Starting phenix.real_space_refine on Sat Mar 7 06:56:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sx3_25492/03_2026/7sx3_25492.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sx3_25492/03_2026/7sx3_25492.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sx3_25492/03_2026/7sx3_25492.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sx3_25492/03_2026/7sx3_25492.map" model { file = "/net/cci-nas-00/data/ceres_data/7sx3_25492/03_2026/7sx3_25492.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sx3_25492/03_2026/7sx3_25492.cif" } resolution = 3.1 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= 1.978 sd= 1.683 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 304 5.16 5 C 24750 2.51 5 N 6265 2.21 5 O 6634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37959 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1386, 11344 Classifications: {'peptide': 1386} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 49, 'TRANS': 1334} Chain breaks: 7 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYS:plan-2': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1256 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 5, 'TRANS': 147} Chain breaks: 3 Chain: "C" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 926 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain breaks: 5 Chain: "D" Number of atoms: 11107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1418, 11107 Classifications: {'peptide': 1418} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PCIS': 1, 'PTRANS': 62, 'TRANS': 1354} Chain breaks: 29 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 222 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'UNK:plan-1': 74} Unresolved non-hydrogen planarities: 74 Chain: "E" Number of atoms: 12977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1611, 12977 Classifications: {'peptide': 1611} Link IDs: {'PCIS': 1, 'PTRANS': 87, 'TRANS': 1522} Chain breaks: 25 Chain: "A" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 349 Unusual residues: {'NAG': 2, 'PEV': 4, 'PGV': 2, 'Y01': 3} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PGV:plan-2': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 8.06, per 1000 atoms: 0.21 Number of scatterers: 37959 At special positions: 0 Unit cell: (202.964, 177.153, 283.914, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 304 16.00 P 6 15.00 O 6634 8.00 N 6265 7.00 C 24750 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 229 " - pdb=" SG CYS A 245 " distance=2.03 Simple disulfide: pdb=" SG CYS A1046 " - pdb=" SG CYS A1057 " distance=2.03 Simple disulfide: pdb=" SG CYS A1405 " - pdb=" SG CYS A1417 " distance=2.04 Simple disulfide: pdb=" SG CYS B 191 " - pdb=" SG CYS B 261 " distance=2.03 Simple disulfide: pdb=" SG CYS B 226 " - pdb=" SG CYS B 313 " distance=2.03 Simple disulfide: pdb=" SG CYS B 304 " - pdb=" SG CYS B 341 " distance=2.03 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 377 " distance=2.02 Simple disulfide: pdb=" SG CYS B 330 " - pdb=" SG CYS B 376 " distance=2.02 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 361 " distance=1.92 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 Links applied NAG-ASN " NAG A2102 " - " ASN A1064 " Time building additional restraints: 3.34 Conformation dependent library (CDL) restraints added in 1.4 seconds 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9044 Finding SS restraints... Secondary structure from input PDB file: 271 helices and 7 sheets defined 79.1% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 35 through 56 removed outlier: 3.667A pdb=" N HIS A 39 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 64 Processing helix chain 'A' and resid 65 through 89 removed outlier: 4.239A pdb=" N TYR A 69 " --> pdb=" O PRO A 65 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 130 Processing helix chain 'A' and resid 137 through 144 removed outlier: 3.790A pdb=" N GLY A 140 " --> pdb=" O SER A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 148 Processing helix chain 'A' and resid 149 through 154 removed outlier: 3.885A pdb=" N ALA A 153 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE A 154 " --> pdb=" O MET A 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 149 through 154' Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 163 through 201 removed outlier: 4.046A pdb=" N ILE A 167 " --> pdb=" O PRO A 163 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY A 201 " --> pdb=" O VAL A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 248 through 252 Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 294 through 309 removed outlier: 3.709A pdb=" N SER A 298 " --> pdb=" O PRO A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 332 removed outlier: 3.727A pdb=" N PHE A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 381 Processing helix chain 'A' and resid 383 through 403 Processing helix chain 'A' and resid 416 through 441 Processing helix chain 'A' and resid 441 through 447 Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 474 through 480 removed outlier: 3.778A pdb=" N GLN A 478 " --> pdb=" O PHE A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 488 Processing helix chain 'A' and resid 489 through 501 Processing helix chain 'A' and resid 502 through 529 removed outlier: 4.209A pdb=" N LEU A 506 " --> pdb=" O PRO A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 553 Processing helix chain 'A' and resid 555 through 567 Processing helix chain 'A' and resid 571 through 589 Processing helix chain 'A' and resid 589 through 603 Processing helix chain 'A' and resid 605 through 616 Processing helix chain 'A' and resid 629 through 631 No H-bonds generated for 'chain 'A' and resid 629 through 631' Processing helix chain 'A' and resid 632 through 637 removed outlier: 4.013A pdb=" N LYS A 636 " --> pdb=" O ARG A 632 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A 637 " --> pdb=" O ILE A 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 632 through 637' Processing helix chain 'A' and resid 659 through 669 Processing helix chain 'A' and resid 713 through 718 removed outlier: 3.671A pdb=" N ARG A 717 " --> pdb=" O SER A 713 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN A 718 " --> pdb=" O ILE A 714 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 713 through 718' Processing helix chain 'A' and resid 718 through 740 Processing helix chain 'A' and resid 818 through 830 Processing helix chain 'A' and resid 835 through 839 removed outlier: 3.616A pdb=" N ILE A 839 " --> pdb=" O PRO A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 856 Processing helix chain 'A' and resid 877 through 883 Processing helix chain 'A' and resid 886 through 904 Processing helix chain 'A' and resid 915 through 938 removed outlier: 3.663A pdb=" N GLN A 919 " --> pdb=" O ALA A 915 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE A 920 " --> pdb=" O PRO A 916 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ALA A 921 " --> pdb=" O THR A 917 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU A 922 " --> pdb=" O LEU A 918 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET A 938 " --> pdb=" O ASN A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 972 Processing helix chain 'A' and resid 980 through 989 Processing helix chain 'A' and resid 990 through 993 Proline residue: A 993 - end of helix No H-bonds generated for 'chain 'A' and resid 990 through 993' Processing helix chain 'A' and resid 994 through 1000 removed outlier: 3.890A pdb=" N LYS A 998 " --> pdb=" O LEU A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1013 removed outlier: 4.492A pdb=" N GLY A1013 " --> pdb=" O GLU A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1040 Processing helix chain 'A' and resid 1053 through 1057 Processing helix chain 'A' and resid 1100 through 1113 removed outlier: 3.717A pdb=" N SER A1113 " --> pdb=" O PHE A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1129 Processing helix chain 'A' and resid 1132 through 1144 removed outlier: 3.850A pdb=" N ILE A1136 " --> pdb=" O HIS A1132 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS A1137 " --> pdb=" O GLY A1133 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A1139 " --> pdb=" O TYR A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1164 removed outlier: 3.935A pdb=" N PHE A1151 " --> pdb=" O GLY A1147 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A1152 " --> pdb=" O LEU A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1185 Processing helix chain 'A' and resid 1197 through 1208 Processing helix chain 'A' and resid 1209 through 1226 removed outlier: 3.534A pdb=" N LYS A1213 " --> pdb=" O HIS A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1229 No H-bonds generated for 'chain 'A' and resid 1227 through 1229' Processing helix chain 'A' and resid 1237 through 1263 removed outlier: 3.607A pdb=" N VAL A1247 " --> pdb=" O THR A1243 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE A1248 " --> pdb=" O MET A1244 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET A1263 " --> pdb=" O LYS A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1271 removed outlier: 4.022A pdb=" N SER A1271 " --> pdb=" O GLY A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1292 Processing helix chain 'A' and resid 1296 through 1312 Processing helix chain 'A' and resid 1313 through 1318 removed outlier: 4.062A pdb=" N LYS A1317 " --> pdb=" O SER A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1318 through 1335 removed outlier: 3.669A pdb=" N LYS A1322 " --> pdb=" O HIS A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1335 through 1358 Processing helix chain 'A' and resid 1374 through 1388 Processing helix chain 'A' and resid 1390 through 1399 Processing helix chain 'A' and resid 1419 through 1437 Processing helix chain 'A' and resid 1437 through 1454 removed outlier: 3.882A pdb=" N LEU A1441 " --> pdb=" O ILE A1437 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A1442 " --> pdb=" O MET A1438 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1478 Processing helix chain 'A' and resid 1489 through 1495 Processing helix chain 'A' and resid 1498 through 1502 removed outlier: 3.545A pdb=" N LEU A1501 " --> pdb=" O ARG A1498 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1522 Processing helix chain 'A' and resid 1530 through 1541 Processing helix chain 'A' and resid 1543 through 1548 Processing helix chain 'A' and resid 1549 through 1598 removed outlier: 4.041A pdb=" N MET A1574 " --> pdb=" O GLN A1570 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TRP A1575 " --> pdb=" O THR A1571 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 removed outlier: 3.741A pdb=" N VAL B 190 " --> pdb=" O ASN B 186 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N CYS B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 186 through 191' Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 230 through 237 Processing helix chain 'B' and resid 259 through 288 removed outlier: 3.763A pdb=" N LYS B 288 " --> pdb=" O SER B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 317 Processing helix chain 'B' and resid 331 through 341 removed outlier: 3.982A pdb=" N LEU B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 17 removed outlier: 3.824A pdb=" N GLU C 12 " --> pdb=" O GLU C 8 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS C 14 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU C 15 " --> pdb=" O ALA C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 38 Processing helix chain 'C' and resid 39 through 41 No H-bonds generated for 'chain 'C' and resid 39 through 41' Processing helix chain 'C' and resid 47 through 54 Processing helix chain 'C' and resid 66 through 79 removed outlier: 4.037A pdb=" N ARG C 75 " --> pdb=" O THR C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 102 through 114 Processing helix chain 'C' and resid 120 through 127 removed outlier: 4.162A pdb=" N GLU C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 145 Processing helix chain 'D' and resid 39 through 55 Processing helix chain 'D' and resid 86 through 105 Processing helix chain 'D' and resid 128 through 141 Processing helix chain 'D' and resid 148 through 165 Processing helix chain 'D' and resid 175 through 180 removed outlier: 3.552A pdb=" N ILE D 179 " --> pdb=" O PRO D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 184 Processing helix chain 'D' and resid 186 through 200 removed outlier: 3.833A pdb=" N HIS D 190 " --> pdb=" O PRO D 186 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LYS D 191 " --> pdb=" O PRO D 187 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASP D 192 " --> pdb=" O PHE D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 206 Processing helix chain 'D' and resid 221 through 234 removed outlier: 4.130A pdb=" N SER D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE D 229 " --> pdb=" O SER D 225 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET D 231 " --> pdb=" O LEU D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 251 removed outlier: 3.805A pdb=" N HIS D 240 " --> pdb=" O ASN D 236 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR D 250 " --> pdb=" O CYS D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 265 removed outlier: 3.744A pdb=" N ASP D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 268 No H-bonds generated for 'chain 'D' and resid 266 through 268' Processing helix chain 'D' and resid 269 through 281 Processing helix chain 'D' and resid 282 through 285 Processing helix chain 'D' and resid 434 through 438 Processing helix chain 'D' and resid 439 through 456 removed outlier: 3.512A pdb=" N CYS D 444 " --> pdb=" O GLU D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 