Starting phenix.real_space_refine on Sat Mar 23 16:58:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sx3_25492/03_2024/7sx3_25492.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sx3_25492/03_2024/7sx3_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sx3_25492/03_2024/7sx3_25492.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sx3_25492/03_2024/7sx3_25492.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sx3_25492/03_2024/7sx3_25492.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sx3_25492/03_2024/7sx3_25492.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 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 Residue "A PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1061": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: 19.80, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 15.22 Conformation dependent library (CDL) restraints added in 6.4 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: 4.58 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: 14.95 Time building geometry restraints manager: 16.27 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: 97.80 - 105.03: 766 105.03 - 112.27: 19975 112.27 - 119.51: 12799 119.51 - 126.75: 18371 126.75 - 133.99: 608 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 2.440 nonbonded pdb=" NH1 ARG A 717 " pdb=" OD1 ASP D 970 " model vdw 2.205 2.520 nonbonded pdb=" O LYS A 998 " pdb=" NH1 ARG A1004 " model vdw 2.233 2.520 nonbonded pdb=" O ALA E1953 " pdb=" OG1 THR E1956 " model vdw 2.246 2.440 nonbonded pdb=" NE ARG E2486 " pdb=" OD2 ASP E2551 " model vdw 2.258 2.520 ... (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 ========== 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: 3.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 16.670 Check model and map are aligned: 0.560 Set scattering table: 0.370 Process input model: 97.550 Find NCS groups from input model: 2.110 Set up NCS constraints: 0.190 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: 0.020 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.060 ------------------------------------------------------------------------------- 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 38800 Z= 0.235 Angle : 0.664 16.668 52519 Z= 0.312 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.12), 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 TRP 0.024 0.001 TRP D 621 HIS 0.006 0.001 HIS E 87 PHE 0.071 0.002 PHE D2220 TYR 0.025 0.002 TYR A1517 ARG 0.016 0.002 ARG D1169 *********************** 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 fitting. rotamer outliers: 0 poor density : 615 time to evaluate : 4.004 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: 0.4983 time to fit residues: 505.5211 Evaluate side-chains 525 residues out of total 4151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 525 time to evaluate : 4.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 393 optimal weight: 3.9990 chunk 353 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 238 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 365 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 222 optimal weight: 0.8980 chunk 271 optimal weight: 2.9990 chunk 423 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 D 797 ASN D1274 HIS D1278 HIS D2137 ASN D2336 HIS D2367 GLN E 349 GLN E2149 GLN E2305 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 38800 Z= 0.315 Angle : 0.635 16.170 52519 Z= 0.320 Chirality : 0.041 0.184 6057 Planarity : 0.004 0.072 6494 Dihedral : 8.653 169.423 5406 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.06 % Allowed : 6.51 % Favored : 92.43 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.13), residues: 4465 helix: 1.68 (0.09), residues: 3134 sheet: -0.05 (0.95), residues: 37 loop : -0.18 (0.19), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 255 HIS 0.009 0.001 HIS E 786 PHE 0.032 0.002 PHE D2220 TYR 0.022 0.002 TYR A1561 ARG 0.006 0.001 ARG E 358 *********************** 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 634 residues out of total 4151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 590 time to evaluate : 4.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 MET cc_start: 0.6646 (mpp) cc_final: 0.6429 (mpp) REVERT: A 79 MET cc_start: 0.7099 (tmm) cc_final: 0.6877 (tmm) REVERT: A 150 MET cc_start: 0.8071 (tpp) cc_final: 0.7689 (tpp) REVERT: A 199 MET cc_start: 0.7602 (mtm) cc_final: 0.7273 (mtm) REVERT: A 256 GLN cc_start: 0.6368 (tp40) cc_final: 0.6162 (mm-40) REVERT: A 824 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7602 (mp0) REVERT: A 892 MET cc_start: 0.7775 (mmm) cc_final: 0.7230 (mmm) REVERT: A 913 MET cc_start: 0.8799 (mtp) cc_final: 0.8537 (mtp) REVERT: A 1203 MET cc_start: 0.7806 (mmp) cc_final: 0.7587 (mmp) REVERT: A 1214 ARG cc_start: 0.7125 (mmt90) cc_final: 0.6620 (ptm160) REVERT: A 1258 MET cc_start: 0.6953 (mmm) cc_final: 0.6703 (mmm) REVERT: A 1268 PHE cc_start: 0.8300 (t80) cc_final: 0.7934 (t80) REVERT: A 1519 MET cc_start: 0.8668 (tpp) cc_final: 0.7942 (tpp) REVERT: A 1532 ASP cc_start: 0.8300 (m-30) cc_final: 0.7903 (m-30) REVERT: B 337 VAL cc_start: 0.8467 (t) cc_final: 0.8224 (t) REVERT: B 378 ASP cc_start: 0.7012 (t0) cc_final: 0.6678 (p0) REVERT: C 13 PHE cc_start: 0.4538 (OUTLIER) cc_final: 0.3474 (m-80) REVERT: C 52 MET cc_start: 0.0461 (mtm) cc_final: 0.0214 (mtm) REVERT: C 73 MET cc_start: 0.3927 (mtt) cc_final: 0.3147 (mtp) REVERT: D 190 HIS cc_start: 0.6650 (OUTLIER) cc_final: 0.6006 (m90) REVERT: D 226 MET cc_start: 0.8579 (tpp) cc_final: 0.8148 (tpp) REVERT: D 444 CYS cc_start: 0.8160 (m) cc_final: 0.7327 (m) REVERT: D 532 GLN cc_start: 0.8580 (tp40) cc_final: 0.7976 (tp-100) REVERT: D 599 GLN cc_start: 0.8017 (pt0) cc_final: 0.7702 (pt0) REVERT: D 625 MET cc_start: 0.8095 (mmt) cc_final: 0.7636 (mmt) REVERT: D 1349 MET cc_start: 0.8385 (mtp) cc_final: 0.8153 (mtp) REVERT: D 2260 ARG cc_start: 0.8310 (ttm-80) cc_final: 0.8071 (ttm-80) REVERT: D 2279 THR cc_start: 0.8700 (m) cc_final: 0.8462 (t) REVERT: D 2335 MET cc_start: 0.7595 (ppp) cc_final: 0.7348 (tmm) REVERT: D 2371 MET cc_start: 0.7139 (tpp) cc_final: 0.6773 (tpp) REVERT: D 2543 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7947 (mm-30) REVERT: