276 MET cc_start: 0.8837 (mpp) cc_final: 0.8608 (mpp) REVERT: F 297 MET cc_start: 0.8264 (ppp) cc_final: 0.7634 (ppp) REVERT: F 322 MET cc_start: 0.7584 (ppp) cc_final: 0.7176 (ppp) REVERT: N 20 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7732 (tpp-160) REVERT: N 204 MET cc_start: 0.9139 (ttm) cc_final: 0.8780 (ttm) REVERT: N 209 PHE cc_start: 0.9633 (m-80) cc_final: 0.9317 (m-80) REVERT: N 283 PHE cc_start: 0.9303 (t80) cc_final: 0.9049 (t80) REVERT: Q 16 MET cc_start: 0.7656 (pmm) cc_final: 0.7348 (pmm) REVERT: Q 60 GLN cc_start: 0.7881 (pp30) cc_final: 0.7616 (pp30) REVERT: Q 92 LYS cc_start: 0.9438 (OUTLIER) cc_final: 0.9147 (ttmm) REVERT: Q 155 MET cc_start: 0.9030 (tpp) cc_final: 0.8464 (ttt) REVERT: Q 195 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8533 (tm-30) outliers start: 143 outliers final: 107 residues processed: 351 average time/residue: 0.2273 time to fit residues: 131.7203 Evaluate side-chains 328 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 212 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 920 VAL Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 802 ASP Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1047 THR Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1186 TYR Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1210 ILE Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1240 VAL Chi-restraints excluded: chain D residue 1268 ASN Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1280 VAL Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain D residue 1355 ARG Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain N residue 186 VAL Chi-restraints excluded: chain N residue 309 VAL Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 6 VAL Chi-restraints excluded: chain Q residue 33 ASP Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 92 LYS Chi-restraints excluded: chain Q residue 128 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 60 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 251 optimal weight: 5.9990 chunk 221 optimal weight: 2.9990 chunk 389 optimal weight: 3.9990 chunk 258 optimal weight: 10.0000 chunk 379 optimal weight: 4.9990 chunk 217 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 332 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 238 GLN ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 702 GLN F 317 ASN ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.108965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.066329 restraints weight = 111646.417| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.11 r_work: 0.2797 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 35831 Z= 0.210 Angle : 0.586 9.207 48869 Z= 0.309 Chirality : 0.043 0.281 5571 Planarity : 0.004 0.060 5984 Dihedral : 16.283 179.657 5982 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.77 % Allowed : 21.57 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -0.92 (0.13), residues: 4138 helix: 0.67 (0.13), residues: 1710 sheet: -1.24 (0.24), residues: 411 loop : -1.63 (0.13), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 93 TYR 0.028 0.001 TYR N 92 PHE 0.015 0.001 PHE N 283 TRP 0.017 0.001 TRP N 276 HIS 0.006 0.001 HIS Q 10 Details of bonding type rmsd covalent geometry : bond 0.00486 (35822) covalent geometry : angle 0.58252 (48857) hydrogen bonds : bond 0.04113 ( 1543) hydrogen bonds : angle 4.62499 ( 4364) metal coordination : bond 0.00819 ( 9) metal coordination : angle 4.23914 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 220 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8423 (p0) REVERT: B 194 GLN cc_start: 0.7879 (tp40) cc_final: 0.7662 (tp40) REVERT: C 239 MET cc_start: 0.9241 (tmm) cc_final: 0.8865 (ppp) REVERT: C 275 ARG cc_start: 0.9500 (mmp80) cc_final: 0.9260 (mmp80) REVERT: C 342 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7153 (p0) REVERT: C 488 MET cc_start: 0.8836 (mmm) cc_final: 0.8580 (mmm) REVERT: C 653 MET cc_start: 0.9039 (tpt) cc_final: 0.8641 (tpt) REVERT: C 903 ARG cc_start: 0.9379 (ptm160) cc_final: 0.9120 (ptp90) REVERT: C 964 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7860 (mm) REVERT: C 1017 GLN cc_start: 0.9398 (OUTLIER) cc_final: 0.8936 (mt0) REVERT: C 1023 HIS cc_start: 0.9106 (m90) cc_final: 0.8678 (m-70) REVERT: C 1025 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.7780 (t80) REVERT: C 1027 LYS cc_start: 0.9185 (mttt) cc_final: 0.8949 (mttt) REVERT: C 1085 MET cc_start: 0.9270 (mmm) cc_final: 