511 Processing helix chain 'D' and resid 519 through 538 removed outlier: 3.552A pdb=" N ALA D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 568 removed outlier: 4.719A pdb=" N LYS D 559 " --> pdb=" O GLN D 555 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TRP D 560 " --> pdb=" O PHE D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 577 removed outlier: 3.501A pdb=" N MET D 572 " --> pdb=" O ARG D 568 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU D 576 " --> pdb=" O MET D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 611 removed outlier: 3.568A pdb=" N GLN D 599 " --> pdb=" O SER D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 614 No H-bonds generated for 'chain 'D' and resid 612 through 614' Processing helix chain 'D' and resid 618 through 635 removed outlier: 4.511A pdb=" N GLU D 622 " --> pdb=" O GLN D 618 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N CYS D 623 " --> pdb=" O SER D 619 " (cutoff:3.500A) Proline residue: D 626 - end of helix Processing helix chain 'D' and resid 643 through 652 removed outlier: 4.277A pdb=" N VAL D 647 " --> pdb=" O GLU D 643 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS D 650 " --> pdb=" O GLU D 646 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET D 651 " --> pdb=" O VAL D 647 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE D 652 " --> pdb=" O LEU D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 667 removed outlier: 3.769A pdb=" N PHE D 667 " --> pdb=" O MET D 663 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 663 through 667' Processing helix chain 'D' and resid 667 through 672 Processing helix chain 'D' and resid 673 through 675 No H-bonds generated for 'chain 'D' and resid 673 through 675' Processing helix chain 'D' and resid 678 through 695 removed outlier: 3.588A pdb=" N GLN D 682 " --> pdb=" O PRO D 678 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN D 684 " --> pdb=" O SER D 680 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA D 685 " --> pdb=" O VAL D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 716 Processing helix chain 'D' and resid 796 through 816 removed outlier: 4.210A pdb=" N CYS D 800 " --> pdb=" O MET D 796 " (cutoff:3.500A) Processing helix chain 'D' and resid 825 through 841 Processing helix chain 'D' and resid 860 through 879 Processing helix chain 'D' and resid 950 through 964 removed outlier: 3.890A pdb=" N ALA D 964 " --> pdb=" O PHE D 960 " (cutoff:3.500A) Processing helix chain 'D' and resid 968 through 984 removed outlier: 3.826A pdb=" N ASN D 974 " --> pdb=" O ASP D 970 " (cutoff:3.500A) Processing helix chain 'D' and resid 987 through 996 removed outlier: 3.873A pdb=" N ARG D 993 " --> pdb=" O LEU D 989 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LYS D 994 " --> pdb=" O TYR D 990 " (cutoff:3.500A) Processing helix chain 'D' and resid 996 through 1007 Processing helix chain 'D' and resid 1007 through 1015 Processing helix chain 'D' and resid 1020 through 1036 removed outlier: 3.698A pdb=" N SER D1024 " --> pdb=" O PHE D1020 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU D1026 " --> pdb=" O GLN D1022 " (cutoff:3.500A) Proline residue: D1029 - end of helix Processing helix chain 'D' and resid 1039 through 1053 removed outlier: 4.026A pdb=" N ILE D1043 " --> pdb=" O HIS D1039 " (cutoff:3.500A) Processing helix chain 'D' and resid 1056 through 1073 removed outlier: 3.847A pdb=" N GLU D1065 " --> pdb=" O PHE D1061 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE D1073 " --> pdb=" O VAL D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1075 through 1080 removed outlier: 3.765A pdb=" N VAL D1079 " --> pdb=" O ASP D1075 " (cutoff:3.500A) Processing helix chain 'D' and resid 1082 through 1100 Processing helix chain 'D' and resid 1104 through 1116 removed outlier: 3.944A pdb=" N ASP D1116 " --> pdb=" O GLY D1112 " (cutoff:3.500A) Processing helix chain 'D' and resid 1119 through 1137 removed outlier: 3.532A pdb=" N THR D1136 " --> pdb=" O PHE D1132 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1155 Processing helix chain 'D' and resid 1162 through 1181 Processing helix chain 'D' and resid 1209 through 1220 Processing helix chain 'D' and resid 1227 through 1232 removed outlier: 4.179A pdb=" N LYS D1232 " --> pdb=" O ARG D1228 " (cutoff:3.500A) Processing helix chain 'D' and resid 1273 through 1290 Processing helix chain 'D' and resid 1298 through 1316 Processing helix chain 'D' and resid 1328 through 1335 Processing helix chain 'D' and resid 1335 through 1352 removed outlier: 3.775A pdb=" N GLY D1344 " --> pdb=" O ALA D1340 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ALA D1346 " --> pdb=" O ILE D1342 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLN D1347 " --> pdb=" O ALA D1343 " (cutoff:3.500A) Processing helix chain 'D' and resid 1352 through 1372 removed outlier: 3.917A pdb=" N HIS D1358 " --> pdb=" O ASN D1354 " (cutoff:3.500A) Proline residue: D1361 - end of helix removed outlier: 3.670A pdb=" N SER D1371 " --> pdb=" O LEU D1367 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N CYS D1372 " --> pdb=" O LYS D1368 " (cutoff:3.500A) Processing helix chain 'D' and resid 1375 through 1380 removed outlier: 4.029A pdb=" N PHE D1379 " --> pdb=" O LEU D1375 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN D1380 " --> pdb=" O ARG D1376 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1375 through 1380' Processing helix chain 'D' and resid 1386 through 1390 removed outlier: 4.040A pdb=" N SER D1389 " --> pdb=" O SER D1386 " (cutoff:3.500A) Processing helix chain 'D' and resid 1391 through 1409 removed outlier: 3.856A pdb=" N GLN D1396 " --> pdb=" O PRO D1392 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET D1397 " --> pdb=" O HIS D1393 " (cutoff:3.500A) Processing helix chain 'D' and resid 1413 through 1433 removed outlier: 4.280A pdb=" N LYS D1418 " --> pdb=" O CYS D1414 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ILE D1419 " --> pdb=" O ASP D1415 " (cutoff:3.500A) Processing helix chain 'D' and resid 2019 through 2037 Processing helix chain 'D' and resid 2037 through 2042 Processing helix chain 'D' and resid 2044 through 2058 removed outlier: 3.589A pdb=" N LEU D2055 " --> pdb=" O SER D2051 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER D2058 " --> pdb=" O ARG D2054 " (cutoff:3.500A) Processing helix chain 'D' and resid 2073 through 2090 Processing helix chain 'D' and resid 2093 through 2100 Processing helix chain 'D' and resid 2107 through 2116 Processing helix chain 'D' and resid 2123 through 2138 Processing helix chain 'D' and resid 2144 through 2159 Processing helix chain 'D' and resid 2169 through 2182 removed outlier: 3.708A pdb=" N ALA D2182 " --> pdb=" O GLN D2178 " (cutoff:3.500A) Processing helix chain 'D' and resid 2183 through 2187 Processing helix chain 'D' and resid 2194 through 2206 removed outlier: 4.109A pdb=" N LEU D2198 " --> pdb=" O LEU D2194 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS D2206 " --> pdb=" O ILE D2202 " (cutoff:3.500A) Processing helix chain 'D' and resid 2209 through 2215 removed outlier: 3.791A pdb=" N SER D2215 " --> pdb=" O ASN D2211 " (cutoff:3.500A) Processing helix chain 'D' and resid 2216 through 2231 Processing helix chain 'D' and resid 2234 through 2249 removed outlier: 3.902A pdb=" N LEU D2238 " --> pdb=" O THR D2234 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG D2247 " --> pdb=" O GLY D2243 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE D2249 " --> pdb=" O CYS D2245 " (cutoff:3.500A) Processing helix chain 'D' and resid 2251 through 2271 removed outlier: 3.601A pdb=" N PHE D2256 " --> pdb=" O GLU D2252 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU D2258 " --> pdb=" O ASP D2254 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N SER D2259 " --> pdb=" O LYS D2255 " (cutoff:3.500A) Processing helix chain 'D' and resid 2277 through 2293 removed outlier: 3.518A pdb=" N LEU D2282 " --> pdb=" O ASP D2278 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP D2291 " --> pdb=" O PHE D2287 " (cutoff:3.500A) Processing helix chain 'D' and resid 2318 through 2323 removed outlier: 3.780A pdb=" N GLN D2323 " --> pdb=" O CYS D2320 " (cutoff:3.500A) Processing helix chain 'D' and resid 2324 through 2334 removed outlier: 3.527A pdb=" N VAL D2328 " --> pdb=" O TYR D2324 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP D2334 " --> pdb=" O ASP D2330 " (cutoff:3.500A) Processing helix chain 'D' and resid 2336 through 2343 Processing helix chain 'D' and resid 2356 through 2378 Processing helix chain 'D' and resid 2383 through 2388 removed outlier: 3.530A pdb=" N TYR D2387 " --> pdb=" O ALA D2383 " (cutoff:3.500A) Processing helix chain 'D' and resid 2389 through 2393 removed outlier: 3.647A pdb=" N TYR D2392 " --> pdb=" O PRO D2389 " (cutoff:3.500A) Processing helix chain 'D' and resid 2407 through 2429 Processing helix chain 'D' and resid 2440 through 2442 No H-bonds generated for 'chain 'D' and resid 2440 through 2442' Processing helix chain 'D' and resid 2443 through 2458 Processing helix chain 'D' and resid 2470 through 2489 removed outlier: 4.183A pdb=" N HIS D2474 " --> pdb=" O CYS D2470 " (cutoff:3.500A) Processing helix chain 'D' and resid 2504 through 2527 Proline residue: D2518 - end of helix removed outlier: 4.037A pdb=" N ASN D2527 " --> pdb=" O LEU D2523 " (cutoff:3.500A) Processing helix chain 'D' and resid 2531 through 2548 Processing helix chain 'D' and resid 2550 through 2566 removed outlier: 3.935A pdb=" N VAL D2554 " --> pdb=" O SER D2550 " (cutoff:3.500A) Proline residue: D2558 - end of helix Proline residue: D2562 - end of helix Processing helix chain 'D' and resid 2575 through 2585 Processing helix chain 'D' and resid 2605 through 2625 Processing helix chain 'E' and resid 22 through 34 removed outlier: 4.043A pdb=" N LEU E 26 " --> pdb=" O ILE E 22 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE E 33 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 55 removed outlier: 4.103A pdb=" N VAL E 47 " --> pdb=" O GLU E 43 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER E 48 " --> pdb=" O ALA E 44 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU E 53 " --> pdb=" O PHE E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 96 Proline residue: E 83 - end of helix Processing helix chain 'E' and resid 108 through 121 Processing helix chain 'E' and resid 182 through 193 Processing helix chain 'E' and resid 194 through 196 No H-bonds generated for 'chain 'E' and resid 194 through 196' Processing helix chain 'E' and resid 214 through 220 removed outlier: 3.689A pdb=" N GLU E 220 " --> pdb=" O GLN E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 339 Processing helix chain 'E' and resid 344 through 365 Processing helix chain 'E' and resid 654 through 665 Processing helix chain 'E' and resid 669 through 687 Processing helix chain 'E' and resid 784 through 798 Processing helix chain 'E' and resid 819 through 836 removed outlier: 3.722A pdb=" N PHE E 823 " --> pdb=" O ARG E 819 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS E 836 " --> pdb=" O THR E 832 " (cutoff:3.500A) Processing helix chain 'E' and resid 838 through 853 removed outlier: 3.713A pdb=" N ASN E 851 " --> pdb=" O ARG E 847 " (cutoff:3.500A) Processing helix chain 'E' and resid 854 through 867 Processing helix chain 'E' and resid 896 through 914 removed outlier: 5.431A pdb=" N LYS E 906 " --> pdb=" O SER E 902 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N SER E 907 " --> pdb=" O ALA E 903 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER E 914 " --> pdb=" O THR E 910 " (cutoff:3.500A) Processing helix chain 'E' and resid 915 through 920 Processing helix chain 'E' and resid 921 through 923 No H-bonds generated for 'chain 'E' and resid 921 through 923' Processing helix chain 'E' and resid 924 through 941 removed outlier: 3.515A pdb=" N GLN E 933 " --> pdb=" O CYS E 929 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA E 941 " --> pdb=" O PHE E 937 " (cutoff:3.500A) Processing helix chain 'E' and resid 944 through 951 removed outlier: 3.789A pdb=" N ARG E 948 " --> pdb=" O ASN E 944 " (cutoff:3.500A) Processing helix chain 'E' and resid 951 through 956 Processing helix chain 'E' and resid 1176 through 1192 Processing helix chain 'E' and resid 1201 through 1208 Processing helix chain 'E' and resid 1214 through 1235 Processing helix chain 'E' and resid 1268 through 1293 removed outlier: 3.752A pdb=" N ALA E1274 " --> pdb=" O GLN E1270 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS E1275 " --> pdb=" O TRP E1271 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU E1276 " --> pdb=" O ASN E1272 " (cutoff:3.500A) Processing helix chain 'E' and resid 1338 through 1360 removed outlier: 3.504A pdb=" N LYS E1342 " --> pdb=" O PRO E1338 " (cutoff:3.500A) Processing helix chain 'E' and resid 1459 through 1469 Processing helix chain 'E' and resid 1484 through 1503 Processing helix chain 'E' and resid 1555 through 1564 Processing helix chain 'E' and resid 1570 through 1579 Processing helix chain 'E' and resid 1584 through 1598 removed outlier: 3.620A pdb=" N GLY E1589 " --> pdb=" O GLU E1585 " (cutoff:3.500A) Proline residue: E1593 - end of helix Processing helix chain 'E' and resid 1599 through 1601 No H-bonds generated for 'chain 'E' and resid 1599 through 1601' Processing helix chain 'E' and resid 1603 through 1621 Processing helix chain 'E' and resid 1621 through 1634 removed outlier: 3.626A pdb=" N VAL E1625 " --> pdb=" O VAL E1621 " (cutoff:3.500A) Processing helix chain 'E' and resid 1637 through 1654 Processing helix chain 'E' and resid 1658 through 1662 Processing helix chain 'E' and resid 1665 through 