E 186 GLU cc_start: 0.7718 (tp30) cc_final: 0.6857 (mm-30) REVERT: E 928 TYR cc_start: 0.8773 (t80) cc_final: 0.8378 (t80) REVERT: E 2843 THR cc_start: 0.9195 (m) cc_final: 0.8657 (p) outliers start: 44 outliers final: 23 residues processed: 617 average time/residue: 0.5142 time to fit residues: 524.2304 Evaluate side-chains 572 residues out of total 4151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 547 time to evaluate : 4.906 ------------------------------------------------------------------------------- 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 351 VAL Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 534 PHE Chi-restraints excluded: chain D residue 672 CYS Chi-restraints excluded: chain D residue 814 LEU Chi-restraints excluded: chain D residue 1076 ILE Chi-restraints excluded: chain D residue 1272 ILE 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 2436 CYS 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 1842 VAL 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 235 optimal weight: 0.5980 chunk 131 optimal weight: 10.0000 chunk 352 optimal weight: 0.0040 chunk 288 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 423 optimal weight: 1.9990 chunk 457 optimal weight: 3.9990 chunk 377 optimal weight: 6.9990 chunk 420 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 340 optimal weight: 0.7980 overall best weight: 1.2796 ------------------------------------------------------------------------------- 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** A1158 ASN A1270 GLN A1531 HIS ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN ** D 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1022 GLN ** D1053 ASN ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 38800 Z= 0.198 Angle : 0.554 9.216 52519 Z= 0.276 Chirality : 0.038 0.209 6057 Planarity : 0.004 0.064 6494 Dihedral : 8.200 163.841 5406 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.16 % Allowed : 9.23 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.13), residues: 4465 helix: 2.00 (0.09), residues: 3147 sheet: -0.58 (0.92), residues: 36 loop : -0.18 (0.18), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP D 255 HIS 0.008 0.001 HIS E 117 PHE 0.026 0.001 PHE D2220 TYR 0.018 0.001 TYR D 239 ARG 0.004 0.000 ARG A1521 *********************** 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 634 residues out of total 4151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 586 time to evaluate : 4.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.7230 (tmm) cc_final: 0.6951 (tmm) REVERT: A 114 MET cc_start: 0.8764 (mmm) cc_final: 0.8552 (mmm) REVERT: A 824 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7587 (mp0) REVERT: A 892 MET cc_start: 0.7747 (mmm) cc_final: 0.7218 (mmm) REVERT: A 1203 MET cc_start: 0.7861 (mmp) cc_final: 0.7521 (mmp) REVERT: A 1214 ARG cc_start: 0.7127 (mmt90) cc_final: 0.6622 (ptm160) REVERT: A 1258 MET cc_start: 0.6760 (mmm) cc_final: 0.5878 (mmm) REVERT: A 1268 PHE cc_start: 0.8269 (t80) cc_final: 0.7929 (t80) REVERT: A 1301 MET cc_start: 0.7301 (mpp) cc_final: 0.6287 (tpt) REVERT: A 1305 CYS cc_start: 0.7949 (m) cc_final: 0.7374 (m) REVERT: A 1519 MET cc_start: 0.8648 (tpp) cc_final: 0.7839 (tpp) REVERT: A 1532 ASP cc_start: 0.8308 (m-30) cc_final: 0.7904 (m-30) REVERT: A 1558 GLN cc_start: 0.8349 (tm-30) cc_final: 0.7939 (mm110) REVERT: B 266 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7642 (tt0) REVERT: B 280 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7305 (mt-10) REVERT: B 330 CYS cc_start: 0.4087 (OUTLIER) cc_final: 0.3880 (p) REVERT: B 337 VAL cc_start: 0.8447 (t) cc_final: 0.8226 (t) REVERT: B 378 ASP cc_start: 0.7202 (t0) cc_final: 0.6630 (p0) REVERT: C 13 PHE cc_start: 0.4582 (OUTLIER) cc_final: 0.3557 (m-80) REVERT: C 73 MET cc_start: 0.4406 (mtt) cc_final: 0.3850 (mtp) REVERT: D 196 TYR cc_start: 0.8695 (m-80) cc_final: 0.8431 (m-80) REVERT: D 226 MET cc_start: 0.8546 (tpp) cc_final: 0.8216 (tpp) REVERT: D 231 MET cc_start: 0.8147 (mpp) cc_final: 0.7793 (mpp) REVERT: D 236 ASN cc_start: 0.8172 (t0) cc_final: 0.7947 (t0) REVERT: D 532 GLN cc_start: 0.8537 (tp40) cc_final: 0.7963 (tp-100) REVERT: D 599 GLN cc_start: 0.7985 (pt0) cc_final: 0.7666 (pt0) REVERT: D 625 MET cc_start: 0.8117 (mmt) cc_final: 0.7788 (mmt) REVERT: D 1077 HIS cc_start: 0.6728 (t-90) cc_final: 0.6512 (t-90) REVERT: D 1349 MET cc_start: 0.8351 (mtp) cc_final: 0.8108 (mtp) REVERT: D 2158 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8407 (ttt) REVERT: D 2260 ARG cc_start: 0.8269 (ttm-80) cc_final: 0.7978 (ttm-80) REVERT: D 2276 LEU cc_start: 0.8785 (mp) cc_final: 0.8489 (tp) REVERT: D 2279 THR cc_start: 0.8624 (m) cc_final: 0.8408 (t) REVERT: D 2335 MET cc_start: 0.7443 (ppp) cc_final: 0.7181 (tmm) REVERT: D 2371 MET cc_start: 0.7104 (tpp) cc_final: 0.6772 (tpp) REVERT: D 2437 LEU cc_start: 0.8402 (mt) cc_final: 0.7759 (pt) REVERT: D 2543 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7873 (mm-30) REVERT: D 2556 LEU cc_start: 0.8056 (mt) cc_final: 0.7824 (mp) REVERT: E 951 LEU cc_start: 0.8601 (mt) cc_final: 0.8338 (mp) REVERT: E 2806 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7162 (tp30) REVERT: E 2841 VAL cc_start: 0.8753 (t) cc_final: 0.8523 (p) REVERT: E 2876 ILE cc_start: 0.7592 (OUTLIER) cc_final: 0.7341 (mp) outliers start: 48 outliers final: 24 residues processed: 615 average time/residue: 0.4988 time to fit residues: 505.9945 Evaluate side-chains 573 residues out of total 4151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 545 time to evaluate : 4.