0.9006 (mmt) REVERT: D 15 GLU cc_start: 0.5632 (OUTLIER) cc_final: 0.4075 (tm-30) REVERT: D 166 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9285 (mm) REVERT: D 192 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.8099 (ptm) REVERT: D 504 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7838 (pt0) REVERT: D 821 MET cc_start: 0.8760 (tpt) cc_final: 0.8447 (tpt) REVERT: D 979 ASN cc_start: 0.9041 (p0) cc_final: 0.8668 (p0) REVERT: D 1355 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8533 (mtp85) REVERT: E 15 ASN cc_start: 0.7004 (t0) cc_final: 0.6141 (t0) REVERT: E 56 GLU cc_start: 0.8506 (tm-30) cc_final: 0.7947 (tm-30) REVERT: E 58 LEU cc_start: 0.8481 (mt) cc_final: 0.8100 (mt) REVERT: F 147 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8598 (pp30) REVERT: F 276 MET cc_start: 0.8828 (mpp) cc_final: 0.8571 (mpp) REVERT: F 297 MET cc_start: 0.8050 (ppp) cc_final: 0.7390 (ppp) REVERT: F 322 MET cc_start: 0.7426 (ppp) cc_final: 0.6983 (ppp) REVERT: F 579 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7952 (pp30) REVERT: N 20 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7719 (tpp-160) REVERT: N 204 MET cc_start: 0.9082 (ttm) cc_final: 0.8587 (ttm) REVERT: N 209 PHE cc_start: 0.9614 (m-80) cc_final: 0.9209 (m-80) REVERT: N 283 PHE cc_start: 0.9278 (t80) cc_final: 0.9031 (t80) REVERT: Q 16 MET cc_start: 0.7707 (pmm) cc_final: 0.7498 (pmm) REVERT: Q 60 GLN cc_start: 0.7996 (pp30) cc_final: 0.7621 (pp30) REVERT: Q 92 LYS cc_start: 0.9435 (OUTLIER) cc_final: 0.9142 (ttmm) REVERT: Q 155 MET cc_start: 0.9043 (tpp) cc_final: 0.8431 (ttt) REVERT: Q 195 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8534 (tm-30) outliers start: 169 outliers final: 118 residues processed: 376 average time/residue: 0.2041 time to fit residues: 127.8353 Evaluate side-chains 343 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 211 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 920 VAL Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain C residue 1025 PHE Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1341 ASP Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1047 THR Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1186 TYR Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1240 VAL Chi-restraints excluded: chain D residue 1268 ASN Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1280 VAL Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain D residue 1355 ARG Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 579 GLN Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain N residue 186 VAL Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 309 VAL Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 6 VAL Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 92 LYS Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 135 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 245 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 163 optimal weight: 10.0000 chunk 113 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 243 optimal weight: 0.8980 chunk 65 optimal weight: 7.9990 chunk 387 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 172 optimal weight: 0.0980 chunk 57 optimal weight: 40.0000 overall best weight: 3.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.109239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.071007 restraints weight = 91478.092| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.01 r_work: 0.2810 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 35831 Z= 0.184 Angle : 0.575 8.523 48869 Z= 0.303 Chirality : 0.043 0.279 5571 Planarity : 0.004 0.059 5984 Dihedral : 16.254 179.753 5980 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.49 % Allowed : 22.47 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -0.77 (0.13), residues: 4138 helix: 0.76 (0.13), residues: 1717 sheet: -1.25 (0.24), residues: 409 loop : -1.50 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 182 TYR 0.028 0.001 TYR N 92 PHE 0.019 0.001 PHE N 196 TRP 0.014 0.001 TRP N 276 HIS 0.008 0.001 HIS Q 10 Details of bonding type rmsd covalent geometry : bond 0.00426 (35822) covalent geometry : angle 0.57162 (48857) hydrogen bonds : bond 0.03954 ( 1543) hydrogen bonds : angle 4.55683 ( 4364) metal coordination : bond 0.00708 ( 9) metal coordination : angle 4.00242 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 220 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 ASN cc_start: 0.8619 (OUTLIER) cc_final: 0.8410 (p0) REVERT: B 194 GLN cc_start: 0.7763 (tp40) cc_final: 0.7547 (tp40) REVERT: C 239 MET cc_start: 0.9231 (tmm) cc_final: 0.8872 (ppp) REVERT: C 325 LEU cc_start: 0.9687 (mm) cc_final: 0.9444 (mm) REVERT: C 342 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7166 (p0) REVERT: C 488 MET cc_start: 0.8869 (mmm) cc_final: 0.8613 (mmm) REVERT: C 653 MET cc_start: 0.9066 (tpt) cc_final: 0.8718 (tpt) REVERT: C 903 ARG cc_start: 0.9389 (ptm160) cc_final: 0.9128 (ptp90) REVERT: C 964 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7912 (mm) REVERT: C 1017 GLN cc_start: 0.9381 (OUTLIER) cc_final: 0.8939 (mt0) REVERT: C 1023 HIS cc_start: 0.9089 (m90) cc_final: 0.8651 (m-70) REVERT: C 1025 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.7782 (t80) REVERT: C 1027 LYS cc_start: 0.9171 (mttt) cc_final: 0.8932 (mttt) REVERT: C 1085 MET cc_start: 0.9247 (mmm) cc_final: 0.8978 (mmt) REVERT: D 15 GLU cc_start: 0.5722 (OUTLIER) cc_final: 0.4166 (tm-30) REVERT: D 166 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9259 (mm) REVERT: D 192 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8125 (ptm) REVERT: D 504 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7680 (pt0) REVERT: D 789 LYS cc_start: 0.5881 (mmtt) cc_final: 0.5453 (mmtp) REVERT: D 821 MET cc_start: 0.8636 (tpt) cc_final: 0.8368 (tpt) REVERT: D 901 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8148 (ttm170) REVERT: D 979 ASN cc_start: 0.9026 (p0) cc_final: 0.8672 (p0) REVERT: D 1189 MET cc_start: 0.8628 (mmp) cc_final: 0.8293 (mmp) REVERT: D 1355 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8533 (mtp85) REVERT: E 15 ASN cc_start: 0.7033 (t0) cc_final: 0.6198 (t0) REVERT: E 56 GLU cc_start: 0.8529 (tm-30) cc_final: 0.7923 (tm-30) REVERT: E 58 LEU cc_start: 0.8539 (mt) cc_final: 0.8151 (mt) REVERT: F 297 MET cc_start: 0.7997 (ppp) cc_final: 0.7365 (ppp) REVERT: F 322 MET cc_start: 0.7414 (ppp) cc_final: 0.6951 (ppp) REVERT: F 579 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7927 (pp30) REVERT: N 20 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7698 (tpp-160) REVERT: N 204 MET cc_start: 0.9109 (ttm) cc_final: 0.8584 (ttm) REVERT: N 209 PHE cc_start: 0.9619 (m-80) cc_final: 0.9194 (m-80) REVERT: N 283 PHE cc_start: 0.9266 (t80) cc_final: 0.8995 (t80) REVERT: Q 60 GLN cc_start: 0.8024 (pp30) cc_final: 0.7713 (pp30) REVERT: Q 92 LYS cc_start: 0.9410 (OUTLIER) cc_final: 0.9154 (ttmm) REVERT: Q 155 MET cc_start: 0.9028 (tpp) cc_final: 0.8369 (ttt) REVERT: Q 195 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8535 (tm-30) outliers start: 159 outliers final: 121 residues processed: 363 average time/residue: 0.2118 time to fit residues: 128.2579 Evaluate side-chains 344 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 209 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 920 VAL Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain C residue 1025 PHE Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1341 ASP Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 345 LYS Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1047 THR Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1186 TYR Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1210 ILE Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1240 VAL Chi-restraints excluded: chain D residue 1268 ASN Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1280 VAL Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain D residue 1355 ARG Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 425 TYR Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 579 GLN Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 39 TYR Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 309 VAL Chi-restraints excluded: chain Q residue 6 VAL Chi-restraints excluded: chain Q residue 33 ASP Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 92 LYS Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 135 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 126 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 383 optimal weight: 8.9990 chunk 88 optimal weight: 20.0000 chunk 79 optimal weight: 9.9990 chunk 295 optimal weight: 6.9990 chunk 310 optimal weight: 0.0570 chunk 68 optimal weight: 20.0000 chunk 60 optimal weight: 8.9990 chunk 416 optimal weight: 6.9990 overall best weight: 5.