1670 removed outlier: 4.246A pdb=" N ILE E1669 " --> pdb=" O GLY E1665 " (cutoff:3.500A) Processing helix chain 'E' and resid 1737 through 1750 Processing helix chain 'E' and resid 1752 through 1756 removed outlier: 3.711A pdb=" N ILE E1756 " --> pdb=" O ILE E1753 " (cutoff:3.500A) Processing helix chain 'E' and resid 1757 through 1763 Processing helix chain 'E' and resid 1844 through 1849 removed outlier: 3.727A pdb=" N CYS E1848 " --> pdb=" O PRO E1844 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA E1849 " --> pdb=" O ALA E1845 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1844 through 1849' Processing helix chain 'E' and resid 1850 through 1858 Processing helix chain 'E' and resid 1869 through 1885 Processing helix chain 'E' and resid 1885 through 1900 removed outlier: 3.766A pdb=" N VAL E1889 " --> pdb=" O ASP E1885 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N HIS E1892 " --> pdb=" O THR E1888 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N PHE E1893 " --> pdb=" O VAL E1889 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR E1898 " --> pdb=" O LEU E1894 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE E1899 " --> pdb=" O GLU E1895 " (cutoff:3.500A) Processing helix chain 'E' and resid 1902 through 1918 Processing helix chain 'E' and resid 1921 through 1942 Processing helix chain 'E' and resid 1946 through 1963 removed outlier: 3.635A pdb=" N PHE E1957 " --> pdb=" O ALA E1953 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TRP E1959 " --> pdb=" O LEU E1955 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLU E1960 " --> pdb=" O THR E1956 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL E1961 " --> pdb=" O PHE E1957 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY E1963 " --> pdb=" O TRP E1959 " (cutoff:3.500A) Processing helix chain 'E' and resid 1969 through 1981 Processing helix chain 'E' and resid 2019 through 2032 removed outlier: 3.669A pdb=" N LEU E2023 " --> pdb=" O GLN E2019 " (cutoff:3.500A) Processing helix chain 'E' and resid 2034 through 2038 Processing helix chain 'E' and resid 2057 through 2062 removed outlier: 3.774A pdb=" N ILE E2061 " --> pdb=" O TYR E2057 " (cutoff:3.500A) Processing helix chain 'E' and resid 2078 through 2110 Processing helix chain 'E' and resid 2112 through 2114 No H-bonds generated for 'chain 'E' and resid 2112 through 2114' Processing helix chain 'E' and resid 2115 through 2130 Processing helix chain 'E' and resid 2132 through 2139 Processing helix chain 'E' and resid 2141 through 2146 removed outlier: 3.856A pdb=" N SER E2146 " --> pdb=" O PHE E2142 " (cutoff:3.500A) Processing helix chain 'E' and resid 2150 through 2175 removed outlier: 3.711A pdb=" N LEU E2154 " --> pdb=" O ALA E2150 " (cutoff:3.500A) Processing helix chain 'E' and resid 2185 through 2200 removed outlier: 3.821A pdb=" N PHE E2189 " --> pdb=" O GLU E2185 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL E2192 " --> pdb=" O LEU E2188 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE E2193 " --> pdb=" O PHE E2189 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN E2194 " --> pdb=" O LEU E2190 " (cutoff:3.500A) Processing helix chain 'E' and resid 2203 through 2221 Processing helix chain 'E' and resid 2221 through 2226 Processing helix chain 'E' and resid 2233 through 2244 Processing helix chain 'E' and resid 2247 through 2278 removed outlier: 8.329A pdb=" N LYS E2267 " --> pdb=" O ILE E2263 " (cutoff:3.500A) Proline residue: E2268 - end of helix Processing helix chain 'E' and resid 2279 through 2281 No H-bonds generated for 'chain 'E' and resid 2279 through 2281' Processing helix chain 'E' and resid 2296 through 2309 removed outlier: 3.703A pdb=" N GLY E2309 " --> pdb=" O GLN E2305 " (cutoff:3.500A) Processing helix chain 'E' and resid 2316 through 2321 Processing helix chain 'E' and resid 2342 through 2357 Processing helix chain 'E' and resid 2360 through 2388 Proline residue: E2375 - end of helix Processing helix chain 'E' and resid 2390 through 2415 Processing helix chain 'E' and resid 2416 through 2420 Processing helix chain 'E' and resid 2480 through 2517 Proline residue: E2492 - end of helix Proline residue: E2509 - end of helix removed outlier: 3.852A pdb=" N LYS E2512 " --> pdb=" O GLY E2508 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE E2513 " --> pdb=" O PRO E2509 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU E2517 " --> pdb=" O ILE E2513 " (cutoff:3.500A) Processing helix chain 'E' and resid 2530 through 2548 removed outlier: 3.991A pdb=" N LEU E2547 " --> pdb=" O SER E2543 " (cutoff:3.500A) Processing helix chain 'E' and resid 2551 through 2556 Processing helix chain 'E' and resid 2557 through 2567 Processing helix chain 'E' and resid 2578 through 2599 removed outlier: 3.954A pdb=" N LEU E2582 " --> pdb=" O VAL E2578 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE E2585 " --> pdb=" O ALA E2581 " (cutoff:3.500A) Processing helix chain 'E' and resid 2599 through 2606 removed outlier: 3.786A pdb=" N ARG E2603 " --> pdb=" O MET E2599 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLN E2605 " --> pdb=" O THR E2601 " (cutoff:3.500A) Processing helix chain 'E' and resid 2608 through 2625 removed outlier: 3.556A pdb=" N ASN E2613 " --> pdb=" O GLU E2609 " (cutoff:3.500A) Processing helix chain 'E' and resid 2626 through 2631 removed outlier: 3.739A pdb=" N PHE E2630 " --> pdb=" O ILE E2627 " (cutoff:3.500A) Processing helix chain 'E' and resid 2632 through 2646 removed outlier: 4.001A pdb=" N SER E2636 " --> pdb=" O PRO E2632 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU E2637 " --> pdb=" O HIS E2633 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET E2646 " --> pdb=" O VAL E2642 " (cutoff:3.500A) Processing helix chain 'E' and resid 2670 through 2688 removed outlier: 3.759A pdb=" N ALA E2676 " --> pdb=" O PRO E2672 " (cutoff:3.500A) Processing helix chain 'E' and resid 2694 through 2699 Processing helix chain 'E' and resid 2700 through 2702 No H-bonds generated for 'chain 'E' and resid 2700 through 2702' Processing helix chain 'E' and resid 2706 through 2714 Processing helix chain 'E' and resid 2715 through 2722 Processing helix chain 'E' and resid 2733 through 2749 removed outlier: 3.733A pdb=" N VAL E2747 " --> pdb=" O THR E2743 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU E2748 " --> pdb=" O VAL E2744 " (cutoff:3.500A) Processing helix chain 'E' and resid 2787 through 2805 Processing helix chain 'E' and resid 2808 through 2811 removed outlier: 3.595A pdb=" N SER E2811 " --> pdb=" O GLN E2808 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2808 through 2811' Processing helix chain 'E' and resid 2812 through 2820 Processing helix chain 'E' and resid 2820 through 2826 removed outlier: 3.813A pdb=" N ALA E2824 " --> pdb=" O VAL E2820 " (cutoff:3.500A) Processing helix chain 'E' and resid 2831 through 2844 removed outlier: 3.535A pdb=" N ASP E2835 " --> pdb=" O LEU E2831 " (cutoff:3.500A) Processing helix chain 'E' and resid 2847 through 2855 Proline residue: E2853 - end of helix Processing helix chain 'E' and resid 2856 through 2861 removed outlier: 3.532A pdb=" N ALA E2861 " --> pdb=" O CYS E2857 " (cutoff:3.500A) Processing helix chain 'E' and resid 2867 through 2871 Processing helix chain 'E' and resid 2872 through 2880 removed outlier: 3.554A pdb=" N LEU E2880 " --> pdb=" O ILE E2876 " (cutoff:3.500A) Processing helix chain 'E' and resid 2890 through 2909 removed outlier: 3.846A pdb=" N LEU E2894 " --> pdb=" O CYS E2890 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA E2896 " --> pdb=" O SER E2892 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU E2897 " --> pdb=" O SER E2893 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 205 through 209 Processing sheet with id=AA2, first strand: chain 'A' and resid 349 through 350 removed outlier: 3.662A pdb=" N VAL A 362 " --> pdb=" O MET A 350 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1045 through 1046 removed outlier: 3.857A pdb=" N LYS A1045 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A1091 " --> pdb=" O LYS A1045 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 1060 through 1064 Processing sheet with id=AA5, first strand: chain 'A' and resid 1484 through 1486 Processing sheet with id=AA6, first strand: chain 'B' and resid 327 through 329 Processing sheet with id=AA7, first strand: chain 'E' and resid 2010 through 2013 2387 hydrogen bonds defined for protein. 7029 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.23 Time building geometry restraints manager: 4.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5968 1.31 - 1.44: 10253 1.44 - 1.57: 22092 1.57 - 1.70: 15 1.70 - 1.83: 472 Bond restraints: 38800 Sorted by residual: bond pdb=" O1 TYS A 287 " pdb=" S TYS A 287 " ideal model delta sigma weight residual 1.462 1.635 -0.173 2.00e-02 2.50e+03 7.47e+01 bond pdb=" OH TYS A 287 " pdb=" S TYS A 287 " ideal model delta sigma weight residual 1.679 1.535 0.144 2.00e-02 2.50e+03 5.21e+01 bond pdb=" C31 PEV A2103 " pdb=" O2 PEV A2103 " ideal model delta sigma weight residual 1.330 1.421 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" C31 PEV A2104 " pdb=" O2 PEV A2104 " ideal model delta sigma weight residual 1.330 1.421 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" C31 PEV A2106 " pdb=" O2 PEV A2106 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.02e+01 ... (remaining 38795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 52182 3.33 - 6.67: 296 6.67 - 10.00: 28 10.00 - 13.33: 7 13.33 - 16.67: 6 Bond angle restraints: 52519 Sorted by residual: angle pdb=" O11 PGV A2107 " pdb=" P PGV A2107 " pdb=" O12 PGV A2107 " ideal model delta sigma weight residual 92.97 109.64 -16.67 3.00e+00 1.11e-01 3.09e+01 angle pdb=" O11 PGV A2108 " pdb=" P PGV A2108 " pdb=" O12 PGV A2108 " ideal model delta sigma weight residual 92.97 109.31 -16.34 3.00e+00 1.11e-01 2.97e+01 angle pdb=" O3P PEV A2104 " pdb=" P PEV A2104 " pdb=" O4P PEV A2104 " ideal model delta sigma weight residual 93.57 109.88 -16.31 3.00e+00 1.11e-01 2.96e+01 angle pdb=" O3P PEV A2105 " pdb=" P PEV A2105 " pdb=" O4P PEV A2105 " ideal model delta sigma weight residual 93.57 109.69 -16.12 3.00e+00 1.11e-01 2.89e+01 angle pdb=" O3P PEV A2103 " pdb=" P PEV A2103 " pdb=" O4P PEV A2103 " ideal model delta sigma weight residual 93.57 109.39 -15.82 3.00e+00 1.11e-01 2.78e+01 ... (remaining 52514 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.21: 22991 34.21 - 68.41: 496 68.41 - 102.62: 60 102.62 - 136.83: 3 136.83 - 171.03: 3 Dihedral angle restraints: 23553 sinusoidal: 9771 harmonic: 13782 Sorted by residual: dihedral pdb=" CB CYS A1405 " pdb=" SG CYS A1405 " pdb=" SG CYS A1417 " pdb=" CB CYS A1417 " ideal model delta sinusoidal sigma weight residual 93.00 36.54 56.46 1 1.00e+01 1.00e-02 4.30e+01 dihedral pdb=" CB CYS A1046 " pdb=" SG CYS A1046 " pdb=" SG CYS A1057 " pdb=" CB CYS A1057 " ideal model delta sinusoidal sigma weight residual -86.00 -128.27 42.27 1 1.00e+01 1.00e-02 2.50e+01 dihedral pdb=" CA GLY E 943 " pdb=" C GLY E 943 " pdb=" N ASN E 944 " pdb=" CA ASN E 944 " ideal model delta harmonic sigma weight residual 180.00 155.63 24.37 0 5.00e+00 4.00e-02 2.38e+01 ... (remaining 23550 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 5144 0.052 - 0.105: 824 0.105 - 0.157: 77 0.157 - 0.210: 10 0.210 - 0.262: 2 Chirality restraints: 6057 Sorted by residual: chirality pdb=" CA PHE C 13 " pdb=" N PHE C 13 " pdb=" C PHE C 13 " pdb=" CB PHE C 13 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C05 PGV A2107 " pdb=" C04 PGV A2107 " pdb=" C06 PGV A2107 " pdb=" O05 PGV A2107 " both_signs ideal model delta sigma weight residual False 2.29 2.51 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CBG Y01 A2111 " pdb=" CAQ Y01 A2111 " pdb=" CBD Y01 A2111 " pdb=" CBI Y01 A2111 " both_signs ideal model delta sigma weight residual False -2.33 -2.52 0.19 2.00e-01 2.50e+01 8.94e-01 ... (remaining 6054 not shown) Planarity restraints: 6495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D2220 " 0.040 2.00e-02 2.50e+03 3.14e-02 1.73e+01 pdb=" CG PHE D2220 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE D2220 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE D2220 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE D2220 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE D2220 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE D2220 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS E 46 " -0.017 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C CYS E 46 " 0.058 2.00e-02 2.50e+03 pdb=" O CYS E 46 " -0.022 2.00e-02 2.50e+03 pdb=" N VAL E 47 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E1765 " 0.049 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO E1766 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO E1766 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO E1766 " 0.042 5.00e-02 4.00e+02 ... (remaining 6492 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3165 2.74 - 3.28: 41211 3.28 - 3.82: 61643 3.82 - 4.36: 71154 4.36 - 4.90: 122354 Nonbonded interactions: 299527 Sorted by model distance: nonbonded pdb=" O PRO E 224 " pdb=" OG1 THR E 230 " model vdw 2.199 3.040 nonbonded pdb=" NH1 ARG A 717 " pdb=" OD1 ASP D 970 " model vdw 2.205 3.120 nonbonded pdb=" O LYS A 998 " pdb=" NH1 ARG A1004 " model vdw 2.233 3.120 nonbonded pdb=" O ALA E1953 " pdb=" OG1 THR E1956 " model vdw 2.246 3.040 nonbonded pdb=" NE ARG E2486 " pdb=" OD2 ASP E2551 " model vdw 2.258 3.120 ... (remaining 299522 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 34.160 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.173 38811 Z= 0.183 Angle : 0.667 16.668 52542 Z= 0.313 Chirality : 0.037 0.262 6057 Planarity : 