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 330 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 672 CYS 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 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 1462 VAL Chi-restraints excluded: chain E residue 1481 HIS Chi-restraints excluded: chain E residue 1741 GLU Chi-restraints excluded: chain E residue 2068 VAL 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 418 optimal weight: 0.4980 chunk 318 optimal weight: 6.9990 chunk 220 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 202 optimal weight: 0.9980 chunk 284 optimal weight: 6.9990 chunk 425 optimal weight: 0.9980 chunk 450 optimal weight: 0.7980 chunk 222 optimal weight: 4.9990 chunk 403 optimal weight: 0.4980 chunk 121 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN A 256 GLN ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1158 ASN A1270 GLN A1587 GLN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 ASN ** D1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2137 ASN E 117 HIS E 349 GLN E1481 HIS E1916 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 38800 Z= 0.159 Angle : 0.530 11.187 52519 Z= 0.262 Chirality : 0.037 0.215 6057 Planarity : 0.004 0.059 6494 Dihedral : 7.838 159.758 5406 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.45 % Allowed : 10.24 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.13), residues: 4465 helix: 2.14 (0.09), residues: 3150 sheet: -0.37 (0.91), residues: 37 loop : -0.19 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP D 255 HIS 0.008 0.001 HIS D 240 PHE 0.023 0.001 PHE A 72 TYR 0.022 0.001 TYR E1764 ARG 0.004 0.000 ARG A1584 *********************** 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 641 residues out of total 4151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 581 time to evaluate : 4.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8747 (mmm) cc_final: 0.8534 (mmm) REVERT: A 824 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7643 (mp0) REVERT: A 850 CYS cc_start: 0.8049 (m) cc_final: 0.7675 (m) REVERT: A 892 MET cc_start: 0.7721 (mmm) cc_final: 0.7208 (mmm) REVERT: A 1203 MET cc_start: 0.7785 (mmp) cc_final: 0.7544 (mmp) REVERT: A 1258 MET cc_start: 0.6721 (mmm) cc_final: 0.6126 (mmm) REVERT: A 1268 PHE cc_start: 0.8226 (t80) cc_final: 0.7896 (t80) REVERT: A 1301 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6770 (tpt) REVERT: A 1515 MET cc_start: 0.8196 (ttm) cc_final: 0.7723 (ttt) REVERT: A 1519 MET cc_start: 0.8603 (tpp) cc_final: 0.7799 (tpp) REVERT: A 1558 GLN cc_start: 0.8312 (tm-30) cc_final: 0.7905 (mm110) REVERT: B 266 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7632 (tt0) REVERT: B 337 VAL cc_start: 0.8496 (t) cc_final: 0.8236 (t) REVERT: B 378 ASP cc_start: 0.7047 (t0) cc_final: 0.6483 (p0) REVERT: C 73 MET cc_start: 0.4515 (mtt) cc_final: 0.4220 (mtp) REVERT: D 182 LEU cc_start: 0.7370 (mt) cc_final: 0.7079 (tp) REVERT: D 196 TYR cc_start: 0.8665 (m-80) cc_final: 0.8462 (m-80) REVERT: D 226 MET cc_start: 0.8490 (tpp) cc_final: 0.8135 (tpp) REVERT: D 532 GLN cc_start: 0.8522 (tp40) cc_final: 0.7949 (tp-100) REVERT: D 599 GLN cc_start: 0.7993 (pt0) cc_final: 0.7659 (pt0) REVERT: D 625 MET cc_start: 0.8073 (mmt) cc_final: 0.7812 (mmt) REVERT: D 796 MET cc_start: 0.7566 (ppp) cc_final: 0.7098 (ppp) REVERT: D 1007 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7305 (mtp) REVERT: D 1349 MET cc_start: 0.8286 (mtp) cc_final: 0.7993 (mtp) REVERT: D 2070 VAL cc_start: 0.8559 (t) cc_final: 0.8324 (m) REVERT: D 2158 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8379 (ttt) REVERT: D 2335 MET cc_start: 0.7322 (ppp) cc_final: 0.7024 (tmm) REVERT: D 2371 MET cc_start: 0.7102 (tpp) cc_final: 0.6788 (tpp) REVERT: D 2437 LEU cc_start: 0.8394 (mt) cc_final: 0.7688 (pt) REVERT: D 2543 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7806 (mm-30) REVERT: D 2556 LEU cc_start: 0.8077 (mt) cc_final: 0.7864 (mp) REVERT: D 2618 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8691 (ttp) REVERT: E 186 GLU cc_start: 0.7783 (tp30) cc_final: 0.6901 (mm-30) REVERT: E 824 ARG cc_start: 0.8036 (mtp85) cc_final: 0.7581 (ttm-80) REVERT: E 933 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8081 (mp10) REVERT: E 951 LEU cc_start: 0.8578 (mt) cc_final: 0.8323 (mp) REVERT: E 2172 MET cc_start: 0.8050 (ttp) cc_final: 0.7782 (ttp) REVERT: E 2841 VAL cc_start: 0.8696 (t) cc_final: 0.8430 (p) REVERT: E 2876 ILE cc_start: 0.7613 (OUTLIER) cc_final: 0.7371 (mp) outliers start: 60 outliers final: 28 residues processed: 614 average time/residue: 0.5220 time to fit residues: 530.4535 Evaluate side-chains 581 residues out of total 4151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 547 time to evaluate : 4.653 ------------------------------------------------------------------------------- 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 A residue 1301 MET 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 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 1007 MET Chi-restraints excluded: chain D residue 1158 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 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 D residue 2618 MET Chi-restraints excluded: chain E residue 786 HIS 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 2000 VAL Chi-restraints excluded: chain E residue 2068 VAL Chi-restraints excluded: chain E residue 2565 MET Chi-restraints excluded: chain E residue 2732 LEU Chi-restraints excluded: chain E residue 2802 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 375 optimal weight: 2.9990 chunk 255 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 335 optimal weight: 8.9990 chunk 185 optimal weight: 7.9990 chunk 384 optimal weight: 3.9990 chunk 311 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 230 optimal weight: 2.9990 chunk 404 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2137 ASN E 117 HIS E 349 GLN E 785 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 38800 Z= 0.235 Angle : 0.554 9.735 52519 Z= 0.275 Chirality : 0.039 0.247 6057 Planarity : 0.004 0.059 6494 Dihedral : 7.701 155.566 5406 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.61 % Allowed : 11.64 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.13), residues: 4465 helix: 2.09 (0.09), residues: 3171 sheet: 0.14 (0.89), residues: 37 loop : -0.22 (0.18), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP D 255 HIS 0.009 0.001 HIS E1230 PHE 0.028 0.002 PHE D2220 TYR 0.025 0.001 TYR D 239 ARG 0.006 0.000 ARG E1234 *********************** 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 649 residues out of total 4151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 582 time to evaluate : 4.