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.108001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.068878 restraints weight = 107398.802| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.17 r_work: 0.2762 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 35831 Z= 0.282 Angle : 0.642 10.289 48869 Z= 0.335 Chirality : 0.045 0.286 5571 Planarity : 0.004 0.059 5984 Dihedral : 16.357 179.548 5976 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.63 % Allowed : 22.84 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -0.83 (0.13), residues: 4138 helix: 0.68 (0.13), residues: 1713 sheet: -1.20 (0.24), residues: 417 loop : -1.51 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 182 TYR 0.026 0.002 TYR Q 104 PHE 0.014 0.001 PHE D 773 TRP 0.015 0.001 TRP N 276 HIS 0.005 0.001 HIS Q 10 Details of bonding type rmsd covalent geometry : bond 0.00655 (35822) covalent geometry : angle 0.63800 (48857) hydrogen bonds : bond 0.04457 ( 1543) hydrogen bonds : angle 4.68269 ( 4364) metal coordination : bond 0.01113 ( 9) metal coordination : angle 4.65301 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 215 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 ASN cc_start: 0.8709 (OUTLIER) cc_final: 0.8459 (p0) REVERT: B 194 GLN cc_start: 0.7741 (tp40) cc_final: 0.7515 (tp40) REVERT: C 239 MET cc_start: 0.9235 (tmm) cc_final: 0.8897 (ppp) REVERT: C 315 MET cc_start: 0.8576 (ptp) cc_final: 0.8342 (mpp) REVERT: C 325 LEU cc_start: 0.9675 (mm) cc_final: 0.9466 (mm) REVERT: C 342 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7158 (p0) REVERT: C 653 MET cc_start: 0.9074 (tpt) cc_final: 0.8706 (tpt) REVERT: C 903 ARG cc_start: 0.9397 (ptm160) cc_final: 0.9080 (ptp90) REVERT: C 964 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7923 (mm) REVERT: C 1023 HIS cc_start: 0.9110 (m90) cc_final: 0.8684 (m-70) REVERT: C 1025 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.7922 (t80) REVERT: C 1027 LYS cc_start: 0.9171 (mttt) cc_final: 0.8940 (mttt) REVERT: C 1085 MET cc_start: 0.9264 (mmm) cc_final: 0.8984 (mmt) REVERT: D 15 GLU cc_start: 0.5792 (OUTLIER) cc_final: 0.4322 (tm-30) REVERT: D 166 LEU cc_start: 0.9543 (OUTLIER) cc_final: 0.9217 (mm) REVERT: D 192 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8146 (ptm) REVERT: D 322 ARG cc_start: 0.8602 (mmm160) cc_final: 0.8376 (mtt90) REVERT: D 821 MET cc_start: 0.8697 (tpt) cc_final: 0.8427 (tpt) REVERT: D 842 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.6982 (mmt180) REVERT: D 901 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8125 (ttm170) REVERT: D 979 ASN cc_start: 0.9073 (p0) cc_final: 0.8741 (p0) REVERT: D 1156 LEU cc_start: 0.8989 (tp) cc_final: 0.8762 (tp) REVERT: D 1189 MET cc_start: 0.8676 (mmp) cc_final: 0.8287 (mmp) REVERT: D 1355 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8624 (mtp85) REVERT: E 15 ASN cc_start: 0.7097 (t0) cc_final: 0.6277 (t0) REVERT: E 56 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8015 (tm-30) REVERT: E 58 LEU cc_start: 0.8465 (mt) cc_final: 0.8169 (mt) REVERT: F 297 MET cc_start: 0.8136 (ppp) cc_final: 0.7578 (ppp) REVERT: F 322 MET cc_start: 0.7696 (ppp) cc_final: 0.7243 (ppp) REVERT: F 579 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7912 (pp30) REVERT: N 20 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7629 (tpp-160) REVERT: N 204 MET cc_start: 0.9156 (ttm) cc_final: 0.8636 (ttm) REVERT: N 209 PHE cc_start: 0.9621 (m-80) cc_final: 0.9194 (m-80) REVERT: N 283 PHE cc_start: 0.9274 (t80) cc_final: 0.9012 (t80) REVERT: Q 58 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8633 (pp) REVERT: Q 60 GLN cc_start: 0.8076 (pp30) cc_final: 0.7772 (pp30) REVERT: Q 92 LYS cc_start: 0.9413 (OUTLIER) cc_final: 0.9123 (ttmm) REVERT: Q 155 MET cc_start: 0.9040 (tpp) cc_final: 0.8388 (ttt) REVERT: Q 195 GLU cc_start: 0.9050 (tm-30) cc_final: 0.8559 (tm-30) outliers start: 164 outliers final: 136 residues processed: 365 average time/residue: 0.2269 time to fit residues: 137.0433 Evaluate side-chains 361 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 211 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 920 VAL Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1025 PHE Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1341 ASP Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 345 LYS Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 775 SER Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 842 ARG Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1047 THR Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1186 