0.006 0.093 6494 Dihedral : 14.786 171.034 14479 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 0.09 (0.12), residues: 4465 helix: 0.39 (0.09), residues: 3072 sheet: -0.33 (0.93), residues: 37 loop : -0.44 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG D1169 TYR 0.025 0.002 TYR A1517 PHE 0.071 0.002 PHE D2220 TRP 0.024 0.001 TRP D 621 HIS 0.006 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00371 (38800) covalent geometry : angle 0.66417 (52519) SS BOND : bond 0.03452 ( 10) SS BOND : angle 3.16740 ( 20) hydrogen bonds : bond 0.13633 ( 2387) hydrogen bonds : angle 5.80839 ( 7029) link_NAG-ASN : bond 0.00153 ( 1) link_NAG-ASN : angle 0.91261 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 615 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 GLN cc_start: 0.6486 (tp40) cc_final: 0.6258 (mm-40) REVERT: A 378 GLN cc_start: 0.4940 (mp10) cc_final: 0.4657 (mp10) REVERT: A 488 ILE cc_start: 0.8538 (mt) cc_final: 0.8291 (mt) REVERT: A 520 MET cc_start: 0.7922 (mmm) cc_final: 0.7708 (mmm) REVERT: A 892 MET cc_start: 0.7714 (mmm) cc_final: 0.7183 (mmm) REVERT: A 1214 ARG cc_start: 0.7102 (mmt90) cc_final: 0.6643 (ptm160) REVERT: A 1268 PHE cc_start: 0.8200 (t80) cc_final: 0.7988 (t80) REVERT: A 1519 MET cc_start: 0.8655 (tpp) cc_final: 0.7988 (tpp) REVERT: A 1532 ASP cc_start: 0.8199 (m-30) cc_final: 0.7771 (m-30) REVERT: A 1566 GLU cc_start: 0.8367 (tp30) cc_final: 0.7768 (tp30) REVERT: B 280 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7284 (mt-10) REVERT: B 315 GLN cc_start: 0.8417 (mm-40) cc_final: 0.8211 (mm-40) REVERT: B 340 ARG cc_start: 0.7986 (mtt90) cc_final: 0.7753 (mtt-85) REVERT: B 378 ASP cc_start: 0.6888 (t0) cc_final: 0.6456 (p0) REVERT: C 146 MET cc_start: 0.5577 (tmm) cc_final: 0.5364 (tmm) REVERT: D 236 ASN cc_start: 0.8063 (t0) cc_final: 0.7823 (t0) REVERT: D 276 MET cc_start: 0.7760 (mmt) cc_final: 0.7397 (mmp) REVERT: D 444 CYS cc_start: 0.8207 (m) cc_final: 0.7286 (m) REVERT: D 599 GLN cc_start: 0.7941 (pt0) cc_final: 0.7651 (pt0) REVERT: D 1349 MET cc_start: 0.8212 (mtp) cc_final: 0.7967 (mtp) REVERT: D 2283 LEU cc_start: 0.9084 (mt) cc_final: 0.8859 (mp) REVERT: D 2371 MET cc_start: 0.7199 (tpp) cc_final: 0.6817 (tpp) REVERT: D 2451 LEU cc_start: 0.8360 (tp) cc_final: 0.8037 (tt) REVERT: E 186 GLU cc_start: 0.7591 (tp30) cc_final: 0.6644 (mm-30) REVERT: E 794 ILE cc_start: 0.8688 (mm) cc_final: 0.8474 (mm) REVERT: E 837 LEU cc_start: 0.8292 (mp) cc_final: 0.7818 (mp) REVERT: E 838 ASP cc_start: 0.6807 (m-30) cc_final: 0.6424 (m-30) REVERT: E 1184 MET cc_start: 0.8704 (mmp) cc_final: 0.8488 (mmm) REVERT: E 1271 TRP cc_start: 0.7947 (t60) cc_final: 0.7729 (t-100) outliers start: 0 outliers final: 0 residues processed: 615 average time/residue: 0.2331 time to fit residues: 237.9586 Evaluate side-chains 525 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 525 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.0970 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 0.0970 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 829 ASN ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1158 ASN A1270 GLN A1365 ASN A1531 HIS ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN D1022 GLN D1274 HIS D1278 HIS D2137 ASN D2367 GLN D2537 HIS E 29 GLN E 349 GLN E2305 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.109089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.080980 restraints weight = 91518.913| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.39 r_work: 0.3077 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 38811 Z= 0.152 Angle : 0.615 18.416 52542 Z= 0.309 Chirality : 0.040 0.209 6057 Planarity : 0.004 0.070 6494 Dihedral : 8.606 169.730 5406 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.92 % Allowed : 6.22 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 1.80 (0.13), residues: 4465 helix: 1.77 (0.09), residues: 3134 sheet: -0.07 (0.93), residues: 37 loop : -0.11 (0.19), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 358 TYR 0.023 0.001 TYR A1517 PHE 0.038 0.002 PHE D 185 TRP 0.031 0.001 TRP D 255 HIS 0.012 0.001 HIS E 786 Details of bonding type rmsd covalent geometry : bond 0.00355 (38800) covalent geometry : angle 0.61111 (52519) SS BOND : bond 0.01526 ( 10) SS BOND : angle 3.41582 ( 20) hydrogen bonds : bond 0.04762 ( 2387) hydrogen bonds : angle 4.25615 ( 7029) link_NAG-ASN : bond 0.00017 ( 1) link_NAG-ASN : angle 1.04078 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 598 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 MET cc_start: 0.7943 (mpp) cc_final: 0.7736 (mpp) REVERT: A 79 MET cc_start: 0.7494 (tmm) cc_final: 0.7259 (tmm) REVERT: A 150 MET cc_start: 0.8311 (tpp) cc_final: 0.7966 (tpp) REVERT: A 382 ARG cc_start: 0.8053 (mpt-90) cc_final: 0.7852 (mmt90) REVERT: A 824 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7764 (mp0) REVERT: A 892 MET cc_start: 0.8478 (mmm) cc_final: 0.7993 (mmm) REVERT: A 1214 ARG cc_start: 0.7248 (mmt90) cc_final: 0.6603 (ptm160) REVERT: A 1268 PHE cc_start: 0.8257 (t80) cc_final: 0.7865 (t80) REVERT: A 1301 MET cc_start: 0.7973 (mpp) cc_final: 0.6759 (tpt) REVERT: A 1305 CYS cc_start: 0.8199 (m) cc_final: 0.7745 (m) REVERT: A 1519 MET cc_start: 0.8716 (tpp) cc_final: 0.7987 (tpp) REVERT: A 1532 ASP cc_start: 0.8743 (m-30) cc_final: 0.8360 (m-30) REVERT: B 330 CYS cc_start: 0.4495 (OUTLIER) cc_final: 0.4042 (t) REVERT: B 340 ARG cc_start: 0.8724 (mtt90) cc_final: 0.8402 (mtt-85) REVERT: B 378 ASP cc_start: 0.7000 (t0) cc_final: 0.6276 (p0) REVERT: C 52 MET cc_start: 0.0557 (mtm) cc_final: 0.0194 (mtm) REVERT: D 190 HIS cc_start: 0.6837 (OUTLIER) cc_final: 0.6174 (m90) REVERT: D 226 MET cc_start: 0.8913 (tpp) cc_final: 0.8516 (tpp) REVERT: D 279 HIS cc_start: 0.8342 (t-90) cc_final: 0.8126 (t-90) REVERT: D 458 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.7077 (p90) REVERT: D 532 GLN cc_start: 0.8805 (tp40) cc_final: 0.8187 (tp-100) REVERT: D 599 GLN cc_start: 0.8196 (pt0) cc_final: 0.7881 (pt0) REVERT: D 625 MET cc_start: 0.8245 (mmt) cc_final: 0.7828 (mmt) REVERT: D 1349 MET cc_start: 0.9172 (mtp) cc_final: 0.8960 (mtp) REVERT: D 2260 ARG cc_start: 0.8480 (ttm-80) cc_final: 0.8212 (ttm-80) REVERT: D 2272 LEU cc_start: 0.8112 (tt) cc_final: 0.7862 (mp) REVERT: D 2279 THR cc_start: 0.8805 (m) cc_final: 0.8549 (t) REVERT: D 2371 MET cc_start: 0.7591 (tpp) cc_final: 0.7127 (tpp) REVERT: D 2539 ILE cc_start: 0.8893 (tp) cc_final: 0.8651 (tp) REVERT: D 2543 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8039 (mm-30) REVERT: E 91 THR cc_start: 0.8413 (m) cc_final: 0.8166 (t) REVERT: E 186 GLU cc_start: 0.7941 (tp30) cc_final: 0.6995 (mm-30) REVERT: E 673 CYS cc_start: 0.8205 (p) cc_final: 0.7991 (m) REVERT: E 928 TYR cc_start: 0.8735 (t80) cc_final: 0.8521 (t80) REVERT: E 1176 ASN cc_start: 0.8759 (t0) cc_final: 0.8510 (t0) REVERT: E 1271 TRP cc_start: 0.8256 (t60) cc_final: 0.7900 (t-100) REVERT: E 2366 MET cc_start: 0.9237 (mmp) cc_final: 0.9010 (mmm) REVERT: E 2579 ARG cc_start: 0.8329 (ttm110) cc_final: 0.7879 (ttm170) REVERT: E 2843 THR cc_start: 0.9233 (m) cc_final: 0.8682 (p) outliers start: 38 outliers final: 21 residues processed: 620 average time/residue: 0.2373 time to fit residues: 243.3795 Evaluate side-chains 571 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 547 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 458 PHE Chi-restraints excluded: chain D residue 534 PHE Chi-restraints excluded: chain D residue 672 CYS Chi-restraints excluded: chain D residue 1076 ILE Chi-restraints excluded: chain D residue 2158 MET Chi-restraints excluded: chain D residue 2173 ILE Chi-restraints excluded: chain D residue 2192 CYS Chi-restraints excluded: chain D residue 2328 VAL Chi-restraints excluded: chain D residue 2339 THR Chi-restraints excluded: chain D residue 2504 THR Chi-restraints excluded: chain E residue 912 CYS Chi-restraints excluded: chain E residue 1211 LEU Chi-restraints excluded: chain E residue 1462 VAL Chi-restraints excluded: chain E residue 1741 GLU Chi-restraints excluded: chain E residue 2621 THR Chi-restraints excluded: chain E residue 2732 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 421 optimal weight: 2.9990 chunk 235 optimal weight: 8.9990 chunk 298 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 401 optimal weight: 0.0980 chunk 412 optimal weight: 0.7980 chunk 145 optimal weight: 5.9990 chunk 378 optimal weight: 5.9990 chunk 279 optimal weight: 30.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1531 HIS B 338 GLN B 348 ASN ** D 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2137 ASN E 117 HIS E 349 GLN ** E1481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.109431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.081086 restraints weight = 91399.511| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.40 r_work: 0.3081 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 38811 Z= 0.127 Angle : 0.555 9.457 52542 Z= 0.277 Chirality : 0.039 0.208 6057 Planarity : 0.004 0.064 6494 Dihedral : 8.163 164.360 5406 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.20 % Allowed : 8.77 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 2.08 (0.13), residues: 4465 helix: 2.02 (0.09), residues: 3145 sheet: -0.49 (0.89), residues: 37 loop : -0.12 (0.19), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E2844 TYR 0.019 0.001 TYR A1517 PHE 0.027 0.001 PHE D2220 TRP 0.046 0.001 TRP D 255 HIS 0.008 0.001 HIS E 117 Details of bonding type rmsd covalent geometry : bond 0.00296 (38800) covalent geometry : angle 0.55423 (52519) SS BOND : bond 0.00261 ( 10) SS BOND : angle 1.54074 ( 20) hydrogen bonds : bond 0.04189 ( 2387) hydrogen bonds : angle 3.99936 ( 7029) link_NAG-ASN : bond 0.00159 ( 1) link_NAG-ASN : angle 0.93005 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 571 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.7523 (tmm) cc_final: 0.7207 (tmm) REVERT: A 80 PHE cc_start: 0.7882 (m-80) cc_final: 0.7629 (m-80) REVERT: A 114 MET cc_start: 0.8777 (mmm) cc_final: 0.8544 (mmm) REVERT: A 150 MET cc_start: 0.8350 (tpp) cc_final: 0.8052 (tpp) REVERT: A 643 MET cc_start: 0.8586 (mmt) cc_final: 0.8069 (mmt) REVERT: A 824 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7731 (mp0) REVERT: A 892 MET cc_start: 0.8460 (mmm) cc_final: 0.8010 (mmm) REVERT: A 913 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8824 (mtp) REVERT: A 1214 ARG cc_start: 0.7310 (mmt90) cc_final: 0.6648 (ptm160) REVERT: A 1258 MET cc_start: 0.6767 (mmm) cc_final: 0.5937 (mmm) REVERT: A 1268 PHE cc_start: 0.8229 (t80) cc_final: 0.7873 (t80) REVERT: A 1301 MET cc_start: 0.7916 (mpp) cc_final: 0.6665 (tpt) REVERT: A 1305 CYS cc_start: 0.8222 (m) cc_final: 0.7755 (m) REVERT: A 1399 MET cc_start: 0.8979 (mtt) cc_final: 0.8774 (mtt) REVERT: A 1515 MET cc_start: 0.8483 (ttm) cc_final: 0.8075 (ttm) REVERT: A 1519 MET cc_start: 0.8638 (tpp) cc_final: 0.7941 (tpp) REVERT: A 1532 ASP cc_start: 0.8751 (m-30) cc_final: 0.8369 (m-30) REVERT: A 1567 VAL cc_start: 0.7702 (p) cc_final: 0.7430 (m) REVERT: B 280 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8166 (mt-10) REVERT: B 315 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8510 (mm-40) REVERT: B 338 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8403 (pt0) REVERT: B 340 ARG cc_start: 0.8678 (mtt90) cc_final: 0.8346 (mtt-85) REVERT: B 378 ASP cc_start: 0.6793 (t0) cc_final: 0.6231 (p0) REVERT: C 13 PHE cc_start: 0.4995 (OUTLIER) cc_final: 0.3795 (m-80) REVERT: C 73 MET cc_start: 0.4148 (mtt) cc_final: 0.3385 (mtp) REVERT: D 196 TYR cc_start: 0.8842 (m-80) cc_final: 0.8624 (m-80) REVERT: D 226 MET cc_start: 0.8902 (tpp) cc_final: 0.8606 (tpp) REVERT: D 231 MET cc_start: 0.8240 (mpp) cc_final: 0.7853 (mpp) REVERT: D 234 THR cc_start: 0.7964 (m) cc_final: 0.7592 (p) REVERT: D 458 PHE cc_start: 0.7264 (OUTLIER) cc_final: 0.6954 (p90) REVERT: D 532 GLN cc_start: 0.8803 (tp40) cc_final: 0.8228 (tp-100) REVERT: D 599 GLN cc_start: 0.8231 (pt0) cc_final: 0.7905 (pt0) REVERT: D 625 MET cc_start: 0.8259 (mmt) cc_final: 0.7902 (mmt) REVERT: D 796 MET cc_start: 0.8074 (ppp) cc_final: 0.7780 (ppp) REVERT: D 1081 LYS cc_start: 0.8713 (mtpt) cc_final: 0.8066 (tmtt) REVERT: D 1349 MET cc_start: 0.9182 (mtp) cc_final: 0.8960 (mtp) REVERT: D 2070 VAL cc_start: 0.8558 (t) cc_final: 0.8147 (m) REVERT: D 2276 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8674 (tp) REVERT: D 2279 THR cc_start: 0.8809 (m) cc_final: 0.8564 (t) REVERT: D 2282 LEU cc_start: 0.9009 (tp) cc_final: 0.8769 (mt) REVERT: D 2335 MET cc_start: 0.7942 (tmm) cc_final: 0.7661 (tmm) REVERT: D 2371 MET cc_start: 0.7616 (tpp) cc_final: 0.7203 (tpp) REVERT: D 2437 LEU cc_start: 0.8677 (mt) cc_final: 0.7916 (pt) REVERT: D 2533 MET cc_start: 0.7917 (tpp) cc_final: 0.7713 (tpp) REVERT: D 2539 ILE cc_start: 0.8920 (tp) cc_final: 0.8695 (tp) REVERT: D 2543 GLU cc_start: 0.8469 (mm-30) cc_final: 0.7977 (mm-30) REVERT: E 91 THR cc_start: 0.8435 (m) cc_final: 0.8204 (t) REVERT: E 673 CYS cc_start: 0.8223 (p) cc_final: 0.7970 (m) REVERT: E 951 LEU cc_start: 0.8652 (mt) cc_final: 0.8325 (mp) REVERT: E 1176 ASN cc_start: 0.8692 (t0) cc_final: 0.8433 (t0) REVERT: E 1937 MET cc_start: 0.8925 (ptp) cc_final: 0.8667 (ptm) REVERT: E 2802 LEU cc_start: 0.8945 (tp) cc_final: 0.8646 (tp) REVERT: E 2876 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.7318 (mp) outliers start: 50 outliers final: 29 residues processed: 600 average time/residue: 0.2208 time to fit residues: 220.4840 Evaluate side-chains 577 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 542 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 1224 SER Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 458 PHE Chi-restraints excluded: chain D residue 534 