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8743 (mmm) cc_final: 0.8531 (mmm) REVERT: A 119 TRP cc_start: 0.8060 (m100) cc_final: 0.6860 (m-10) REVERT: A 824 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7780 (mp0) REVERT: A 834 ASP cc_start: 0.8121 (t70) cc_final: 0.7822 (t70) REVERT: A 850 CYS cc_start: 0.8060 (m) cc_final: 0.7686 (m) REVERT: A 913 MET cc_start: 0.8842 (mtp) cc_final: 0.8580 (mtp) REVERT: A 1203 MET cc_start: 0.7889 (mmp) cc_final: 0.7597 (mmp) REVERT: A 1258 MET cc_start: 0.6812 (mmm) cc_final: 0.6034 (mmm) REVERT: A 1268 PHE cc_start: 0.8255 (t80) cc_final: 0.7939 (t80) REVERT: A 1301 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.6762 (tpt) REVERT: A 1515 MET cc_start: 0.8207 (ttm) cc_final: 0.7693 (ttt) REVERT: A 1519 MET cc_start: 0.8596 (tpp) cc_final: 0.7810 (tpp) REVERT: A 1565 GLU cc_start: 0.7757 (mp0) cc_final: 0.7205 (mp0) REVERT: A 1573 ARG cc_start: 0.7347 (ptm160) cc_final: 0.6753 (ttp80) REVERT: B 266 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7619 (tt0) REVERT: B 280 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7415 (mt-10) REVERT: B 337 VAL cc_start: 0.8481 (t) cc_final: 0.8247 (t) REVERT: B 378 ASP cc_start: 0.7020 (t0) cc_final: 0.6504 (p0) REVERT: D 182 LEU cc_start: 0.7288 (mt) cc_final: 0.7005 (tp) REVERT: D 226 MET cc_start: 0.8328 (tpp) cc_final: 0.8048 (tpp) REVERT: D 532 GLN cc_start: 0.8557 (tp40) cc_final: 0.7988 (tp-100) REVERT: D 599 GLN cc_start: 0.8081 (pt0) cc_final: 0.7724 (pt0) REVERT: D 625 MET cc_start: 0.8177 (mmt) cc_final: 0.7948 (mmt) REVERT: D 645 ARG cc_start: 0.7692 (ttm110) cc_final: 0.7438 (ttm-80) REVERT: D 796 MET cc_start: 0.7749 (ppp) cc_final: 0.7516 (ppp) REVERT: D 963 MET cc_start: 0.9031 (mtp) cc_final: 0.8827 (mtm) REVERT: D 1007 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7277 (mtp) REVERT: D 1349 MET cc_start: 0.8358 (mtp) cc_final: 0.8107 (mtp) REVERT: D 2158 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8381 (ttt) REVERT: D 2260 ARG cc_start: 0.8303 (ttm-80) cc_final: 0.7999 (ttm-80) REVERT: D 2335 MET cc_start: 0.7207 (ppp) cc_final: 0.6919 (tmm) REVERT: D 2371 MET cc_start: 0.7210 (tpp) cc_final: 0.6883 (tpp) REVERT: D 2437 LEU cc_start: 0.8405 (mt) cc_final: 0.7704 (pt) REVERT: D 2543 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7830 (mm-30) REVERT: D 2618 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8723 (ttp) REVERT: E 186 GLU cc_start: 0.7610 (tp30) cc_final: 0.6692 (mm-30) REVERT: E 824 ARG cc_start: 0.8106 (mtp85) cc_final: 0.7662 (ttm-80) REVERT: E 933 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8050 (mp10) REVERT: E 951 LEU cc_start: 0.8684 (mt) cc_final: 0.8436 (mp) REVERT: E 1453 TYR cc_start: 0.7970 (m-80) cc_final: 0.7675 (m-80) REVERT: E 2172 MET cc_start: 0.8176 (ttp) cc_final: 0.7865 (ttp) REVERT: E 2384 GLN cc_start: 0.7808 (tm-30) cc_final: 0.7521 (tm-30) REVERT: E 2395 ARG cc_start: 0.8274 (mmt180) cc_final: 0.8031 (mmt180) REVERT: E 2841 VAL cc_start: 0.8785 (t) cc_final: 0.8441 (p) REVERT: E 2876 ILE cc_start: 0.7632 (OUTLIER) cc_final: 0.7383 (mp) outliers start: 67 outliers final: 39 residues processed: 622 average time/residue: 0.5055 time to fit residues: 513.4411 Evaluate side-chains 592 residues out of total 4151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 547 time to evaluate : 4.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 876 HIS 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 220 ASN Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 534 PHE Chi-restraints excluded: chain D residue 672 CYS Chi-restraints excluded: chain D residue 1007 MET 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 2504 THR 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 790 LEU 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 2732 LEU Chi-restraints excluded: chain E residue 2802 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 151 optimal weight: 0.9980 chunk 405 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 264 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 450 optimal weight: 0.9990 chunk 374 optimal weight: 4.9990 chunk 208 optimal weight: 0.0870 chunk 37 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 chunk 236 optimal weight: 20.0000 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2137 ASN E 29 GLN E 117 HIS E 349 GLN E2613 ASN ** E2734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 38800 Z= 0.154 Angle : 0.529 11.385 52519 Z= 0.260 Chirality : 0.037 0.194 6057 Planarity : 0.004 0.056 6494 Dihedral : 7.460 153.177 5406 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.42 % Allowed : 12.48 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.13), residues: 4465 helix: 2.25 (0.09), residues: 3156 sheet: -0.20 (0.90), residues: 36 loop : -0.20 (0.18), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP D 255 HIS 0.009 0.001 HIS E 786 PHE 0.022 0.001 PHE E2630 TYR 0.021 0.001 TYR D 264 ARG 0.005 0.000 ARG D2386 *********************** 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 635 residues out of total 4151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 576 time to evaluate : 4.326 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 114 MET cc_start: 0.8740 (mmm) cc_final: 0.8530 (mmm) REVERT: A 119 TRP cc_start: 0.8005 (m100) cc_final: 0.6419 (m-10) REVERT: A 588 LEU cc_start: 0.8307 (mt) cc_final: 0.8046 (mp) REVERT: A 824 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7788 (mp0) REVERT: A 850 CYS cc_start: 0.8044 (m) cc_final: 0.7603 (m) REVERT: A 1203 MET cc_start: 0.7958 (mmp) cc_final: 0.7630 (mmp) REVERT: A 1258 MET cc_start: 0.6692 (mmm) cc_final: 0.5896 (mmm) REVERT: A 1268 PHE cc_start: 0.8239 (t80) cc_final: 0.7862 (t80) REVERT: A 1301 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.6770 (tpt) REVERT: A 1515 MET cc_start: 0.8119 (ttm) cc_final: 0.7863 (ttp) REVERT: A 1519 MET cc_start: 0.8569 (tpp) cc_final: 0.7740 (tpp) REVERT: A 1558 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8045 (mm110) REVERT: A 1565 GLU cc_start: 0.7773 (mp0) cc_final: 0.7385 (mp0) REVERT: A 1573 ARG cc_start: 0.7332 (ptm160) cc_final: 0.6739 (ttp80) REVERT: B 266 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7605 (tt0) REVERT: B 337 VAL cc_start: 0.8493 (t) cc_final: 0.8208 (t) REVERT: D 182 LEU cc_start: 0.7377 (mt) cc_final: 0.7084 (tp) REVERT: D 226 MET cc_start: 0.8287 (tpp) cc_final: 