TYR Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1240 VAL Chi-restraints excluded: chain D residue 1268 ASN Chi-restraints excluded: chain D residue 1271 SER Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1280 VAL Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain D residue 1355 ARG Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 425 TYR Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 579 GLN Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 39 TYR Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 309 VAL Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 6 VAL Chi-restraints excluded: chain Q residue 33 ASP Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 92 LYS Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 135 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 286 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 338 optimal weight: 7.9990 chunk 232 optimal weight: 0.0770 chunk 370 optimal weight: 10.0000 chunk 33 optimal weight: 0.0170 chunk 223 optimal weight: 0.8980 chunk 84 optimal weight: 8.9990 chunk 354 optimal weight: 1.9990 chunk 251 optimal weight: 0.5980 chunk 284 optimal weight: 4.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 834 GLN C1008 GLN C1256 GLN ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 GLN ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 286 ASN ** N 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.110995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.070711 restraints weight = 93732.782| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.13 r_work: 0.2856 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 35831 Z= 0.110 Angle : 0.552 12.153 48869 Z= 0.289 Chirality : 0.042 0.289 5571 Planarity : 0.004 0.054 5984 Dihedral : 16.088 179.909 5976 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.44 % Allowed : 24.22 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -0.45 (0.13), residues: 4138 helix: 1.02 (0.13), residues: 1713 sheet: -1.02 (0.25), residues: 391 loop : -1.31 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 363 TYR 0.025 0.001 TYR N 92 PHE 0.017 0.001 PHE N 196 TRP 0.019 0.001 TRP N 276 HIS 0.007 0.001 HIS Q 10 Details of bonding type rmsd covalent geometry : bond 0.00226 (35822) covalent geometry : angle 0.54978 (48857) hydrogen bonds : bond 0.03448 ( 1543) hydrogen bonds : angle 4.38936 ( 4364) metal coordination : bond 0.00290 ( 9) metal coordination : angle 3.39150 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 229 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7857 (tp30) REVERT: C 239 MET cc_start: 0.9263 (tmm) cc_final: 0.8897 (ppp) REVERT: C 275 ARG cc_start: 0.9482 (mmm160) cc_final: 0.9260 (mmp80) REVERT: C 325 LEU cc_start: 0.9671 (mm) cc_final: 0.9446 (mm) REVERT: C 342 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.6892 (p0) REVERT: C 542 ARG cc_start: 0.7783 (mpp80) cc_final: 0.7508 (mtt90) REVERT: C 653 MET cc_start: 0.9048 (tpt) cc_final: 0.8672 (tpt) REVERT: C 903 ARG cc_start: 0.9398 (ptm160) cc_final: 0.9156 (ptp90) REVERT: C 1023 HIS cc_start: 0.9097 (m90) cc_final: 0.8842 (m-70) REVERT: C 1025 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.7824 (t80) REVERT: C 1085 MET cc_start: 0.9219 (mmm) cc_final: 0.8984 (mmt) REVERT: C 1232 MET cc_start: 0.8991 (mmm) cc_final: 0.8771 (mmp) REVERT: D 15 GLU cc_start: 0.5735 (OUTLIER) cc_final: 0.4382 (tm-30) REVERT: D 166 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9256 (mm) REVERT: D 704 GLU cc_start: 0.5912 (OUTLIER) cc_final: 0.5581 (pp20) REVERT: D 821 MET cc_start: 0.8635 (tpt) cc_final: 0.8415 (tpt) REVERT: D 873 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8128 (mt-10) REVERT: D 901 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8784 (ptm-80) REVERT: D 979 ASN cc_start: 0.8997 (p0) cc_final: 0.8674 (p0) REVERT: D 1156 LEU cc_start: 0.8985 (tp) cc_final: 0.8708 (tp) REVERT: D 1189 MET cc_start: 0.8644 (mmp) cc_final: 0.8248 (mmp) REVERT: E 15 ASN cc_start: 0.6751 (t0) cc_final: 0.6020 (t0) REVERT: E 44 ASP cc_start: 0.6364 (m-30) cc_final: 0.6108 (m-30) REVERT: E 56 GLU cc_start: 0.8477 (tm-30) cc_final: 0.7798 (tm-30) REVERT: E 58 LEU cc_start: 0.8520 (mt) cc_final: 0.7991 (mt) REVERT: F 276 MET cc_start: 0.8860 (ptp) cc_final: 0.8646 (mpp) REVERT: F 297 MET cc_start: 0.8066 (ppp) cc_final: 0.7474 (ppp) REVERT: F 322 MET cc_start: 0.7573 (ppp) cc_final: 0.7102 (ppp) REVERT: F 579 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7936 (pp30) REVERT: N 20 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7784 (tpp-160) REVERT: N 196 PHE cc_start: 0.9050 (m-10) cc_final: 0.8849 (m-10) REVERT: N 204 MET cc_start: 0.9131 (ttm) cc_final: 0.8582 (ttm) REVERT: N 209 PHE cc_start: 0.9619 (m-80) cc_final: 0.9194 (m-80) REVERT: N 283 PHE cc_start: 0.9295 (t80) cc_final: 0.9040 (t80) REVERT: Q 60 GLN cc_start: 0.8031 (pp30) cc_final: 0.7694 (pp30) REVERT: Q 92 LYS cc_start: 0.9395 (OUTLIER) cc_final: 0.9170 (ttmm) REVERT: Q 155 MET cc_start: 0.9028 (tpp) cc_final: 0.8414 (ttt) REVERT: Q 195 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8533 (tm-30) outliers start: 122 outliers final: 85 residues processed: 340 average time/residue: 0.2149 time to fit residues: 121.3009 Evaluate side-chains 308 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 213 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 920 VAL Chi-restraints excluded: chain C residue 1025 PHE Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1341 ASP Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1047 THR Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1186 TYR Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1210 ILE Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1268 ASN Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1280 VAL Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 425 TYR Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 579 GLN Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 309 VAL Chi-restraints excluded: chain Q residue 33 ASP Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 92 LYS Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 135 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 168 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 327 optimal weight: 20.0000 chunk 143 optimal weight: 0.8980 chunk 382 optimal weight: 6.9990 chunk 372 optimal weight: 9.9990 chunk 196 optimal weight: 4.9990 chunk 173 optimal weight: 0.6980 chunk 57 optimal weight: 50.0000 chunk 256 optimal weight: 0.8980 chunk 361 optimal weight: 0.9980 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.110336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.068748 restraints weight = 99449.318| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.06 r_work: 0.2839 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35831 Z= 0.130 Angle : 0.566 12.385 48869 Z= 0.293 Chirality : 0.042 0.253 5571 Planarity : 0.004 0.054 5984 Dihedral : 16.000 179.808 5971 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.94 % Allowed : 24.68 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -0.34 (0.13), residues: 4138 helix: 1.07 (0.13), residues: 1713 sheet: -0.87 (0.25), residues: 405 loop : -1.24 (0.14), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 363 TYR 0.031 0.001 TYR N 92 PHE 0.016 0.001 PHE N 196 TRP 0.017 0.001 TRP N 276 HIS 0.008 0.001 HIS Q 10 Details of bonding type rmsd covalent geometry : bond 0.00294 (35822) covalent geometry : angle 0.56306 (48857) hydrogen bonds : bond 0.03514 ( 1543) hydrogen bonds : angle 4.35699 ( 4364) metal coordination : bond 0.00451 ( 9) metal coordination : angle 3.44422 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 216 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7864 (tp30) REVERT: C 239 MET cc_start: 0.9247 (tmm) cc_final: 0.8863 (ppp) REVERT: C 315 MET cc_start: 0.8750 (ptp) cc_final: 0.8394 (mpp) REVERT: C 325 LEU cc_start: 0.9658 (mm) cc_final: 0.9422 (mm) REVERT: C 342 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.6814 (p0) REVERT: C 653 MET cc_start: 0.9004 (tpt) cc_final: 0.8657 (tpt) REVERT: C 903 ARG cc_start: 0.9403 (ptm160) cc_final: 0.9160 (ptp90) REVERT: C 1023 HIS cc_start: 0.9064 (m90) cc_final: 0.8814 (m-70) REVERT: C 1025 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7737 (t80) REVERT: C 1085 MET cc_start: 0.9242 (mmm) cc_final: 0.8975 (mmt) REVERT: D 15 GLU cc_start: 0.5764 (OUTLIER) cc_final: 0.4392 (tm-30) REVERT: D 166 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9254 (mm) REVERT: D 504 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7648 (pt0) REVERT: D 704 GLU cc_start: 0.5838 (OUTLIER) cc_final: 0.5469 (pp20) REVERT: D 789 LYS cc_start: 0.5788 (mmtt) cc_final: 0.5508 (mmtp) REVERT: D 873 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8119 (mt-10) REVERT: D 901 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8778 (ptm-80) REVERT: D 979 ASN