Starting phenix.real_space_refine on Sun Aug 24 19:32:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jy4_36719/08_2025/8jy4_36719.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jy4_36719/08_2025/8jy4_36719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jy4_36719/08_2025/8jy4_36719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jy4_36719/08_2025/8jy4_36719.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jy4_36719/08_2025/8jy4_36719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jy4_36719/08_2025/8jy4_36719.map" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.053 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 S 57 5.16 5 C 7139 2.51 5 N 1820 2.21 5 O 1978 1.98 5 H 11252 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22246 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 22246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1383, 22246 Classifications: {'peptide': 1383} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 1339} Chain breaks: 3 Time building chain proxies: 3.38, per 1000 atoms: 0.15 Number of scatterers: 22246 At special positions: 0 Unit cell: (104.86, 128.4, 146.59, 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 57 16.00 O 1978 8.00 N 1820 7.00 C 7139 6.00 H 11252 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 26 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 590.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2618 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 6 sheets defined 70.4% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 12 through 17 removed outlier: 3.606A pdb=" N ASP A 17 " --> pdb=" O SER A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 31 Processing helix chain 'A' and resid 33 through 44 Processing helix chain 'A' and resid 45 through 54 removed outlier: 4.583A pdb=" N VAL A 51 " --> pdb=" O GLN A 47 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER A 54 " --> pdb=" O HIS A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 88 removed outlier: 3.609A pdb=" N LEU A 66 " --> pdb=" O THR A 62 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 121 removed outlier: 3.690A pdb=" N TYR A 101 " --> pdb=" O PRO A 97 " (cutoff:3.500A) Proline residue: A 104 - end of helix Processing helix chain 'A' and resid 129 through 157 removed outlier: 3.549A pdb=" N ILE A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY A 143 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLN A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 184 removed outlier: 3.651A pdb=" N LEU A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.831A pdb=" N THR A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 222 through 226 removed outlier: 3.514A pdb=" N VAL A 226 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 266 removed outlier: 3.609A pdb=" N HIS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 334 removed outlier: 7.335A pdb=" N MET A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL A 321 " --> pdb=" O THR A 317 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER A 325 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU A 328 " --> pdb=" O LYS A 324 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VAL A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 351 removed outlier: 3.823A pdb=" N GLN A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 405 removed outlier: 3.875A pdb=" N GLY A 360 " --> pdb=" O TYR A 356 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR A 381 " --> pdb=" O CYS A 377 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A 384 " --> pdb=" O CYS A 380 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY A 389 " --> pdb=" O CYS A 385 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A 395 " --> pdb=" O LYS A 391 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR A 401 " --> pdb=" O MET A 397 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 416 through 423 removed outlier: 3.674A pdb=" N ASN A 422 " --> pdb=" O GLY A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 437 removed outlier: 3.567A pdb=" N ASP A 433 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 441 Processing helix chain 'A' and resid 442 through 460 removed outlier: 3.584A pdb=" N GLU A 458 " --> pdb=" O PHE A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 508 removed outlier: 3.873A pdb=" N GLY A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) Proline residue: A 475 - end of helix removed outlier: 4.060A pdb=" N LYS A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASN A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER A 507 " --> pdb=" O ASN A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 515 removed outlier: 3.555A pdb=" N PHE A 515 " --> pdb=" O ILE A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 552 removed outlier: 3.699A pdb=" N PHE A 521 " --> pdb=" O TRP A 517 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN A 535 " --> pdb=" O LYS A 531 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA A 538 " --> pdb=" O LYS A 534 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 569 removed outlier: 3.668A pdb=" N SER A 558 " --> pdb=" O PRO A 554 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 559 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL A 566 " --> pdb=" O PHE A 562 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASP A 569 " --> pdb=" O TYR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 581 Processing helix chain 'A' and resid 582 through 618 removed outlier: 3.733A pdb=" N ASN A 587 " --> pdb=" O ILE A 583 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N PHE A 591 " --> pdb=" O ASN A 587 " (cutoff:3.500A) Proline residue: A 592 - end of helix Proline residue: A 597 - end of helix removed outlier: 3.812A pdb=" N SER A 601 " --> pdb=" O PRO A 597 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER A 602 " --> pdb=" O MET A 598 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER A 607 " --> pdb=" O MET A 603 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL A 608 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 613 " --> pdb=" O SER A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 686 Processing helix chain 'A' and resid 714 through 721 Processing helix chain 'A' and resid 726 through 737 Processing helix chain 'A' and resid 738 through 746 removed outlier: 3.774A pdb=" N ASP A 742 " --> pdb=" O ALA A 738 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU A 744 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N MET A 745 " --> pdb=" O PRO A 741 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU A 746 " --> pdb=" O ASP A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 778 removed outlier: 3.673A pdb=" N ASN A 778 " --> pdb=" O ALA A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 803 Processing helix chain 'A' and resid 824 through 828 Processing helix chain 'A' and resid 848 through 852 removed outlier: 3.626A pdb=" N LYS A 851 " --> pdb=" O LEU A 848 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS A 852 " --> pdb=" O LEU A 849 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 848 through 852' Processing helix chain 'A' and resid 964 through 975 Processing helix chain 'A' and resid 975 through 1005 removed outlier: 3.619A pdb=" N PHE A 981 " --> pdb=" O PHE A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1009 Processing helix chain 'A' and resid 1016 through 1065 removed outlier: 3.800A pdb=" N GLN A1034 " --> pdb=" O LEU A1030 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY A1035 " --> pdb=" O GLY A1031 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA A1041 " --> pdb=" O PHE A1037 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TRP A1044 " --> pdb=" O ILE A1040 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS A1057 " --> pdb=" O SER A1053 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS A1058 " --> pdb=" O ASN A1054 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A1061 " --> pdb=" O HIS A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1075 removed outlier: 3.841A pdb=" N PHE A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1084 removed outlier: 3.966A pdb=" N ILE A1080 " --> pdb=" O PRO A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1094 removed outlier: 4.008A pdb=" N ASP A1092 " --> pdb=" O ILE A1088 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A1094 " --> pdb=" O THR A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1118 removed outlier: 4.102A pdb=" N SER A1101 " --> pdb=" O GLN A1097 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A1108 " --> pdb=" O THR A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1168 removed outlier: 4.021A pdb=" N ILE A1126 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE A1128 " --> pdb=" O THR A1124 " (cutoff:3.500A) Proline residue: A1129 - end of helix removed outlier: 3.748A pdb=" N PHE A1140 " --> pdb=" O SER A1136 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER A1143 " --> pdb=" O MET A1139 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A1146 " --> pdb=" O VAL A1142 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLN A1147 " --> pdb=" O SER A1143 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A1157 " --> pdb=" O SER A1153 " (cutoff:3.500A) Proline residue: A1158 - end of helix Processing helix chain 'A' and resid 1169 through 1177 removed outlier: 3.667A pdb=" N ILE A1173 " --> pdb=" O GLY A1169 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A1175 " --> pdb=" O PRO A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1213 removed outlier: 3.732A pdb=" N VAL A1188 " --> pdb=" O LYS A1184 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG A1189 " --> pdb=" O HIS A1185 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR A1192 " --> pdb=" O VAL A1188 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN A1193 " --> pdb=" O ARG A1189 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N CYS A1196 " --> pdb=" O THR A1192 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER A1199 " --> pdb=" O LYS A1195 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A1203 " --> pdb=" O SER A1199 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A1207 " --> pdb=" O SER A1203 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA A1208 " --> pdb=" O ASN A1204 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG A1210 " --> pdb=" O TRP A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1229 removed outlier: 3.973A pdb=" N VAL A1219 " --> pdb=" O GLY A1215 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A1222 " --> pdb=" O THR A1218 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1246 removed outlier: 3.961A