0.7942 (tpp) REVERT: D 599 GLN cc_start: 0.8057 (pt0) cc_final: 0.7701 (pt0) REVERT: D 645 ARG cc_start: 0.7680 (ttm110) cc_final: 0.7433 (ttm-80) REVERT: D 1007 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7240 (mtp) REVERT: D 1349 MET cc_start: 0.8245 (mtp) cc_final: 0.7934 (mtp) REVERT: D 2070 VAL cc_start: 0.8556 (t) cc_final: 0.8268 (m) REVERT: D 2204 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8740 (tt) REVERT: D 2260 ARG cc_start: 0.8297 (ttm-80) cc_final: 0.7995 (ttm-80) REVERT: D 2335 MET cc_start: 0.7173 (ppp) cc_final: 0.6878 (tmm) REVERT: D 2371 MET cc_start: 0.7313 (tpp) cc_final: 0.7001 (tpp) REVERT: D 2437 LEU cc_start: 0.8377 (mt) cc_final: 0.7709 (pt) REVERT: D 2543 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7931 (mm-30) REVERT: D 2556 LEU cc_start: 0.8119 (mt) cc_final: 0.7827 (mp) REVERT: E 182 MET cc_start: 0.8072 (mmt) cc_final: 0.7618 (mmm) REVERT: E 186 GLU cc_start: 0.7721 (tp30) cc_final: 0.6964 (mm-30) REVERT: E 200 LYS cc_start: 0.8474 (pttt) cc_final: 0.8187 (ptpt) REVERT: E 824 ARG cc_start: 0.8084 (mtp85) cc_final: 0.7706 (ttm-80) REVERT: E 933 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.8002 (mp10) REVERT: E 951 LEU cc_start: 0.8632 (mt) cc_final: 0.8341 (mp) REVERT: E 1453 TYR cc_start: 0.7954 (m-80) cc_final: 0.7662 (m-80) REVERT: E 2172 MET cc_start: 0.8028 (ttp) cc_final: 0.7751 (ttp) REVERT: E 2384 GLN cc_start: 0.7824 (tm-30) cc_final: 0.7426 (tm-30) REVERT: E 2556 GLU cc_start: 0.7813 (tp30) cc_final: 0.7591 (mm-30) REVERT: E 2841 VAL cc_start: 0.8741 (t) cc_final: 0.8382 (p) REVERT: E 2876 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.7358 (mp) outliers start: 59 outliers final: 31 residues processed: 608 average time/residue: 0.5418 time to fit residues: 546.2469 Evaluate side-chains 585 residues out of total 4151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 549 time to evaluate : 4.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 571 VAL Chi-restraints excluded: chain D residue 672 CYS Chi-restraints excluded: chain D residue 1007 MET Chi-restraints excluded: chain D residue 1288 MET Chi-restraints excluded: chain D residue 2204 LEU 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 D residue 2618 MET Chi-restraints excluded: chain E residue 860 ASP Chi-restraints excluded: chain E residue 933 GLN Chi-restraints excluded: chain E residue 1574 SER 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 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 434 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 256 optimal weight: 0.5980 chunk 329 optimal weight: 0.0470 chunk 255 optimal weight: 0.4980 chunk 379 optimal weight: 0.9990 chunk 251 optimal weight: 0.6980 chunk 449 optimal weight: 0.0670 chunk 281 optimal weight: 10.0000 chunk 273 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2137 ASN E 117 HIS E 349 GLN E 785 ASN E 841 GLN E2037 GLN ** E2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2379 GLN ** E2734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 38800 Z= 0.138 Angle : 0.514 11.246 52519 Z= 0.252 Chirality : 0.036 0.238 6057 Planarity : 0.004 0.053 6494 Dihedral : 7.080 149.599 5406 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.23 % Allowed : 12.77 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.13), residues: 4465 helix: 2.30 (0.09), residues: 3168 sheet: 0.07 (0.93), residues: 36 loop : -0.13 (0.18), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 255 HIS 0.003 0.000 HIS E2867 PHE 0.023 0.001 PHE A1199 TYR 0.017 0.001 TYR A1420 ARG 0.005 0.000 ARG E2383 *********************** 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 636 residues out of total 4151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 585 time to evaluate : 4.306 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 114 MET cc_start: 0.8725 (mmm) cc_final: 0.8516 (mmm) REVERT: A 817 MET cc_start: 0.3690 (pmm) cc_final: 0.3440 (pmm) REVERT: A 824 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7784 (mp0) REVERT: A 850 CYS cc_start: 0.8067 (m) cc_final: 0.7583 (m) REVERT: A 1203 MET cc_start: 0.7957 (mmp) cc_final: 0.7336 (mmp) REVERT: A 1258 MET cc_start: 0.6673 (mmm) cc_final: 0.5851 (mmm) REVERT: A 1268 PHE cc_start: 0.8201 (t80) cc_final: 0.7840 (t80) REVERT: A 1301 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6810 (tpt) REVERT: A 1515 MET cc_start: 0.7973 (ttm) cc_final: 0.7719 (ttp) REVERT: A 1519 MET cc_start: 0.8527 (tpp) cc_final: 0.7700 (tpp) REVERT: A 1558 GLN cc_start: 0.8410 (tm-30) cc_final: 0.7962 (mm110) REVERT: A 1573 ARG cc_start: 0.7299 (ptm160) cc_final: 0.6705 (ttp80) REVERT: B 227 ASN cc_start: 0.8203 (p0) cc_final: 0.7985 (p0) REVERT: B 266 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7589 (tt0) REVERT: B 337 VAL cc_start: 0.8465 (t) cc_final: 0.8172 (t) REVERT: D 182 LEU cc_start: 0.7060 (mt) cc_final: 0.6712 (tp) REVERT: D 226 MET cc_start: 0.8236 (tpp) cc_final: 0.8020 (tpp) REVERT: D 231 MET cc_start: 0.7777 (mpp) cc_final: 0.7540 (mpp) REVERT: D 260 TYR cc_start: 0.7153 (OUTLIER) cc_final: 0.6106 (t80) REVERT: D 276 MET cc_start: 0.7311 (mmm) cc_final: 0.6700 (mmm) REVERT: D 280 TYR cc_start: 0.8051 (m-80) cc_final: 0.7809 (m-80) REVERT: D 599 GLN cc_start: 0.8028 (pt0) cc_final: 0.7702 (pt0) REVERT: D 645 ARG cc_start: 0.7647 (ttm110) cc_final: 0.7277 (ttm-80) REVERT: D 2070 VAL cc_start: 0.8336 (t) cc_final: 0.8113 (m) REVERT: D 2158 MET cc_start: 0.8440 (mtp) cc_final: 0.8021 (ttt) REVERT: D 2204 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8704 (tt) REVERT: D 2335 MET cc_start: 0.7229 (ppp) cc_final: 0.6924 (tmm) REVERT: D 2371 MET cc_start: 0.7292 (tpp) cc_final: 0.7022 (tpp) REVERT: D 2413 ARG cc_start: 0.7552 (ttm110) cc_final: 0.7249 (ttm110) REVERT: D 2424 THR cc_start: 0.8096 (m) cc_final: 0.7812 (m) REVERT: D 2437 LEU cc_start: 0.8386 (mt) cc_final: 0.7675 (pt) REVERT: D 2543 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7844 (mm-30) REVERT: D 2556 LEU cc_start: 0.8117 (mt) cc_final: 0.7820 (mp) REVERT: D 2610 TRP cc_start: 0.8183 (t60) cc_final: 0.7860 (t60) REVERT: E 182 MET cc_start: 0.8021 (mmt) cc_final: 0.7551 (mmm) REVERT: E 186 GLU cc_start: 0.7718 (tp30) cc_final: 0.6946 (mm-30) REVERT: E 200 LYS