cc_start: 0.9030 (p0) cc_final: 0.8700 (p0) REVERT: D 1156 LEU cc_start: 0.8986 (tp) cc_final: 0.8696 (tp) REVERT: D 1189 MET cc_start: 0.8625 (mmp) cc_final: 0.8190 (mmp) REVERT: D 1262 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8259 (mtm180) REVERT: E 15 ASN cc_start: 0.6839 (t0) cc_final: 0.6072 (t0) REVERT: E 56 GLU cc_start: 0.8477 (tm-30) cc_final: 0.7760 (tm-30) REVERT: E 58 LEU cc_start: 0.8484 (mt) cc_final: 0.7930 (mt) REVERT: F 276 MET cc_start: 0.8865 (ptp) cc_final: 0.8654 (mpp) REVERT: F 297 MET cc_start: 0.8014 (ppp) cc_final: 0.7430 (ppp) REVERT: F 322 MET cc_start: 0.7495 (ppp) cc_final: 0.7032 (ppp) REVERT: F 579 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7948 (pp30) REVERT: N 196 PHE cc_start: 0.9071 (m-10) cc_final: 0.8817 (m-10) REVERT: N 204 MET cc_start: 0.9065 (ttm) cc_final: 0.8491 (ttm) REVERT: N 209 PHE cc_start: 0.9598 (m-80) cc_final: 0.9125 (m-80) REVERT: N 283 PHE cc_start: 0.9289 (t80) cc_final: 0.9025 (t80) REVERT: Q 60 GLN cc_start: 0.7993 (pp30) cc_final: 0.7700 (pp30) REVERT: Q 92 LYS cc_start: 0.9391 (OUTLIER) cc_final: 0.9171 (ttmm) REVERT: Q 155 MET cc_start: 0.9038 (tpp) cc_final: 0.8439 (ttt) REVERT: Q 195 GLU cc_start: 0.9004 (tm-30) cc_final: 0.8550 (tm-30) outliers start: 104 outliers final: 85 residues processed: 313 average time/residue: 0.2118 time to fit residues: 110.7279 Evaluate side-chains 310 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 214 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 920 VAL Chi-restraints excluded: chain C residue 1025 PHE Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1341 ASP Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1047 THR Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1186 TYR Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1210 ILE Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1262 ARG Chi-restraints excluded: chain D residue 1268 ASN Chi-restraints excluded: chain D residue 1280 VAL Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 425 TYR Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 579 GLN Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 309 VAL Chi-restraints excluded: chain Q residue 33 ASP Chi-restraints excluded: chain Q residue 92 LYS Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 135 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 90 optimal weight: 20.0000 chunk 266 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 322 optimal weight: 0.9980 chunk 265 optimal weight: 1.9990 chunk 262 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 359 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 232 optimal weight: 4.9990 chunk 392 optimal weight: 50.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.109664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.071456 restraints weight = 100177.451| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.07 r_work: 0.2814 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 35831 Z= 0.168 Angle : 0.595 12.690 48869 Z= 0.306 Chirality : 0.042 0.248 5571 Planarity : 0.004 0.054 5984 Dihedral : 16.006 179.751 5965 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.96 % Allowed : 24.76 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -0.35 (0.13), residues: 4138 helix: 1.03 (0.13), residues: 1712 sheet: -0.83 (0.26), residues: 399 loop : -1.22 (0.14), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 363 TYR 0.032 0.001 TYR N 92 PHE 0.016 0.001 PHE N 196 TRP 0.021 0.001 TRP N 276 HIS 0.007 0.001 HIS Q 10 Details of bonding type rmsd covalent geometry : bond 0.00386 (35822) covalent geometry : angle 0.59254 (48857) hydrogen bonds : bond 0.03749 ( 1543) hydrogen bonds : angle 4.42057 ( 4364) metal coordination : bond 0.00644 ( 9) metal coordination : angle 3.65579 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 216 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7897 (tp30) REVERT: C 239 MET cc_start: 0.9241 (tmm) cc_final: 0.8867 (ppp) REVERT: C 315 MET cc_start: 0.8751 (ptp) cc_final: 0.8359 (mpp) REVERT: C 325 LEU cc_start: 0.9669 (mm) cc_final: 0.9441 (mm) REVERT: C 342 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.6959 (p0) REVERT: C 653 MET cc_start: 0.9016 (tpt) cc_final: 0.8660 (tpt) REVERT: C 903 ARG cc_start: 0.9398 (ptm160) cc_final: 0.9038 (ptp90) REVERT: C 1023 HIS cc_start: 0.9087 (m90) cc_final: 0.8639 (m-70) REVERT: C 1025 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.7754 (t80) REVERT: C 