PHE Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 672 CYS Chi-restraints excluded: chain D residue 1158 ILE Chi-restraints excluded: chain D residue 2158 MET Chi-restraints excluded: chain D residue 2192 CYS Chi-restraints excluded: chain D residue 2276 LEU Chi-restraints excluded: chain D residue 2328 VAL Chi-restraints excluded: chain D residue 2356 THR Chi-restraints excluded: chain D residue 2361 LEU Chi-restraints excluded: chain D residue 2504 THR Chi-restraints excluded: chain D residue 2541 LEU Chi-restraints excluded: chain D residue 2561 LEU Chi-restraints excluded: chain E residue 857 ASN Chi-restraints excluded: chain E residue 1211 LEU Chi-restraints excluded: chain E residue 1481 HIS Chi-restraints excluded: chain E residue 1842 VAL Chi-restraints excluded: chain E residue 2068 VAL Chi-restraints excluded: chain E residue 2565 MET Chi-restraints excluded: chain E residue 2621 THR Chi-restraints excluded: chain E residue 2732 LEU Chi-restraints excluded: chain E residue 2876 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 392 optimal weight: 0.0040 chunk 355 optimal weight: 4.9990 chunk 275 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 423 optimal weight: 1.9990 chunk 252 optimal weight: 0.9980 chunk 394 optimal weight: 0.0020 chunk 334 optimal weight: 0.0040 chunk 388 optimal weight: 7.9990 chunk 254 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 overall best weight: 0.4012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1531 HIS A1587 GLN B 348 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 ASN D2137 ASN E 117 HIS E 349 GLN E1481 HIS E1916 ASN E2011 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.110630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.082449 restraints weight = 91405.669| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.42 r_work: 0.3112 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 38811 Z= 0.105 Angle : 0.527 11.086 52542 Z= 0.261 Chirality : 0.037 0.166 6057 Planarity : 0.004 0.060 6494 Dihedral : 7.773 160.577 5406 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.40 % Allowed : 9.66 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 2.22 (0.13), residues: 4465 helix: 2.14 (0.09), residues: 3160 sheet: -0.60 (0.86), residues: 37 loop : -0.13 (0.18), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1584 TYR 0.019 0.001 TYR D 239 PHE 0.023 0.001 PHE A 72 TRP 0.051 0.001 TRP D 255 HIS 0.007 0.001 HIS D 240 Details of bonding type rmsd covalent geometry : bond 0.00223 (38800) covalent geometry : angle 0.52600 (52519) SS BOND : bond 0.00677 ( 10) SS BOND : angle 1.66218 ( 20) hydrogen bonds : bond 0.03594 ( 2387) hydrogen bonds : angle 3.84259 ( 7029) link_NAG-ASN : bond 0.00210 ( 1) link_NAG-ASN : angle 0.89797 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 578 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.7469 (tmm) cc_final: 0.7193 (tmm) REVERT: A 114 MET cc_start: 0.8769 (mmm) cc_final: 0.8524 (mmm) REVERT: A 631 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8064 (pp) REVERT: A 643 MET cc_start: 0.8257 (mmt) cc_final: 0.7690 (mmt) REVERT: A 824 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7730 (mp0) REVERT: A 850 CYS cc_start: 0.8308 (m) cc_final: 0.7893 (m) REVERT: A 892 MET cc_start: 0.8152 (mmm) cc_final: 0.7671 (mmm) REVERT: A 913 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8780 (mtp) REVERT: A 1258 MET cc_start: 0.6485 (mmm) cc_final: 0.5809 (mmm) REVERT: A 1268 PHE cc_start: 0.8189 (t80) cc_final: 0.7827 (t80) REVERT: A 1301 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7133 (tpt) REVERT: A 1515 MET cc_start: 0.8255 (ttm) cc_final: 0.7770 (ttm) REVERT: A 1519 MET cc_start: 0.8608 (tpp) cc_final: 0.7768 (tpp) REVERT: A 1531 HIS cc_start: 0.7462 (OUTLIER) cc_final: 0.7078 (m-70) REVERT: A 1532 ASP cc_start: 0.8527 (m-30) cc_final: 0.8111 (m-30) REVERT: A 1558 GLN cc_start: 0.8402 (tm-30) cc_final: 0.7883 (mm110) REVERT: A 1567 VAL cc_start: 0.7658 (p) cc_final: 0.7387 (m) REVERT: B 266 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7608 (tt0) REVERT: B 340 ARG cc_start: 0.8567 (mtt90) cc_final: 0.8236 (mtt-85) REVERT: B 378 ASP cc_start: 0.6950 (t0) cc_final: 0.6187 (p0) REVERT: C 13 PHE cc_start: 0.4821 (OUTLIER) cc_final: 0.3427 (m-80) REVERT: C 73 MET cc_start: 0.3803 (mtt) cc_final: 0.3509 (mtp) REVERT: D 182 LEU cc_start: 0.7075 (mt) cc_final: 0.6698 (tp) REVERT: D 226 MET cc_start: 0.8813 (tpp) cc_final: 0.8439 (tpp) REVERT: D 234 THR cc_start: 0.7877 (m) cc_final: 0.7584 (p) REVERT: D 246 CYS cc_start: 0.8762 (t) cc_final: 0.7844 (p) REVERT: D 247 LEU cc_start: 0.8385 (tp) cc_final: 0.7962 (tp) REVERT: D 279 HIS cc_start: 0.8085 (t-90) cc_final: 0.7713 (t70) REVERT: D 532 GLN cc_start: 0.8712 (tp40) cc_final: 0.8110 (tp-100) REVERT: D 599 GLN cc_start: 0.8136 (pt0) cc_final: 0.7793 (pt0) REVERT: D 625 MET cc_start: 0.8128 (mmt) cc_final: 0.7889 (mmt) REVERT: D 1081 LYS cc_start: 0.8509 (mtpt) cc_final: 0.7969 (tmtt) REVERT: D 1349 MET cc_start: 0.8919 (mtp) cc_final: 0.8617 (mtp) REVERT: D 2070 VAL cc_start: 0.8348 (t) cc_final: 0.8051 (m) REVERT: D 2279 THR cc_start: 0.8634 (m) cc_final: 0.8411 (t) REVERT: D 2282 LEU cc_start: 0.8974 (tp) cc_final: 0.8763 (mt) REVERT: D 2335 MET cc_start: 0.7827 (tmm) cc_final: 0.7501 (tmm) REVERT: D 2371 MET cc_start: 0.7493 (tpp) cc_final: 0.7124 (tpp) REVERT: D 2437 LEU cc_start: 0.8536 (mt) cc_final: 0.7784 (pt) REVERT: D 2618 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8743 (ttp) REVERT: E 186 GLU cc_start: 0.7675 (tp30) cc_final: 0.6668 (mm-30) REVERT: E 673 CYS cc_start: 0.8174 (p) cc_final: 0.7901 (m) REVERT: E 824 ARG cc_start: 0.7936 (mtp85) cc_final: 0.7491 (ttm-80) REVERT: E 933 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8184 (mp10) REVERT: E 934 LEU cc_start: 0.9108 (tt) cc_final: 0.8878 (tt) REVERT: E 951 LEU cc_start: 0.8604 (mt) cc_final: 0.8277 (mp) REVERT: E 1176 ASN cc_start: 0.8562 (t0) cc_final: 0.8309 (t0) REVERT: E 1948 MET cc_start: 0.7843 (mmp) cc_final: 0.7606 (mmp) REVERT: E 2172 MET cc_start: 0.8448 (ttp) cc_final: 0.8183 (ttp) REVERT: E 2876 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7293 (mp) outliers start: 58 outliers final: 26 residues processed: 611 average time/residue: 0.2233 time to fit residues: 227.0910 Evaluate side-chains 576 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 542 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 1224 SER Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1301 MET Chi-restraints excluded: chain A residue 1531 HIS Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 534 PHE Chi-restraints excluded: chain D residue 1158 ILE Chi-restraints excluded: chain D residue 2173 ILE Chi-restraints excluded: chain D residue 2192 CYS Chi-restraints excluded: chain D residue 2356 THR Chi-restraints excluded: chain D residue 2361 LEU Chi-restraints excluded: chain D residue 2368 ILE Chi-restraints excluded: chain D residue 2541 LEU Chi-restraints excluded: chain D residue 2561 LEU Chi-restraints excluded: chain D residue 2618 MET Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 857 ASN Chi-restraints excluded: chain E residue 933 GLN Chi-restraints excluded: chain E residue 1211 LEU Chi-restraints excluded: chain E residue 1741 GLU Chi-restraints excluded: chain E residue 1842 VAL Chi-restraints excluded: chain E residue 2565 MET Chi-restraints excluded: chain E residue 2621 THR Chi-restraints excluded: chain E residue 2732 LEU Chi-restraints excluded: chain E residue 2816 LEU Chi-restraints excluded: chain E residue 2876 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 40 optimal weight: 0.0980 chunk 110 optimal weight: 10.0000 chunk 166 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 204 optimal weight: 2.9990 chunk 286 optimal weight: 1.9990 chunk 346 optimal weight: 4.9990 chunk 399 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1270 GLN A1531 HIS ** A1587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 GLN B 348 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2137 ASN E 117 HIS E 349 GLN E2011 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.108589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.080159 restraints weight = 91211.691| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.40 r_work: 0.3063 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 38811 Z= 0.156 Angle : 0.561 10.560 52542 Z= 0.278 Chirality : 0.039 0.165 6057 Planarity : 0.004 0.059 6494 Dihedral : 7.637 155.344 5406 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.49 % Allowed : 10.96 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.16 (0.13), residues: 4465 helix: 2.09 (0.09), residues: 3158 sheet: -0.23 (0.84), residues: 37 loop : -0.16 (0.18), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D2386 TYR 0.016 0.001 TYR A1517 PHE 0.029 0.002 PHE D2220 TRP 0.043 0.001 TRP D 255 HIS 0.036 0.001 HIS A1531 Details of bonding type rmsd covalent geometry : bond 0.00380 (38800) covalent geometry : angle 0.56021 (52519) SS BOND : bond 0.00228 ( 10) SS BOND : angle 1.79274 ( 20) hydrogen bonds : bond 0.04147 ( 2387) hydrogen bonds : angle 3.87292 ( 7029) link_NAG-ASN : bond 0.00003 ( 1) link_NAG-ASN : angle 1.12804 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 579 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.7684 (tmm) cc_final: 0.7405 (tmm) REVERT: A 114 MET cc_start: 0.8683 (mmm) cc_final: 0.8460 (mmm) REVERT: A 588 LEU cc_start: 0.8395 (mt) cc_final: 0.8064 (mp) REVERT: A 631 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8030 (pp) REVERT: A 643 MET cc_start: 0.8554 (mmt) cc_final: 0.8061 (mmt) REVERT: A 658 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8765 (pt) REVERT: A 824 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7807 (mp0) REVERT: A 850 CYS cc_start: 0.8523 (m) cc_final: 0.8066 (m) REVERT: A 892 MET cc_start: 0.8507 (mmm) cc_final: 0.8056 (mmm) REVERT: A 913 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8878 (mtp) REVERT: A 1258 MET cc_start: 0.6406 (mmm) cc_final: 0.5930 (mmm) REVERT: A 1268 PHE cc_start: 0.8239 (t80) cc_final: 0.7909 (t80) REVERT: A 1301 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7257 (tpt) REVERT: A 1515 MET cc_start: 0.8466 (ttm) cc_final: 0.8191 (ttp) REVERT: A 1519 MET cc_start: 0.8652 (tpp) cc_final: 0.7877 (tpp) REVERT: A 1558 GLN cc_start: 0.8477 (tm-30) cc_final: 0.7899 (mm110) REVERT: A 1565 GLU cc_start: 0.7949 (mp0) cc_final: 0.7571 (mp0) REVERT: A 1573 ARG cc_start: 0.7365 (ptm160) cc_final: 0.6726 (ttp80) REVERT: B 266 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7616 (tt0) REVERT: B 340 ARG cc_start: 0.8725 (mtt90) cc_final: 0.8359 (mtt-85) REVERT: B 378 ASP cc_start: 0.6932 (t0) cc_final: 0.6271 (p0) REVERT: C 13 PHE cc_start: 0.4935 (OUTLIER) cc_final: 0.3684 (m-80) REVERT: C 73 MET cc_start: 0.4463 (mtt) cc_final: 0.3948 (mtt) REVERT: C 77 MET cc_start: 0.4343 (mtt) cc_final: 0.3769 (mmt) REVERT: D 182 LEU cc_start: 0.7207 (mt) cc_final: 0.6727 (tp) REVERT: D 197 LEU cc_start: 0.8413 (tp) cc_final: 0.8141 (mt) REVERT: D 226 MET cc_start: 0.8806 (tpp) cc_final: 0.8430 (tpp) REVERT: D 231 MET cc_start: 0.8071 (mpp) cc_final: 0.7801 (mpp) REVERT: D 532 GLN cc_start: 0.8829 (tp40) cc_final: 0.8253 (tp-100) REVERT: D 599 GLN cc_start: 0.8278 (pt0) cc_final: 0.7917 (pt0) REVERT: D 645 ARG cc_start: 0.8053 (ttm110) cc_final: 0.7714 (ttm-80) REVERT: D 796 MET cc_start: 0.8173 (ppp) cc_final: 0.7806 (ppp) REVERT: D 1081 LYS cc_start: 0.8647 (mtpt) cc_final: 0.7935 (tmtt) REVERT: D 2070 VAL cc_start: 0.8507 (t) cc_final: 0.8124 (m) REVERT: D 2158 MET cc_start: 0.8991 (ttt) cc_final: 0.8777 (ttt) REVERT: D 2260 ARG cc_start: 0.8459 (ttm-80) cc_final: 0.8154 (ttm-80) REVERT: D 2282 LEU cc_start: 0.9061 (tp) cc_final: 0.8819 (mt) REVERT: D 2335 MET cc_start: 0.8150 (tmm) cc_final: 0.7839 (tmm) REVERT: D 2371 MET cc_start: 0.7683 (tpp) cc_final: 0.7284 (tpp) REVERT: D 2437 LEU cc_start: 0.8665 (mt) cc_final: 0.7935 (pt) REVERT: D 2481 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8034 (mm) REVERT: D 2543 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8056 (mm-30) REVERT: D 2618 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8717 (ttp) REVERT: E 186 GLU cc_start: 0.7860 (tp30) cc_final: 0.7085 (mm-30) REVERT: E 200 LYS cc_start: 0.8481 (pttt) cc_final: 0.8172 (ptpt) REVERT: E 673 CYS cc_start: 0.8263 (p) cc_final: 0.8000 (m) REVERT: E 933 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8226 (mp10) REVERT: E 951 LEU cc_start: 0.8822 (mt) cc_final: 0.8489 (mp) REVERT: E 1176 ASN cc_start: 0.8710 (t0) cc_final: 0.8437 (t0) REVERT: E 1937 MET cc_start: 0.8935 (ptp) cc_final: 0.8691 (ptm) REVERT: E 2172 MET cc_start: 0.8753 (ttp) cc_final: 0.8470 (ttp) REVERT: E 2827 LYS cc_start: 0.8539 (tppt) cc_final: 0.8167 (tppt) REVERT: E 2876 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.7357 (mp) outliers start: 62 outliers final: 35 residues processed: 617 average time/residue: 0.2351 time to fit residues: 240.1559 Evaluate side-chains 597 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 553 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 1224 SER Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1292 PHE Chi-restraints excluded: chain A residue 1301 MET Chi-restraints excluded: chain A residue 1574 MET Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 534 PHE Chi-restraints excluded: chain D residue 672 CYS Chi-restraints excluded: chain D residue 1158 ILE Chi-restraints excluded: chain D residue 1272 ILE Chi-restraints excluded: chain D residue 1288 MET Chi-restraints excluded: chain D residue 2173 ILE Chi-restraints excluded: chain D residue 2192 CYS Chi-restraints excluded: chain D residue 2356 THR Chi-restraints