cc_start: 0.8496 (pttt) cc_final: 0.8234 (ptpt) REVERT: E 218 MET cc_start: 0.7900 (ttm) cc_final: 0.7532 (ttm) REVERT: E 824 ARG cc_start: 0.7949 (mtp85) cc_final: 0.7549 (ttm-80) REVERT: E 933 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7951 (mp10) REVERT: E 1453 TYR cc_start: 0.7933 (m-80) cc_final: 0.7637 (m-80) REVERT: E 1606 MET cc_start: 0.8321 (tpp) cc_final: 0.8072 (tpp) REVERT: E 2172 MET cc_start: 0.7919 (ttp) cc_final: 0.7627 (ttp) REVERT: E 2384 GLN cc_start: 0.7715 (tm-30) cc_final: 0.7372 (tm-30) REVERT: E 2556 GLU cc_start: 0.7780 (tp30) cc_final: 0.7566 (mm-30) REVERT: E 2791 SER cc_start: 0.8147 (t) cc_final: 0.7786 (p) REVERT: E 2841 VAL cc_start: 0.8706 (t) cc_final: 0.8335 (p) REVERT: E 2876 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7350 (mp) outliers start: 51 outliers final: 35 residues processed: 616 average time/residue: 0.5202 time to fit residues: 530.7683 Evaluate side-chains 591 residues out of total 4151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 551 time to evaluate : 3.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 631 LEU 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 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 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 1158 ILE 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 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 790 LEU 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 1574 SER 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 2388 VAL Chi-restraints excluded: chain E residue 2565 MET 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 2843 THR 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 277 optimal weight: 0.7980 chunk 179 optimal weight: 0.8980 chunk 268 optimal weight: 0.2980 chunk 135 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 285 optimal weight: 0.9980 chunk 306 optimal weight: 10.0000 chunk 222 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 353 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN D 190 HIS ** D1053 ASN ** 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 E1454 HIS ** E2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2696 HIS ** E2734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 38800 Z= 0.155 Angle : 0.529 14.081 52519 Z= 0.257 Chirality : 0.037 0.316 6057 Planarity : 0.004 0.056 6494 Dihedral : 6.955 147.584 5406 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.40 % Allowed : 13.11 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.13), residues: 4465 helix: 2.33 (0.09), residues: 3169 sheet: 0.09 (0.92), residues: 36 loop : -0.15 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 119 HIS 0.003 0.000 HIS E1926 PHE 0.032 0.001 PHE E2630 TYR 0.019 0.001 TYR A1561 ARG 0.004 0.000 ARG D2386 *********************** 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 627 residues out of total 4151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 569 time to evaluate : 4.794 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 114 MET cc_start: 0.8714 (mmm) cc_final: 0.8497 (mmm) REVERT: A 119 TRP cc_start: 0.7901 (m100) cc_final: 0.6449 (m-10) REVERT: A 817 MET cc_start: 0.3697 (pmm) cc_final: 0.3474 (pmm) REVERT: A 824 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7872 (mp0) REVERT: A 850 CYS cc_start: 0.8054 (m) cc_final: 0.7634 (m) REVERT: A 913 MET cc_start: 0.8791 (mtp) cc_final: 0.8525 (mtp) REVERT: A 1203 MET cc_start: 0.7948 (mmp) cc_final: 0.7292 (mmp) REVERT: A 1258 MET cc_start: 0.6658 (mmm) cc_final: 0.5847 (mmm) REVERT: A 1268 PHE cc_start: 0.8208 (t80) cc_final: 0.7816 (t80) REVERT: A 1301 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.6835 (tpt) REVERT: A 1515 MET cc_start: 0.7950 (ttm) cc_final: 0.7699 (ttp) REVERT: A 1519 MET cc_start: 0.8509 (tpp) cc_final: 0.7699 (tpp) REVERT: A 1558 GLN cc_start: 0.8416 (tm-30) cc_final: 0.7967 (mm110) REVERT: A 1565 GLU cc_start: 0.7731 (mp0) cc_final: 0.7402 (mp0) REVERT: A 1573 ARG cc_start: 0.7346 (ptm160) cc_final: 0.6760 (ttp80) REVERT: B 266 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7592 (tt0) REVERT: B 337 VAL cc_start: 0.8465 (t) cc_final: 0.8174 (t) REVERT: D 182 LEU cc_start: 0.6923 (mt) cc_final: 0.6634 (tp) REVERT: D 189 LEU cc_start: 0.8831 (mt) cc_final: 0.8535 (tp) REVERT: D 226 MET cc_start: 0.8204 (tpp) cc_final: 0.7888 (tpp) REVERT: D 231 MET cc_start: 0.7785 (mpp) cc_final: 0.7499 (mpp) REVERT: D 260 TYR cc_start: 0.7225 (OUTLIER) cc_final: 0.6226 (t80) REVERT: D 276 MET cc_start: 0.7358 (mmm) cc_final: 0.6792 (mmm) REVERT: D 599 GLN cc_start: 0.8033 (pt0) cc_final: 0.7706 (pt0) REVERT: D 645 ARG cc_start: 0.7650 (ttm110) cc_final: 0.7286 (ttm-80) REVERT: D 796 MET cc_start: 0.7642 (ppp) cc_final: 0.7322 (ppp) REVERT: D 2070 VAL cc_start: 0.8330 (t) cc_final: 0.8104 (m) REVERT: D 2204 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8689 (tt) REVERT: D 2332 MET cc_start: 0.7342 (tpp) cc_final: 0.6929 (mtt) REVERT: D 2335 MET cc_start: 0.7226 (ppp) cc_final: 0.6931 (tmm) REVERT: D 2371 MET cc_start: 0.7296 (tpp) cc_final: 0.7030 (tpp) REVERT: D 2437 LEU cc_start: 0.8368 (mt) cc_final: 0.7640 (pt) REVERT: D 2543 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7853 (mm-30) REVERT: E 182 MET cc_start: 0.7976 (mmt) cc_final: 0.7495 (mmm) REVERT: E 186 GLU cc_start: 0.7703 (tp30) cc_final: 0.6938 (mm-30) REVERT: E 824 ARG cc_start: 0.7971 (mtp85) cc_final: 0.7566 (ttm-80) REVERT: E 933 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7968 (mp10) REVERT: E 1453 TYR cc_start: 0.7949 (m-80) cc_final: 0.7657 (m-80) REVERT: E 2172 MET cc_start: 0.7975 (ttp) cc_final: 0.7659 (ttp) REVERT: E 2791 SER cc_start: 0.8155 (t) cc_final: 0.7791 (p) REVERT: E 2841 VAL cc_start: 0.8729 (t) cc_final: 0.8322 (p) REVERT: E 2844 ARG cc_start: 0.8322 (mtm110) cc_final: 0.7941 (mtm110) REVERT: E 2876 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7358 (mp) outliers start: 58 outliers final: 38 residues processed: 605 average time/residue: 0.5085 time to fit residues: 510.1243 Evaluate side-chains 595 residues out of total 4151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 552 time to evaluate : 3.