1027 LYS cc_start: 0.9152 (mttt) cc_final: 0.8910 (mttt) REVERT: C 1085 MET cc_start: 0.9269 (mmm) cc_final: 0.8983 (mmt) REVERT: D 15 GLU cc_start: 0.5774 (OUTLIER) cc_final: 0.4385 (tm-30) REVERT: D 81 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7239 (tmm-80) REVERT: D 166 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9259 (mm) REVERT: D 504 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7683 (pt0) REVERT: D 704 GLU cc_start: 0.5945 (OUTLIER) cc_final: 0.5585 (pp20) REVERT: D 873 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8133 (mt-10) REVERT: D 901 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8790 (ptm-80) REVERT: D 979 ASN cc_start: 0.9059 (p0) cc_final: 0.8739 (p0) REVERT: D 1189 MET cc_start: 0.8661 (mmp) cc_final: 0.8325 (mmp) REVERT: D 1262 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8382 (mtm180) REVERT: E 15 ASN cc_start: 0.6971 (t0) cc_final: 0.6233 (t0) REVERT: E 56 GLU cc_start: 0.8458 (tm-30) cc_final: 0.7730 (tm-30) REVERT: E 58 LEU cc_start: 0.8452 (mt) cc_final: 0.7897 (mt) REVERT: F 297 MET cc_start: 0.7972 (ppp) cc_final: 0.7352 (ppp) REVERT: F 322 MET cc_start: 0.7500 (ppp) cc_final: 0.7048 (ppp) REVERT: F 579 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7940 (pp30) REVERT: N 196 PHE cc_start: 0.9118 (m-10) cc_final: 0.8838 (m-10) REVERT: N 204 MET cc_start: 0.9064 (ttm) cc_final: 0.8484 (ttm) REVERT: N 209 PHE cc_start: 0.9592 (m-80) cc_final: 0.9109 (m-80) REVERT: N 283 PHE cc_start: 0.9284 (t80) cc_final: 0.9020 (t80) REVERT: Q 60 GLN cc_start: 0.8044 (pp30) cc_final: 0.7736 (pp30) REVERT: Q 92 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.9187 (ttmm) REVERT: Q 155 MET cc_start: 0.9041 (tpp) cc_final: 0.8442 (ttt) REVERT: Q 195 GLU cc_start: 0.9019 (tm-30) cc_final: 0.8546 (tm-30) outliers start: 105 outliers final: 87 residues processed: 313 average time/residue: 0.2123 time to fit residues: 110.7467 Evaluate side-chains 310 residues out of total 3541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 211 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 920 VAL Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 1025 PHE Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1341 ASP Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1047 THR Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1186 TYR Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1210 ILE Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1262 ARG Chi-restraints excluded: chain D residue 1268 ASN Chi-restraints excluded: chain D residue 1280 VAL Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 425 TYR Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 579 GLN Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 309 VAL Chi-restraints excluded: chain Q residue 33 ASP Chi-restraints excluded: chain Q residue 92 LYS Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 135 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 24 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 112 optimal weight: 0.3980 chunk 256 optimal weight: 4.9990 chunk 162 optimal weight: 30.0000 chunk 242 optimal weight: 1.9990 chunk 238 optimal weight: 0.0670 chunk 287 optimal weight: 20.0000 chunk 227 optimal weight: 1.9990 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.111011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.070632 restraints weight = 113060.330| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.30 r_work: 0.2833 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 35831 Z= 0.112 Angle : 0.570 13.313 48869 Z= 0.293 Chirality : 0.042 0.251 5571 Planarity : 0.004 0.053 5984 Dihedral : 15.896 179.956 5963 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.82 % Allowed : 24.84 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -0.23 (0.13), residues: 4138 helix: 1.11 (0.13), residues: 1715 sheet: -0.77 (0.26), residues: 400 loop : -1.13 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 363 TYR 0.032 0.001 TYR N 92 PHE 0.015 0.001 PHE N 196 TRP 0.019 0.001 TRP N 276 HIS 0.006 0.000 HIS Q 10 Details of bonding type rmsd covalent geometry : bond 0.00248 (35822) covalent geometry : angle 0.56800 (48857) hydrogen bonds : bond 0.03375 ( 1543) hydrogen bonds : angle 4.32244 ( 4364) metal coordination : bond 0.00341 ( 9) metal coordination : angle 3.26656 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10828.40 seconds wall clock time: 185 minutes 13.47 seconds (11113.47 seconds total)