excluded: chain D residue 2361 LEU Chi-restraints excluded: chain D residue 2481 LEU Chi-restraints excluded: chain D residue 2561 LEU Chi-restraints excluded: chain D residue 2618 MET Chi-restraints excluded: chain E residue 857 ASN Chi-restraints excluded: chain E residue 933 GLN Chi-restraints excluded: chain E residue 1211 LEU Chi-restraints excluded: chain E residue 1462 VAL Chi-restraints excluded: chain E residue 1741 GLU Chi-restraints excluded: chain E residue 1842 VAL Chi-restraints excluded: chain E residue 1899 ILE Chi-restraints excluded: chain E residue 2000 VAL Chi-restraints excluded: chain E residue 2068 VAL Chi-restraints excluded: chain E residue 2224 LEU Chi-restraints excluded: chain E residue 2565 MET Chi-restraints excluded: chain E residue 2621 THR Chi-restraints excluded: chain E residue 2732 LEU Chi-restraints excluded: chain E residue 2802 LEU Chi-restraints excluded: chain E residue 2816 LEU Chi-restraints excluded: chain E residue 2876 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 47 optimal weight: 3.9990 chunk 387 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 453 optimal weight: 0.6980 chunk 222 optimal weight: 3.9990 chunk 427 optimal weight: 3.9990 chunk 197 optimal weight: 0.9980 chunk 181 optimal weight: 0.8980 chunk 232 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 268 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN A 876 HIS ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1270 GLN A1587 GLN B 338 GLN B 348 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1053 ASN D2137 ASN ** D2537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 HIS E 349 GLN E 785 ASN E2011 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.109446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.081348 restraints weight = 90737.977| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.40 r_work: 0.3084 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 38811 Z= 0.111 Angle : 0.532 11.719 52542 Z= 0.262 Chirality : 0.038 0.265 6057 Planarity : 0.004 0.057 6494 Dihedral : 7.387 150.400 5406 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.73 % Allowed : 11.59 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.26 (0.13), residues: 4465 helix: 2.17 (0.09), residues: 3160 sheet: -0.33 (0.86), residues: 37 loop : -0.14 (0.18), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D2386 TYR 0.016 0.001 TYR A1517 PHE 0.024 0.001 PHE D2220 TRP 0.040 0.001 TRP D 255 HIS 0.008 0.001 HIS D 240 Details of bonding type rmsd covalent geometry : bond 0.00254 (38800) covalent geometry : angle 0.53180 (52519) SS BOND : bond 0.00247 ( 10) SS BOND : angle 1.41664 ( 20) hydrogen bonds : bond 0.03696 ( 2387) hydrogen bonds : angle 3.75794 ( 7029) link_NAG-ASN : bond 0.00150 ( 1) link_NAG-ASN : angle 1.10998 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 582 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.7538 (tmm) cc_final: 0.7251 (tmm) REVERT: A 114 MET cc_start: 0.8682 (mmm) cc_final: 0.8453 (mmm) REVERT: A 256 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.7047 (mm-40) REVERT: A 569 HIS cc_start: 0.6810 (m170) cc_final: 0.6438 (m170) REVERT: A 643 MET cc_start: 0.8263 (mmt) cc_final: 0.7712 (mmt) REVERT: A 658 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8694 (pt) REVERT: A 824 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7876 (mp0) REVERT: A 850 CYS cc_start: 0.8308 (m) cc_final: 0.7846 (m) REVERT: A 892 MET cc_start: 0.8210 (mmm) cc_final: 0.7727 (mmm) REVERT: A 913 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8842 (mtp) REVERT: A 1258 MET cc_start: 0.6178 (mmm) cc_final: 0.5741 (mmm) REVERT: A 1268 PHE cc_start: 0.8222 (t80) cc_final: 0.7885 (t80) REVERT: A 1301 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7163 (tpt) REVERT: A 1515 MET cc_start: 0.8275 (ttm) cc_final: 0.7967 (ttp) REVERT: A 1519 MET cc_start: 0.8602 (tpp) cc_final: 0.7625 (tpp) REVERT: A 1558 GLN cc_start: 0.8392 (tm-30) cc_final: 0.7898 (mm110) REVERT: A 1573 ARG cc_start: 0.7293 (ptm160) cc_final: 0.6655 (ttp80) REVERT: B 266 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7608 (tt0) REVERT: B 340 ARG cc_start: 0.8517 (mtt90) cc_final: 0.8204 (mtt-85) REVERT: C 13 PHE cc_start: 0.4866 (OUTLIER) cc_final: 0.3630 (m-80) REVERT: C 73 MET cc_start: 0.4330 (OUTLIER) cc_final: 0.4001 (mtt) REVERT: C 77 MET cc_start: 0.4296 (mtt) cc_final: 0.3722 (mmt) REVERT: D 182 LEU cc_start: 0.7147 (mt) cc_final: 0.6701 (tp) REVERT: D 197 LEU cc_start: 0.8338 (tp) cc_final: 0.8105 (mt) REVERT: D 226 MET cc_start: 0.8685 (tpp) cc_final: 0.8334 (tpp) REVERT: D 231 MET cc_start: 0.8025 (mpp) cc_final: 0.7600 (mpp) REVERT: D 236 ASN cc_start: 0.8214 (t0) cc_final: 0.8008 (t0) REVERT: D 280 TYR cc_start: 0.8367 (m-80) cc_final: 0.8052 (m-80) REVERT: D 599 GLN cc_start: 0.8234 (pt0) cc_final: 0.7855 (pt0) REVERT: D 645 ARG cc_start: 0.7883 (ttm110) cc_final: 0.7574 (ttm-80) REVERT: D 796 MET cc_start: 0.7919 (ppp) cc_final: 0.7619 (ppp) REVERT: D 963 MET cc_start: 0.9241 (ttm) cc_final: 0.9010 (mtp) REVERT: D 968 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7385 (tm-30) REVERT: D 1081 LYS cc_start: 0.8499 (mtpt) cc_final: 0.7936 (tmtt) REVERT: D 2070 VAL cc_start: 0.8395 (t) cc_final: 0.8126 (m) REVERT: D 2158 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8656 (ttt) REVERT: D 2192 CYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6778 (m) REVERT: D 2204 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8716 (tt) REVERT: D 2282 LEU cc_start: 0.9006 (tp) cc_final: 0.8794 (mt) REVERT: D 2335 MET cc_start: 0.7903 (tmm) cc_final: 0.7644 (tmm) REVERT: D 2371 MET cc_start: 0.7533 (tpp) cc_final: 0.7167 (tpp) REVERT: D 2437 LEU cc_start: 0.8554 (mt) cc_final: 0.7830 (pt) REVERT: D 2481 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7879 (mm) REVERT: D 2543 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7970 (mm-30) REVERT: D 2618 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8687 (ttp) REVERT: E 182 MET cc_start: 0.7898 (mmt) cc_final: 0.7288 (mmm) REVERT: E 186 GLU cc_start: 0.7856 (tp30) cc_final: 0.7066 (mm-30) REVERT: E 200 LYS cc_start: 0.8436 (pttt) cc_final: 0.8154 (ptpt) REVERT: E 673 CYS cc_start: 0.8209 (p) cc_final: 0.7921 (m) REVERT: E 861 PHE cc_start: 0.8856 (t80) cc_final: 0.8475 (t80) REVERT: E 933 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8119 (mp10) REVERT: E 951 LEU cc_start: 0.8715 (mt) cc_final: 0.8403 (mp) REVERT: E 1176 ASN cc_start: 0.8578 (t0) cc_final: 0.8339 (t0) REVERT: E 1937 MET cc_start: 0.8781 (ptp) cc_final: 0.8528 (ptm) REVERT: E 2172 MET cc_start: 0.8496 (ttp) cc_final: 0.8201 (ttp) REVERT: E 2556 GLU cc_start: 0.8534 (tp30) cc_final: 0.8259 (mm-30) REVERT: E 2827 LYS cc_start: 0.8497 (tppt) cc_final: 0.8110 (tppt) REVERT: E 2876 ILE cc_start: 0.7538 (OUTLIER) cc_final: 0.7309 (mp) outliers start: 72 outliers final: 37 residues processed: 626 average time/residue: 0.2312 time to fit residues: 240.4355 Evaluate side-chains 605 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 555 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain A residue 1224 SER Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1292 PHE Chi-restraints excluded: chain A residue 1301 MET Chi-restraints excluded: chain A residue 1574 MET Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 534 PHE Chi-restraints excluded: chain D residue 672 CYS Chi-restraints excluded: chain D residue 1158 ILE Chi-restraints excluded: chain D residue 1288 MET Chi-restraints excluded: chain D residue 2158 MET Chi-restraints excluded: chain D residue 2173 ILE Chi-restraints excluded: chain D residue 2192 CYS Chi-restraints excluded: chain D residue 2204 LEU Chi-restraints excluded: chain D residue 2263 VAL Chi-restraints excluded: chain D residue 2328 VAL Chi-restraints excluded: chain D residue 2356 THR Chi-restraints excluded: chain D residue 2361 LEU Chi-restraints excluded: chain D residue 2481 LEU Chi-restraints excluded: chain D residue 2541 LEU Chi-restraints excluded: chain D residue 2561 LEU Chi-restraints excluded: chain D residue 2618 MET Chi-restraints excluded: chain E residue 785 ASN Chi-restraints excluded: chain E residue 857 ASN Chi-restraints excluded: chain E residue 933 GLN Chi-restraints excluded: chain E residue 1211 LEU Chi-restraints excluded: chain E residue 1462 VAL Chi-restraints excluded: chain E residue 1741 GLU Chi-restraints excluded: chain E residue 1842 VAL Chi-restraints excluded: chain E residue 2068 VAL Chi-restraints excluded: chain E residue 2565 MET Chi-restraints excluded: chain E residue 2621 THR Chi-restraints excluded: chain E residue 2697 VAL Chi-restraints excluded: chain E residue 2732 LEU Chi-restraints excluded: chain E residue 2802 LEU Chi-restraints excluded: chain E residue 2816 LEU Chi-restraints excluded: chain E residue 2876 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 462 optimal weight: 0.1980 chunk 371 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 212 optimal weight: 0.7980 chunk 166 optimal weight: 20.0000 chunk 209 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 383 optimal weight: 0.7980 chunk 180 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 876 HIS ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1270 GLN ** A1587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 GLN B 348 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2137 ASN D2360 HIS ** D2537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 HIS E 349 GLN E2011 GLN E2379 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.109114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.080910 restraints weight = 90915.419| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.40 r_work: 0.3076 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 38811 Z= 0.123 Angle : 0.546 11.625 52542 Z= 0.268 Chirality : 0.038 0.225 6057 Planarity : 0.004 0.055 6494 Dihedral : 7.270 148.556 5406 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.40 % Allowed : 12.34 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.29 (0.13), residues: 4465 helix: 2.20 (0.09), residues: 3156 sheet: -0.19 (0.87), residues: 37 loop : -0.14 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E1562 TYR 0.024 0.001 TYR D 264 PHE 0.027 0.001 PHE D2220 TRP 0.036 0.001 TRP D 255 HIS 0.007 0.001 HIS E 786 Details of bonding type rmsd covalent geometry : bond 0.00290 (38800) covalent geometry : angle 0.54558 (52519) SS BOND : bond 0.00220 ( 10) SS BOND : angle 1.43535 ( 20) hydrogen bonds : bond 0.03776 ( 2387) hydrogen bonds : angle 3.75472 ( 7029) link_NAG-ASN : bond 0.00091 ( 1) link_NAG-ASN : angle 1.14348 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 577 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.7797 (tmm) cc_final: 0.7496 (tmm) REVERT: A 114 MET cc_start: 0.8675 (mmm) cc_final: 0.8451 (mmm) REVERT: A 569 HIS cc_start: 0.7072 (m170) cc_final: 0.6709 (m170) REVERT: A 643 MET cc_start: 0.8538 (mmt) cc_final: 0.8028 (mmt) REVERT: A 658 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8777 (pt) REVERT: A 824 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7914 (mp0) REVERT: A 850 CYS cc_start: 0.8482 (m) cc_final: 0.8051 (m) REVERT: A 892 MET cc_start: 0.8473 (mmm) cc_final: 0.8012 (mmm) REVERT: A 913 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8922 (mtp) REVERT: A 1203 MET cc_start: 0.8092 (mmp) cc_final: 0.7712 (mmt) REVERT: A 1258 MET cc_start: 0.6173 (mmm) cc_final: 0.5695 (mmm) REVERT: A 1268 PHE cc_start: 0.8229 (t80) cc_final: 0.7885 (t80) REVERT: A 1301 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7316 (tpt) REVERT: A 1515 MET cc_start: 0.8327 (ttm) cc_final: 0.8015 (ttp) REVERT: A 1519 MET cc_start: 0.8635 (tpp) cc_final: 0.7739 (tpp) REVERT: A 1558 GLN cc_start: 0.8465 (tm-30) cc_final: 0.7943 (mm110) REVERT: A 1565 GLU cc_start: 0.7925 (mp0) cc_final: 0.7544 (mp0) REVERT: A 1573 ARG cc_start: 0.7352 (ptm160) cc_final: 0.6702 (ttp80) REVERT: B 266 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7606 (tt0) REVERT: B 340 ARG cc_start: 0.8717 (mtt90) cc_final: 0.8391 (mtt-85) REVERT: C 77 MET cc_start: 0.4308 (mtt) cc_final: 0.3794 (mmt) REVERT: C 110 MET cc_start: 0.8908 (ppp) cc_final: 0.8630 (ppp) REVERT: D 182 LEU cc_start: 0.7165 (mt) cc_final: 0.6612 (tp) REVERT: D 197 LEU cc_start: 0.8381 (tp) cc_final: 0.8105 (mt) REVERT: D 226 MET cc_start: 0.8768 (tpp) cc_final: 0.8415 (tpp) REVERT: D 231 MET cc_start: 0.8179 (mpp) cc_final: 0.7909 (mpp) REVERT: D 532 GLN cc_start: 0.8850 (tp40) cc_final: 0.8276 (tp-100) REVERT: D 599 GLN cc_start: 0.8343 (pt0) cc_final: 0.7975 (pt0) REVERT: D 645 ARG cc_start: 0.8018 (ttm110) cc_final: 0.7692 (ttm-80) REVERT: D 963 MET cc_start: 0.9331 (ttm) cc_final: 0.9109 (mtp) REVERT: D 968 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7692 (tm-30) REVERT: D 1081 LYS cc_start: 0.8628 (mtpt) cc_final: 0.7963 (tmtt) REVERT: D 1189 PHE cc_start: 0.7904 (t80) cc_final: 0.7696 (t80) REVERT: D 2070 VAL cc_start: 0.8398 (t) cc_final: 0.8087 (m) REVERT: D 2192 CYS cc_start: 0.7525 (t) cc_final: 0.6940 (m) REVERT: D 2204 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8734 (tt) REVERT: D 2282 LEU cc_start: 0.9074 (tp) cc_final: 0.8863 (mt) REVERT: D 2335 MET cc_start: 0.8082 (tmm) cc_final: 0.7793 (tmm) REVERT: D 2371 MET cc_start: 0.7791 (tpp) cc_final: 0.7395 (tpp) REVERT: D 2437 LEU cc_start: 0.8666 (mt) cc_final: 0.7943 (pt) REVERT: D 2533 MET cc_start: 0.7987 (tpp) cc_final: 0.7746 (tpp) REVERT: D 2543 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8021 (mm-30) REVERT: D 2610 TRP cc_start: 0.8488 (t60) cc_final: 0.8186 (t60) REVERT: D 2618 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8685 (ttp) REVERT: E 186 GLU