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 631 LEU 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 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 260 TYR Chi-restraints excluded: chain D residue 534 PHE Chi-restraints excluded: chain D residue 827 LEU Chi-restraints excluded: chain D residue 1100 VAL Chi-restraints excluded: chain D residue 1158 ILE Chi-restraints excluded: chain D residue 2173 ILE Chi-restraints excluded: chain D residue 2187 VAL Chi-restraints excluded: chain D residue 2204 LEU Chi-restraints excluded: chain D residue 2263 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 D residue 2618 MET 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 1574 SER 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 408 optimal weight: 0.7980 chunk 430 optimal weight: 5.9990 chunk 392 optimal weight: 6.9990 chunk 418 optimal weight: 7.9990 chunk 251 optimal weight: 0.0970 chunk 182 optimal weight: 6.9990 chunk 328 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 378 optimal weight: 0.8980 chunk 395 optimal weight: 6.9990 chunk 417 optimal weight: 1.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 841 GLN ** E2734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 38800 Z= 0.221 Angle : 0.557 11.834 52519 Z= 0.272 Chirality : 0.038 0.285 6057 Planarity : 0.004 0.056 6494 Dihedral : 6.952 146.181 5406 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.37 % Allowed : 13.23 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.13), residues: 4465 helix: 2.27 (0.09), residues: 3173 sheet: 0.05 (0.91), residues: 36 loop : -0.20 (0.18), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D2610 HIS 0.005 0.001 HIS E1926 PHE 0.028 0.001 PHE E2630 TYR 0.018 0.001 TYR E2795 ARG 0.004 0.000 ARG A1545 *********************** 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 634 residues out of total 4151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 577 time to evaluate : 4.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8715 (mmm) cc_final: 0.8494 (mmm) REVERT: A 119 TRP cc_start: 0.7912 (m100) cc_final: 0.6487 (m-10) REVERT: A 299 TYR cc_start: 0.8374 (m-80) cc_final: 0.7930 (m-80) REVERT: A 824 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7871 (mp0) REVERT: A 850 CYS cc_start: 0.8104 (m) cc_final: 0.7627 (m) REVERT: A 1203 MET cc_start: 0.7904 (mmp) cc_final: 0.7220 (mmp) REVERT: A 1258 MET cc_start: 0.6653 (mmm) cc_final: 0.5855 (mmm) REVERT: A 1268 PHE cc_start: 0.8226 (t80) cc_final: 0.7850 (t80) REVERT: A 1301 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.6862 (tpt) REVERT: A 1515 MET cc_start: 0.8010 (ttm) cc_final: 0.7532 (ttt) REVERT: A 1519 MET cc_start: 0.8528 (tpp) cc_final: 0.7727 (tpp) REVERT: A 1558 GLN cc_start: 0.8409 (tm-30) cc_final: 0.7964 (mm110) REVERT: A 1573 ARG cc_start: 0.7369 (ptm160) cc_final: 0.6741 (ttp80) REVERT: B 266 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7566 (tt0) REVERT: B 280 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7407 (mt-10) REVERT: B 337 VAL cc_start: 0.8445 (t) cc_final: 0.8192 (t) REVERT: D 182 LEU cc_start: 0.6905 (mt) cc_final: 0.6544 (tp) REVERT: D 197 LEU cc_start: 0.8323 (tp) cc_final: 0.8015 (mt) REVERT: D 226 MET cc_start: 0.8235 (tpp) cc_final: 0.8022 (tpp) REVERT: D 231 MET cc_start: 0.7839 (mpp) cc_final: 0.7569 (mpp) REVERT: D 260 TYR cc_start: 0.7288 (OUTLIER) cc_final: 0.6293 (t80) REVERT: D 276 MET cc_start: 0.7397 (mmm) cc_final: 0.6829 (mmm) REVERT: D 599 GLN cc_start: 0.8088 (pt0) cc_final: 0.7762 (pt0) REVERT: D 645 ARG cc_start: 0.7666 (ttm110) cc_final: 0.7414 (ttm-80) REVERT: D 796 MET cc_start: 0.7625 (ppp) cc_final: 0.7407 (ppp) REVERT: D 1007 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7208 (mtp) REVERT: D 2158 MET cc_start: 0.8769 (ttt) cc_final: 0.8380 (ttt) REVERT: D 2260 ARG cc_start: 0.8283 (ttm-80) cc_final: 0.8063 (ttm-80) REVERT: D 2335 MET cc_start: 0.7237 (ppp) cc_final: 0.6962 (tmm) REVERT: D 2371 MET cc_start: 0.7310 (tpp) cc_final: 0.7013 (tpp) REVERT: D 2437 LEU cc_start: 0.8380 (mt) cc_final: 0.7675 (pt) REVERT: D 2543 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7851 (mm-30) REVERT: E 87 HIS cc_start: 0.8561 (OUTLIER) cc_final: 0.8190 (m-70) REVERT: E 186 GLU cc_start: 0.7778 (tp30) cc_final: 0.7026 (mm-30) REVERT: E 824 ARG cc_start: 0.8049 (mtp85) cc_final: 0.7680 (ttm-80) REVERT: E 933 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8000 (mp10) REVERT: E 2172 MET cc_start: 0.8146 (ttp) cc_final: 0.7834 (ttp) REVERT: E 2791 SER cc_start: 0.8176 (t) cc_final: 0.7815 (p) REVERT: E 2827 LYS cc_start: 0.8503 (tppt) cc_final: 0.8132 (tppt) REVERT: E 2841 VAL cc_start: 0.8715 (t) cc_final: 0.8345 (p) REVERT: E 2854 PHE cc_start: 0.8068 (t80) cc_final: 0.7740 (t80) REVERT: E 2876 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.7394 (mp) outliers start: 57 outliers final: 44 residues processed: 609 average time/residue: 0.5042 time to fit residues: 506.8495 Evaluate side-chains 607 residues out of total 4151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 557 time to evaluate : 4.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 631 LEU 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 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 330 CYS Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 220 ASN 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 827 LEU Chi-restraints excluded: chain D residue 1007 MET Chi-restraints excluded: chain D residue 1100 VAL Chi-restraints excluded: chain D residue 1158 ILE Chi-restraints excluded: chain D residue 1416 ILE 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 2356 THR Chi-restraints excluded: chain D residue 2360 HIS 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 D residue 2618 MET Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 790 LEU 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 1481 HIS Chi-restraints excluded: chain E residue 1574 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 274 optimal weight: 4.9990 chunk 442 optimal weight: 2.9990 chunk 270 optimal weight: 0.9980 chunk 209 optimal weight: 0.6980 chunk 307 optimal weight: 5.9990 chunk 464 optimal weight: 2.9990 chunk 427 optimal weight: 2.9990 chunk 369 optimal weight: 0.1980 chunk 38 optimal weight: 3.9990 chunk 285 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 825 HIS ** D1053 ASN ** 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 ** E2734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 38800 Z= 0.206 Angle : 0.565 15.077 52519 Z= 0.274 Chirality : 0.038 0.281 6057 Planarity : 0.004 0.054 6494 Dihedral : 6.896 144.619 5406 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.13 % Allowed : 13.64 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.13), residues: 4465 helix: 2.25 (0.09), residues: 3177 sheet: 0.02 (0.89), residues: 36 loop : -0.21 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP D2610 HIS 0.007 0.001 HIS D2360 PHE 0.028 0.001 PHE E2630 TYR 0.023 0.001 TYR A1561 ARG 0.004 0.000 ARG A1545 ********************** 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 610 residues out of total 4151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 563 time to evaluate : 4.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8715 (mmm) cc_final: 0.8497 (mmm) REVERT: A 299 TYR cc_start: 0.8369 (m-80) cc_final: 0.7925 (m-80) REVERT: A 824 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7871 (mp0) REVERT: A 850 CYS cc_start: 0.8115 (m) cc_final: 0.7652 (m) REVERT: A 913 MET cc_start: 0.8757 (mtp) cc_final: 0.8518 (mtp) REVERT: A 1203 MET cc_start: 0.7950 (mmp) cc_final: 0.7343 (mmt) REVERT: A 1214 ARG cc_start: 0.7067 (mmt90) cc_final: 0.6779 (mmt-90) REVERT: A 1258 MET cc_start: 0.6666 (mmm) cc_final: 0.6051 (mmm) REVERT: A 1268 PHE cc_start: 0.8227 (t80) cc_final: 0.7854 (t80) REVERT: A 1301 MET cc_start: 0.7459 (OUTLIER) cc_final: 0.6857 (tpt) REVERT: A 1515 MET cc_start: 0.8004 (ttm) cc_final: 0.7711 (ttp) REVERT: A 1519 MET cc_start: 0.8536 (tpp) cc_final: 0.7595 (tpp) REVERT: A 1558 GLN cc_start: 0.8410 (tm-30) cc_final: 0.7985 (mm110) REVERT: A 1565 GLU cc_start: 0.7778 (mp0) cc_final: 0.7249 (mp0) REVERT: A 1573 ARG cc_start: 0.7353 (ptm160) cc_final: 0.6712 (ttp80) REVERT: B 266 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7573 (tt0) REVERT: B 337 VAL cc_start: 0.8468 (t) cc_final: 0.8178 (t) REVERT: D 182 LEU cc_start: 0.6965 (mt) cc_final: 0.6581 (tp) REVERT: D 197 LEU cc_start: 0.8411 (tp) cc_final: 0.8070 (mt) REVERT: D 226 MET cc_start: 0.8207 (tpp) cc_final: 0.8002 (tpp) REVERT: D 231 MET cc_start: 0.7849 (mpp) cc_final: 0.7567 (mpp) REVERT: D 260 TYR cc_start: 0.7320 (OUTLIER) cc_final: 0.6273 (t80) REVERT: D 276 MET cc_start: 0.7403 (mmm) cc_final: 0.6831 (mmm) REVERT: D 599 GLN cc_start: 0.8074 (pt0) cc_final: 0.7749 (pt0) REVERT: D 645 ARG cc_start: 0.7671 (ttm110) cc_final: 0.7289 (ttm-80) REVERT: D 796 MET cc_start: 0.7770 (ppp) cc_final: 0.7558 (ppp) REVERT: D 1007 MET cc_start: 0.7790 (mtm) cc_final: 0.7252 (mtp) REVERT: D 2158 MET cc_start: 0.8778 (ttt) cc_final: 0.8398 (ttt) REVERT: D 2260 ARG cc_start: 0.8280 (ttm-80) cc_final: 0.8069 (ttm-80) REVERT: D 2335 MET cc_start: 0.7241 (ppp) cc_final: 0.6963 (tmm) REVERT: D 2371 MET cc_start: 0.7316 (tpp) cc_final: 0.7022 (tpp) REVERT: D 2437 LEU cc_start: 0.8364 (mt) cc_final: 0.7677 (pt) REVERT: D 2543 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7824 (mm-30) REVERT: E 87 HIS cc_start: 0.8567 (OUTLIER) cc_final: 0.8153 (m-70) REVERT: E 186 GLU cc_start: 0.7781 (tp30) cc_final: 0.7030 (mm-30) REVERT: E 824 ARG cc_start: 0.8040 (mtp85) cc_final: 0.7663 (ttm-80) REVERT: E 861 PHE cc_start: 0.8769 (t80) cc_final: 0.8453 (t80) REVERT: E 933 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7976 (mp10) REVERT: E 2172 MET cc_start: 0.8108 (ttp) cc_final: 0.7812 (ttp) REVERT: E 2791 SER cc_start: 0.8179 (t) cc_final: 0.7814 (p) REVERT: E 2827 LYS cc_start: 0.8476 (tppt) cc_final: 0.8129 (tppt) REVERT: E 2841 VAL cc_start: 0.8718 (t) cc_final: 0.8344 (p) REVERT: E 2844 ARG cc_start: 0.8526 (mtm110) cc_final: 0.8275 (mtm110) REVERT: E 2854 PHE cc_start: 0.8063 (t80) cc_final: 0.7774 (t80) REVERT: E 2876 ILE cc_start: 0.7634 (OUTLIER) cc_final: 0.7392 (mp) outliers start: 47 outliers final: 40 residues processed: 591 average time/residue: 0.5067 time to fit residues: 491.1621 Evaluate side-chains 599 residues out of total 4151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 554 time to evaluate : 4.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 631 LEU 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 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 827 LEU Chi-restraints excluded: chain D residue 1100 VAL Chi-restraints excluded: chain D residue 1158 ILE Chi-restraints excluded: chain D residue 1416 ILE 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 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 D residue 2618 MET Chi-restraints excluded: chain E residue 87 HIS Chi-restraints excluded: chain E residue 790 LEU 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 1574 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 293 optimal weight: 10.0000 chunk 393 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 340 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 102 optimal weight: 0.0050 chunk 370 optimal weight: 0.9980 chunk 154 optimal weight: 0.3980 chunk 380 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2137 ASN E 117 HIS E 349 GLN E 841 GLN ** E2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2734 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.110358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.082574 restraints weight = 90490.913| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.36 r_work: 0.3112 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 38800 Z= 0.151 Angle : 0.541 14.115 52519 Z= 0.261 Chirality : 0.037 0.267 6057 Planarity : 0.004 0.053 6494 Dihedral : 6.678 143.566 5406 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.20 % Allowed : 13.73 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.13), residues: 4465 helix: 2.34 (0.09), residues: 3172 sheet: 0.02 (0.89), residues: 36 loop : -0.21 (0.18), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP D2610 HIS 0.004 0.000 HIS A 844 PHE 0.029 0.001 PHE E2630 TYR 0.019 0.001 TYR A1561 ARG 0.004 0.000 ARG E2844 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11295.71 seconds wall clock time: 203 minutes 13.89 seconds (12193.89 seconds total)