cc_start: 0.7958 (tp30) cc_final: 0.7151 (mm-30) REVERT: E 200 LYS cc_start: 0.8450 (pttt) cc_final: 0.8167 (ptpt) REVERT: E 673 CYS cc_start: 0.8276 (p) cc_final: 0.7992 (m) REVERT: E 924 ASN cc_start: 0.8544 (m-40) cc_final: 0.8298 (m-40) REVERT: E 933 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8213 (mp10) REVERT: E 934 LEU cc_start: 0.9096 (tt) cc_final: 0.8834 (tt) REVERT: E 951 LEU cc_start: 0.8817 (mt) cc_final: 0.8488 (mp) REVERT: E 1176 ASN cc_start: 0.8684 (t0) cc_final: 0.8420 (t0) REVERT: E 1606 MET cc_start: 0.8956 (tpp) cc_final: 0.8745 (tpp) REVERT: E 1937 MET cc_start: 0.8914 (ptp) cc_final: 0.8693 (ptm) REVERT: E 2172 MET cc_start: 0.8689 (ttp) cc_final: 0.8403 (ttp) REVERT: E 2556 GLU cc_start: 0.8710 (tp30) cc_final: 0.8459 (mm-30) REVERT: E 2646 MET cc_start: 0.7672 (pmm) cc_final: 0.7137 (pmm) REVERT: E 2823 MET cc_start: 0.8172 (tpp) cc_final: 0.7593 (tmm) REVERT: E 2827 LYS cc_start: 0.8523 (tppt) cc_final: 0.8132 (tppt) REVERT: E 2876 ILE cc_start: 0.7529 (OUTLIER) cc_final: 0.7294 (mp) outliers start: 58 outliers final: 37 residues processed: 612 average time/residue: 0.2222 time to fit residues: 226.7193 Evaluate side-chains 597 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 553 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain A residue 1224 SER Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1292 PHE Chi-restraints excluded: chain A residue 1301 MET Chi-restraints excluded: chain A residue 1574 MET Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 534 PHE Chi-restraints excluded: chain D residue 672 CYS Chi-restraints excluded: chain D residue 1158 ILE Chi-restraints excluded: chain D residue 1288 MET Chi-restraints excluded: chain D residue 2173 ILE Chi-restraints excluded: chain D residue 2204 LEU Chi-restraints excluded: chain D residue 2263 VAL Chi-restraints excluded: chain D residue 2328 VAL Chi-restraints excluded: chain D residue 2356 THR Chi-restraints excluded: chain D residue 2360 HIS Chi-restraints excluded: chain D residue 2361 LEU Chi-restraints excluded: chain D residue 2561 LEU Chi-restraints excluded: chain D residue 2618 MET Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 933 GLN Chi-restraints excluded: chain E residue 1211 LEU Chi-restraints excluded: chain E residue 1462 VAL Chi-restraints excluded: chain E residue 1685 VAL Chi-restraints excluded: chain E residue 1741 GLU Chi-restraints excluded: chain E residue 1842 VAL Chi-restraints excluded: chain E residue 2068 VAL Chi-restraints excluded: chain E residue 2565 MET Chi-restraints excluded: chain E residue 2621 THR Chi-restraints excluded: chain E residue 2697 VAL Chi-restraints excluded: chain E residue 2732 LEU Chi-restraints excluded: chain E residue 2802 LEU Chi-restraints excluded: chain E residue 2816 LEU Chi-restraints excluded: chain E residue 2876 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 238 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 218 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 161 optimal weight: 7.9990 chunk 202 optimal weight: 0.7980 chunk 214 optimal weight: 0.9980 chunk 359 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 chunk 127 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1270 GLN ** A1587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 GLN B 348 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1053 ASN D2137 ASN ** D2537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 HIS E 349 GLN E 785 ASN E1454 HIS E2011 GLN E2696 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.109197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.081015 restraints weight = 90605.611| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.39 r_work: 0.3085 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 38811 Z= 0.113 Angle : 0.543 11.400 52542 Z= 0.264 Chirality : 0.037 0.199 6057 Planarity : 0.004 0.057 6494 Dihedral : 7.094 147.447 5406 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.40 % Allowed : 12.80 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.33 (0.13), residues: 4465 helix: 2.22 (0.09), residues: 3157 sheet: -0.24 (0.90), residues: 36 loop : -0.11 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1545 TYR 0.021 0.001 TYR D 264 PHE 0.031 0.001 PHE E2630 TRP 0.033 0.001 TRP D 255 HIS 0.016 0.001 HIS D2360 Details of bonding type rmsd covalent geometry : bond 0.00261 (38800) covalent geometry : angle 0.54197 (52519) SS BOND : bond 0.00217 ( 10) SS BOND : angle 1.33107 ( 20) hydrogen bonds : bond 0.03634 ( 2387) hydrogen bonds : angle 3.71547 ( 7029) link_NAG-ASN : bond 0.00127 ( 1) link_NAG-ASN : angle 1.12858 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 576 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.7786 (tmm) cc_final: 0.7516 (tmm) REVERT: A 114 MET cc_start: 0.8673 (mmm) cc_final: 0.8449 (mmm) REVERT: A 643 MET cc_start: 0.8528 (mmt) cc_final: 0.8006 (mmt) REVERT: A 658 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8774 (pt) REVERT: A 824 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7932 (mp0) REVERT: A 850 CYS cc_start: 0.8425 (m) cc_final: 0.7908 (m) REVERT: A 892 MET cc_start: 0.8465 (mmm) cc_final: 0.8009 (mmm) REVERT: A 913 MET cc_start: 0.9146 (OUTLIER) cc_final: 0.8922 (mtp) REVERT: A 1203 MET cc_start: 0.8106 (mmp) cc_final: 0.7687 (mmp) REVERT: A 1258 MET cc_start: 0.6144 (mmm) cc_final: 0.5662 (mmm) REVERT: A 1268 PHE cc_start: 0.8228 (t80) cc_final: 0.7882 (t80) REVERT: A 1301 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7308 (tpt) REVERT: A 1515 MET cc_start: 0.8251 (ttm) cc_final: 0.7926 (ttp) REVERT: A 1519 MET cc_start: 0.8621 (tpp) cc_final: 0.7703 (tpp) REVERT: A 1558 GLN cc_start: 0.8471 (tm-30) cc_final: 0.7934 (mm110) REVERT: A 1565 GLU cc_start: 0.7866 (mp0) cc_final: 0.7369 (mp0) REVERT: A 1573 ARG cc_start: 0.7343 (ptm160) cc_final: 0.6696 (ttp80) REVERT: B 266 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7609 (tt0) REVERT: B 330 CYS cc_start: 0.4791 (OUTLIER) cc_final: 0.4440 (p) REVERT: B 340 ARG cc_start: 0.8695 (mtt90) cc_final: 0.8376 (mtt-85) REVERT: C 77 MET cc_start: 0.4404 (mtt) cc_final: 0.3851 (mmt) REVERT: C 110 MET cc_start: 0.8830 (ppp) cc_final: 0.8585 (ppp) REVERT: D 182 LEU cc_start: 0.7145 (mt) cc_final: 0.6567 (tp) REVERT: D 197 LEU cc_start: 0.8453 (tp) cc_final: 0.8137 (mt) REVERT: D 226 MET cc_start: 0.8803 (tpp) cc_final: 0.8517 (tpp) REVERT: D 231 MET cc_start: 0.8142 (mpp) cc_final: 0.7792 (mpp) REVERT: D 276 MET cc_start: 0.8016 (mmm) cc_final: 0.7473 (mmm) REVERT: D 599 GLN cc_start: 0.8346 (pt0) cc_final: 0.7979 (pt0) REVERT: D 645 ARG cc_start: 0.8017 (ttm110) cc_final: 0.7691 (ttm-80) REVERT: D 963 MET cc_start: 0.9318 (ttm) cc_final: 0.9105 (mtp) REVERT: D 1081 LYS cc_start: 0.8606 (mtpt) cc_final: 0.7937 (tmtt) REVERT: D 1189 PHE cc_start: 0.7873 (t80) cc_final: 0.7657 (t80) REVERT: D 2070 VAL cc_start: 0.8371 (t) cc_final: 0.8069 (m) REVERT: D 2192 CYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7019 (m) REVERT: D 2204 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8732 (tt) REVERT: D 2282 LEU cc_start: 0.9063 (tp) cc_final: 0.8853 (mt) REVERT: D 2335 MET cc_start: 0.8068 (tmm) cc_final: 0.7781 (tmm) REVERT: D 2371 MET cc_start: 0.7768 (tpp) cc_final: 0.7414 (tpp) REVERT: D 2437 LEU cc_start: 0.8684 (mt) cc_final: 0.7935 (pt) REVERT: D 2543 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8019 (mm-30) REVERT: E 87 HIS cc_start: 0.8740 (m-70) cc_final: 0.8333 (m-70) REVERT: E 182 MET cc_start: 0.7921 (mmt) cc_final: 0.7719 (mmt) REVERT: E 186 GLU cc_start: 0.7945 (tp30) cc_final: 0.7126 (mm-30) REVERT: E 191 LEU cc_start: 0.8816 (mp) cc_final: 0.8576 (mp) REVERT: E 200 LYS cc_start: 0.8549 (pttt) cc_final: 0.8268 (ptpt) REVERT: E 673 CYS cc_start: 0.8280 (p) cc_final: 0.7985 (m) REVERT: E 861 PHE cc_start: 0.8954 (t80) cc_final: 0.8611 (t80) REVERT: E 933 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8161 (mp10) REVERT: E 934 LEU cc_start: 0.9105 (tt) cc_final: 0.8870 (tt) REVERT: E 1176 ASN cc_start: 0.8669 (t0) cc_final: 0.8340 (t0) REVERT: E 1937 MET cc_start: 0.8904 (ptp) cc_final: 0.8685 (ptm) REVERT: E 2172 MET cc_start: 0.8650 (ttp) cc_final: 0.8382 (ttp) REVERT: E 2556 GLU cc_start: 0.8685 (tp30) cc_final: 0.8432 (mm-30) REVERT: E 2631 LEU cc_start: 0.8434 (tt) cc_final: 0.8175 (mt) REVERT: E 2646 MET cc_start: 0.7703 (pmm) cc_final: 0.7187 (pmm) REVERT: E 2823 MET cc_start: 0.8194 (tpp) cc_final: 0.7632 (tmm) REVERT: E 2827 LYS cc_start: 0.8496 (tppt) cc_final: 0.8117 (tppt) outliers start: 58 outliers final: 39 residues processed: 611 average time/residue: 0.2370 time to fit residues: 241.6775 Evaluate side-chains 606 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 560 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain A residue 1224 SER Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1301 MET Chi-restraints excluded: chain A residue 1574 MET Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 534 PHE Chi-restraints excluded: chain D residue 672 CYS Chi-restraints excluded: chain D residue 1158 ILE Chi-restraints excluded: chain D residue 1288 MET Chi-restraints excluded: chain D residue 2173 ILE Chi-restraints excluded: chain D residue 2192 CYS Chi-restraints excluded: chain D residue 2204 LEU Chi-restraints excluded: chain D residue 2263 VAL Chi-restraints excluded: chain D residue 2328 VAL Chi-restraints excluded: chain D residue 2356 THR Chi-restraints excluded: chain D residue 2361 LEU Chi-restraints excluded: chain D residue 2561 LEU Chi-restraints excluded: chain D residue 2618 MET Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 785 ASN Chi-restraints excluded: chain E residue 857 ASN Chi-restraints excluded: chain E residue 933 GLN Chi-restraints excluded: chain E residue 1211 LEU Chi-restraints excluded: chain E residue 1291 LEU Chi-restraints excluded: chain E residue 1462 VAL Chi-restraints excluded: chain E residue 1685 VAL Chi-restraints excluded: chain E residue 1741 GLU Chi-restraints excluded: chain E residue 1842 VAL Chi-restraints excluded: chain E residue 2000 VAL Chi-restraints excluded: chain E residue 2068 VAL Chi-restraints excluded: chain E residue 2621 THR Chi-restraints excluded: chain E residue 2697 VAL Chi-restraints excluded: chain E residue 2732 LEU Chi-restraints excluded: chain E residue 2802 LEU Chi-restraints excluded: chain E residue 2816 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 460 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 297 optimal weight: 4.9990 chunk 194 optimal weight: 0.8980 chunk 287 optimal weight: 9.9990 chunk 368 optimal weight: 0.0270 chunk 233 optimal weight: 0.7980 chunk 356 optimal weight: 1.9990 chunk 337 optimal weight: 2.9990 chunk 317 optimal weight: 0.2980 chunk 161 optimal weight: 20.0000 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1270 GLN A1587 GLN B 338 GLN B 348 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2137 ASN ** D2537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 HIS E 349 GLN E 785 ASN E 786 HIS E 841 GLN E2011 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.109649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.081431 restraints weight = 91405.503| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.42 r_work: 0.3087 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 38811 Z= 0.110 Angle : 0.545 14.660 52542 Z= 0.264 Chirality : 0.037 0.185 6057 Planarity : 0.004 0.056 6494 Dihedral : 6.931 146.354 5406 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.42 % Allowed : 12.87 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.36 (0.13), residues: 4465 helix: 2.25 (0.09), residues: 3162 sheet: -0.07 (0.90), residues: 37 loop : -0.11 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1562 TYR 0.019 0.001 TYR D 264 PHE 0.028 0.001 PHE E2630 TRP 0.028 0.001 TRP D 255 HIS 0.011 0.001 HIS E 786 Details of bonding type rmsd covalent geometry : bond 0.00253 (38800) covalent geometry : angle 0.54420 (52519) SS BOND : bond 0.00218 ( 10) SS BOND : angle 1.28353 ( 20) hydrogen bonds : bond 0.03547 ( 2387) hydrogen bonds : angle 3.67850 ( 7029) link_NAG-ASN : bond 0.00133 ( 1) link_NAG-ASN : angle 1.12446 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 574 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.7698 (tmm) cc_final: 0.7408 (tmm) REVERT: A 114 MET cc_start: 0.8673 (mmm) cc_final: 0.8441 (mmm) REVERT: A 299 TYR cc_start: 0.8392 (m-80) cc_final: 0.7954 (m-80) REVERT: A 533 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8072 (pt0) REVERT: A 643 MET cc_start: 0.8246 (mmt) cc_final: 0.7678 (mmt) REVERT: A 658 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8692 (pt) REVERT: A 824 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7909 (mp0) REVERT: A 850 CYS cc_start: 0.8356 (m) cc_final: 0.7799 (m) REVERT: A 892 MET cc_start: 0.8213 (mmm) cc_final: 0.7679 (mmm) REVERT: A 913 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8834 (mtp) REVERT: A 1203 MET cc_start: 0.8103 (mmp) cc_final: 0.7777 (mmm) REVERT: A 1268 PHE cc_start: 0.8213 (t80) cc_final: 0.7881 (t80) REVERT: A 1301 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7150 (tpt) REVERT: A 1515 MET cc_start: 0.8062 (ttm) cc_final: 0.7576 (ttm) REVERT: A 1519 MET cc_start: 0.8552 (tpp) cc_final: 0.7621 (tpp) REVERT: A 1558 GLN cc_start: 0.8414 (tm-30) cc_final: 0.7929 (mm110) REVERT: A 1565 GLU cc_start: 0.7788 (mp0) cc_final: 0.7281 (mp0) REVERT: A 1573 ARG cc_start: 0.7304 (ptm160) cc_final: 0.6670 (ttp80) REVERT: B 266 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7562 (tt0) REVERT: B 330 CYS cc_start: 0.4729 (OUTLIER) cc_final: 0.4355 (p) REVERT: B 340 ARG cc_start: 0.8534 (mtt90) cc_final: 0.8238 (mtt-85) REVERT: C 77 MET cc_start: 0.4652 (mtt) cc_final: 0.4120 (mmt) REVERT: D 182 LEU cc_start: 0.6963 (mt) cc_final: 0.6482 (tp) REVERT: D 197 LEU cc_start: 0.8467 (tp) cc_final: 0.8194 (mt) REVERT: D 226 MET cc_start: 0.8692 (tpp) cc_final: 0.8299 (tpp) REVERT: D 231 MET cc_start: 0.8015 (mpp) cc_final: 0.7769 (mpp) REVERT: D 260 TYR cc_start: 0.7555 (OUTLIER) cc_final: 0.6729 (t80) REVERT: D 599 GLN cc_start: 0.8238 (pt0) cc_final: 0.7884 (pt0) REVERT: D 645 ARG cc_start: 0.7859 (ttm110) cc_final: 0.7552 (ttm-80) REVERT: D 796 MET cc_start: 0.8044 (ppp) cc_final: 0.7765 (ppp) REVERT: D 963 MET cc_start: 0.9235 (ttm) cc_final: 0.9027 (mtp) REVERT: D 1081 LYS cc_start: 0.8470 (mtpt) cc_final: 0.7902 (tmtt) REVERT: D 2070 VAL cc_start: 0.8318 (t) cc_final: 0.8037 (m) REVERT: D 2192 CYS cc_start: 0.7386 (OUTLIER) cc_final: 0.6906 (m) REVERT: D 2204 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8687 (tt) REVERT: D 2335 MET cc_start: 0.7897 (tmm) cc_final: 0.7605 (tmm) REVERT: D 2371 MET cc_start: 0.7612 (tpp) cc_final: 0.7270 (tpp) REVERT: D 2437 LEU cc_start: 0.8556 (mt) cc_final: 0.7819 (pt) REVERT: D 2533 MET cc_start: 0.7905 (tpp) cc_final: 0.7670 (tpp) REVERT: D 2543 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7946 (mm-30) REVERT: E 87 HIS cc_start: 0.8591 (OUTLIER) cc_final: 0.8161 (m-70) REVERT: E 186 GLU cc_start: 0.7833 (tp30) cc_final: 0.7038 (mm-30) REVERT: E 191 LEU cc_start: 0.8773 (mp) cc_final: 0.8526 (mp) REVERT: E 200 LYS cc_start: 0.8527 (pttt) cc_final: 0.8269 (ptpt) REVERT: E 673 CYS cc_start: 0.8226 (p) cc_final: 0.7925 (m) REVERT: E 785 ASN cc_start: 0.7533 (OUTLIER) cc_final: 0.7238 (t0) REVERT: E 861 PHE cc_start: 0.8891 (t80) cc_final: 0.8571 (t80) REVERT: E 933 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8106 (mp10) REVERT: E 934 LEU cc_start: 0.9079 (tt) cc_final: 0.8876 (tt) REVERT: E 1176 ASN cc_start: 0.8534 (t0) cc_final: 0.8229 (t0) REVERT: E 1902 ARG cc_start: 0.7954 (mtm-85) cc_final: 0.7178 (mtp180) REVERT: E 1937 MET cc_start: 0.8764 (ptp) cc_final: 0.8539 (ptm) REVERT: E 2172 MET cc_start: 0.8478 (ttp) cc_final: 0.8194 (ttp) REVERT: E 2631 LEU cc_start: 0.8339 (tt) cc_final: 0.8094 (mt) REVERT: E 2646 MET cc_start: 0.7587 (pmm) cc_final: 0.7079 (pmm) REVERT: E 2823 MET cc_start: 0.8026 (tpp) cc_final: 0.7470 (tmm) REVERT: E 2827 LYS cc_start: 0.8509 (tppt) cc_final: 0.8115 (tppt) outliers start: 59 outliers final: 39 residues processed: 611 average time/residue: 0.2289 time to fit residues: 233.1164 Evaluate side-chains 601 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 552 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain A residue 1224 SER Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1301 MET Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 534 PHE Chi-restraints excluded: chain D residue 672 CYS Chi-restraints excluded: chain D residue 1158 ILE Chi-restraints excluded: chain D residue 1288 MET Chi-restraints excluded: chain D residue 2173 ILE Chi-restraints excluded: chain D residue 2192 CYS Chi-restraints excluded: chain D residue 2204 LEU Chi-restraints excluded: chain D residue 2263 VAL Chi-restraints excluded: chain D residue 2328 VAL Chi-restraints excluded: chain D residue 2356 THR Chi-restraints excluded: chain D residue 2361 LEU Chi-restraints excluded: chain D residue 2368 ILE Chi-restraints excluded: chain D residue 2561 LEU Chi-restraints excluded: chain D residue 2618 MET Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 785 ASN Chi-restraints excluded: chain E residue 857 ASN Chi-restraints excluded: chain E residue 933 GLN Chi-restraints excluded: chain E residue 1211 LEU Chi-restraints excluded: chain E residue 1291 LEU Chi-restraints excluded: chain E residue 1462 VAL Chi-restraints excluded: chain E residue 1685 VAL Chi-restraints excluded: chain E residue 1741 GLU Chi-restraints excluded: chain E residue 1842 VAL Chi-restraints excluded: chain E residue 2000 VAL Chi-restraints excluded: chain E residue 2068 VAL Chi-restraints excluded: chain E residue 2621 THR Chi-restraints excluded: chain E residue 2697 VAL Chi-restraints excluded: chain E residue 2732 LEU Chi-restraints excluded: chain E residue 2802 LEU Chi-restraints excluded: chain E residue 2816 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 261 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 353 optimal weight: 0.7980 chunk 53 optimal weight: 0.0060 chunk 189 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 325 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 300 optimal weight: 2.9990 chunk 446 optimal weight: 0.0770 overall best weight: 0.4754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 HIS ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1270 GLN ** A1587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 GLN B 348 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2137 ASN D2360 HIS ** D2537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 HIS E 349 GLN E 785 ASN ** E 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2011 GLN ** E2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.110227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.082121 restraints weight = 90736.273| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.41 r_work: 0.3102 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 38811 Z= 0.103 Angle : 0.548 12.614 52542 Z= 0.265 Chirality : 0.037 0.178 6057 Planarity : 0.004 0.054 6494 Dihedral : 6.777 145.230 5406 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.16 % Allowed : 13.25 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.39 (0.13), residues: 4465 helix: 2.27 (0.09), residues: 3167 sheet: -0.26 (0.90), residues: 36 loop : -0.11 (0.18), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1545 TYR 0.022 0.001 TYR D 264 PHE 0.029 0.001 PHE E2630 TRP 0.035 0.001 TRP D2610 HIS 0.004 0.000 HIS D2537 Details of bonding type rmsd covalent geometry : bond 0.00229 (38800) covalent geometry : angle 0.54761 (52519) SS BOND : bond 0.00290 ( 10) SS BOND : angle 1.23602 ( 20) hydrogen bonds : bond 0.03372 ( 2387) hydrogen bonds : angle 3.65177 ( 7029) link_NAG-ASN : bond 0.00184 ( 1) link_NAG-ASN : angle 1.07791 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8930 Ramachandran restraints generated. 4465 Oldfield, 0 Emsley, 4465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 563 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.7681 (tmm) cc_final: 0.7389 (tmm) REVERT: A 114 MET cc_start: 0.8668 (mmm) cc_final: 0.8435 (mmm) REVERT: A 533 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8042 (pt0) REVERT: A 643 MET cc_start: 0.8251 (mmt) cc_final: 0.7683 (mmt) REVERT: A 658 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8697 (pt) REVERT: A 824 GLU cc_start: 0.8381 (mm-30) cc_final: 0.7962 (mp0) REVERT: A 850 CYS cc_start: 0.8342 (m) cc_final: 0.7785 (m) REVERT: A 892 MET cc_start: 0.8191 (mmm) cc_final: 0.7668 (mmm) REVERT: A 913 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8840 (mtp) REVERT: A 1203 MET cc_start: 0.8152 (mmp) cc_final: 0.7821 (mmm) REVERT: A 1268 PHE cc_start: 0.8213 (t80) cc_final: 0.7881 (t80) REVERT: A 1301 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7130 (tpt) REVERT: A 1515 MET cc_start: 0.8035 (ttm) cc_final: 0.7551 (ttm) REVERT: A 1519 MET cc_start: 0.8544 (tpp) cc_final: 0.7617 (tpp) REVERT: A 1558 GLN cc_start: 0.8410 (tm-30) cc_final: 0.7926 (mm110) REVERT: A 1565 GLU cc_start: 0.7793 (mp0) cc_final: 0.7275 (mp0) REVERT: A 1566 GLU cc_start: 0.8385 (tp30) cc_final: 0.7748 (tp30) REVERT: A 1573 ARG cc_start: 0.7323 (ptm160) cc_final: 0.6678 (ttp80) REVERT: B 266 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7559 (tt0) REVERT: B 340 ARG cc_start: 0.8491 (mtt90) cc_final: 0.8201 (mtt-85) REVERT: C 77 MET cc_start: 0.4804 (mtt) cc_final: 0.4261 (mmt) REVERT: D 182 LEU cc_start: 0.6824 (mt) cc_final: 0.6352 (tp) REVERT: D 197 LEU cc_start: 0.8375 (tp) cc_final: 0.8045 (mt) REVERT: D 260 TYR cc_start: 0.7362 (OUTLIER) cc_final: 0.6368 (t80) REVERT: D 264 TYR cc_start: 0.6360 (m-10) cc_final: 0.6090 (m-10) REVERT: D 599 GLN cc_start: 0.8227 (pt0) cc_final: 0.7874 (pt0) REVERT: D 645 ARG cc_start: 0.7842 (ttm110) cc_final: 0.7405 (ttm-80) REVERT: D 694 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8582 (tt0) REVERT: D 796 MET cc_start: 0.7956 (ppp) cc_final: 0.7726 (ppp) REVERT: D 963 MET cc_start: 0.9224 (ttm) cc_final: 0.8994 (mtp) REVERT: D 1081 LYS cc_start: 0.8467 (mtpt) cc_final: 0.7902 (tmtt) REVERT: D 1326 MET cc_start: 0.8441 (mmp) cc_final: 0.8166 (mtm) REVERT: D 2070 VAL cc_start: 0.8219 (t) cc_final: 0.7933 (m) REVERT: D 2192 CYS cc_start: 0.7314 (OUTLIER) cc_final: 0.6859 (m) REVERT: D 2335 MET cc_start: 0.7923 (tmm) cc_final: 0.7646 (tmm) REVERT: D 2371 MET cc_start: 0.7600 (tpp) cc_final: 0.7266 (tpp) REVERT: D 2437 LEU cc_start: 0.8520 (mt) cc_final: 0.7789 (pt) REVERT: D 2543 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7947 (mm-30) REVERT: E 87 HIS cc_start: 0.8578 (OUTLIER) cc_final: 0.8197 (m-70) REVERT: E 186 GLU cc_start: 0.7861 (tp30) cc_final: 0.7057 (mm-30) REVERT: E 191 LEU cc_start: 0.8764 (mp) cc_final: 0.8530 (mp) REVERT: E 212 LEU cc_start: 0.7289 (tp) cc_final: 0.7072 (mt) REVERT: E 673 CYS cc_start: 0.8233 (p) cc_final: 0.7920 (m) REVERT: E 861 PHE cc_start: 0.8875 (t80) cc_final: 0.8591 (t80) REVERT: E 933 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8077 (mp10) REVERT: E 934 LEU cc_start: 0.9055 (tt) cc_final: 0.8850 (tt) REVERT: E 1176 ASN cc_start: 0.8512 (t0) cc_final: 0.8208 (t0) REVERT: E 1902 ARG cc_start: 0.7924 (mtm-85) cc_final: 0.7163 (mtp180) REVERT: E 1937 MET cc_start: 0.8757 (ptp) cc_final: 0.8531 (ptm) REVERT: E 2172 MET cc_start: 0.8405 (ttp) cc_final: 0.8127 (ttp) REVERT: E 2631 LEU cc_start: 0.8300 (tt) cc_final: 0.8069 (mt) REVERT: E 2646 MET cc_start: 0.7513 (pmm) cc_final: 0.6960 (pmm) REVERT: E 2791 SER cc_start: 0.8121 (t) cc_final: 0.7758 (p) REVERT: E 2823 MET cc_start: 0.8024 (tpp) cc_final: 0.7445 (tmm) REVERT: E 2827 LYS cc_start: 0.8520 (tppt) cc_final: 0.8140 (tppt) outliers start: 48 outliers final: 38 residues processed: 592 average time/residue: 0.2320 time to fit residues: 227.0106 Evaluate side-chains 593 residues out of total 4151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 548 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain A residue 1224 SER Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1289 VAL Chi-restraints excluded: chain A residue 1292 PHE Chi-restraints excluded: chain A residue 1301 MET Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 260 TYR Chi-restraints excluded: chain D residue 534 PHE Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 1158 ILE Chi-restraints excluded: chain D residue 1288 MET Chi-restraints excluded: chain D residue 2173 ILE Chi-restraints excluded: chain D residue 2192 CYS Chi-restraints excluded: chain D residue 2204 LEU Chi-restraints excluded: chain D residue 2263 VAL Chi-restraints excluded: chain D residue 2360 HIS Chi-restraints excluded: chain D residue 2361 LEU Chi-restraints excluded: chain D residue 2368 ILE Chi-restraints excluded: chain D residue 2561 LEU Chi-restraints excluded: chain D residue 2618 MET Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 785 ASN Chi-restraints excluded: chain E residue 857 ASN Chi-restraints excluded: chain E residue 933 GLN Chi-restraints excluded: chain E residue 1211 LEU Chi-restraints excluded: chain E residue 1291 LEU Chi-restraints excluded: chain E residue 1685 VAL Chi-restraints excluded: chain E residue 1741 GLU Chi-restraints excluded: chain E residue 1842 VAL Chi-restraints excluded: chain E residue 2000 VAL Chi-restraints excluded: chain E residue 2068 VAL Chi-restraints excluded: chain E residue 2621 THR Chi-restraints excluded: chain E residue 2732 LEU Chi-restraints excluded: chain E residue 2802 LEU Chi-restraints excluded: chain E residue 2816 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 441 optimal weight: 1.9990 chunk 211 optimal weight: 0.7980 chunk 135 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 219 optimal weight: 0.7980 chunk 356 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 HIS A 844 HIS ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1270 GLN ** A1587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 GLN B 348 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2137 ASN ** D2537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 HIS E 349 GLN E 841 GLN E2011 GLN ** E2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.110227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.082207 restraints weight = 91333.031| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.37 r_work: 0.3106 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 38811 Z= 0.111 Angle : 0.556 11.949 52542 Z= 0.268 Chirality : 0.037 0.173 6057 Planarity : 0.004 0.055 6494 Dihedral : 6.733 144.363 5406 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.25 % Allowed : 13.37 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.39 (0.13), residues: 4465 helix: 2.28 (0.09), residues: 3161 sheet: -0.12 (0.88), residues: 37 loop : -0.15 (0.18), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1545 TYR 0.035 0.001 TYR D 264 PHE 0.028 0.001 PHE E2630 TRP 0.051 0.001 TRP D2610 HIS 0.020 0.001 HIS E1230 Details of bonding type rmsd covalent geometry : bond 0.00259 (38800) covalent geometry : angle 0.55579 (52519) SS BOND : bond 0.00221 ( 10) SS BOND : angle 1.23169 ( 20) hydrogen bonds : bond 0.03450 ( 2387) hydrogen bonds : angle 3.65844 ( 7029) link_NAG-ASN : bond 0.00127 ( 1) link_NAG-ASN : angle 1.08758 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14645.18 seconds wall clock time: 249 minutes 30.28 seconds (14970.28 seconds total)