pdb=" N PHE A1240 " --> pdb=" O ASP A1236 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A1241 " --> pdb=" O THR A1237 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A1245 " --> pdb=" O VAL A1241 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A1246 " --> pdb=" O LEU A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1266 removed outlier: 3.976A pdb=" N ASN A1253 " --> pdb=" O THR A1249 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP A1254 " --> pdb=" O GLN A1250 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A1256 " --> pdb=" O LEU A1252 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A1259 " --> pdb=" O LEU A1255 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A1261 " --> pdb=" O ARG A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1277 removed outlier: 3.682A pdb=" N TYR A1275 " --> pdb=" O ARG A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1348 removed outlier: 3.590A pdb=" N THR A1344 " --> pdb=" O LYS A1340 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A1348 " --> pdb=" O THR A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1368 No H-bonds generated for 'chain 'A' and resid 1366 through 1368' Processing helix chain 'A' and resid 1369 through 1375 Processing helix chain 'A' and resid 1391 through 1396 Processing helix chain 'A' and resid 1402 through 1413 Processing helix chain 'A' and resid 1415 through 1422 Processing helix chain 'A' and resid 1424 through 1427 Processing helix chain 'A' and resid 1431 through 1435 Processing helix chain 'A' and resid 1438 through 1454 Processing helix chain 'A' and resid 1468 through 1483 Processing helix chain 'A' and resid 1494 through 1498 Processing helix chain 'A' and resid 1517 through 1524 Processing helix chain 'A' and resid 1526 through 1533 Processing sheet with id=AA1, first strand: chain 'A' and resid 627 through 629 removed outlier: 6.189A pdb=" N ARG A 628 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 654 through 657 removed outlier: 5.440A pdb=" N ALA A 642 " --> pdb=" O ASP A 656 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N SER A 643 " --> pdb=" O VAL A 691 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU A 689 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.176A pdb=" N ALA A 702 " --> pdb=" O LEU A 783 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU A 830 " --> pdb=" O LEU A 666 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1317 through 1324 removed outlier: 7.256A pdb=" N ARG A1318 " --> pdb=" O GLN A1306 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLN A1306 " --> pdb=" O ARG A1318 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE A1320 " --> pdb=" O ASN A1304 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N PHE A1302 " --> pdb=" O ILE A1359 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE A1359 " --> pdb=" O PHE A1302 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ASN A1304 " --> pdb=" O GLN A1357 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLN A1357 " --> pdb=" O ASN A1304 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1377 through 1380 removed outlier: 6.471A pdb=" N LYS A1329 " --> pdb=" O LYS A1503 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N MET A1505 " --> pdb=" O LYS A1329 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLY A1331 " --> pdb=" O MET A1505 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N LEU A1507 " --> pdb=" O GLY A1331 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL A1333 " --> pdb=" O LEU A1507 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU A1514 " --> pdb=" O VAL A1506 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ASP A1508 " --> pdb=" O ILE A1512 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ILE A1512 " --> pdb=" O ASP A1508 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1389 through 1390 638 hydrogen bonds defined for protein. 1860 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: 5.17 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11234 1.03 - 1.23: 19 1.23 - 1.42: 4631 1.42 - 1.62: 6502 1.62 - 1.81: 94 Bond restraints: 22480 Sorted by residual: bond pdb=" CA PHE A1084 " pdb=" CB PHE A1084 " ideal model delta sigma weight residual 1.528 1.545 -0.017 1.35e-02 5.49e+03 1.61e+00 bond pdb=" CA ASP A 786 " pdb=" CB ASP A 786 " ideal model delta sigma weight residual 1.522 1.530 -0.007 7.00e-03 2.04e+04 1.10e+00 bond pdb=" CA CYS A 142 " pdb=" C CYS A 142 " ideal model delta sigma weight residual 1.523 1.508 0.014 1.41e-02 5.03e+03 1.05e+00 bond pdb=" CA ASP A 786 " pdb=" C ASP A 786 " ideal model delta sigma weight residual 1.531 1.524 0.008 7.40e-03 1.83e+04 1.03e+00 bond pdb=" CB TRP A 46 " pdb=" CG TRP A 46 " ideal model delta sigma weight residual 1.498 1.528 -0.030 3.10e-02 1.04e+03 9.39e-01 ... (remaining 22475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 38153 1.11 - 2.22: 2395 2.22 - 3.33: 126 3.33 - 4.45: 41 4.45 - 5.56: 5 Bond angle restraints: 40720 Sorted by residual: angle pdb=" N VAL A 840 " pdb=" CA VAL A 840 " pdb=" C VAL A 840 " ideal model delta sigma weight residual 111.62 109.07 2.55 7.90e-01 1.60e+00 1.05e+01 angle pdb=" N LYS A 757 " pdb=" CA LYS A 757 " pdb=" CB LYS A 757 " ideal model delta sigma weight residual 114.17 110.52 3.65 1.14e+00 7.69e-01 1.03e+01 angle pdb=" N ILE A1040 " pdb=" CA ILE A1040 " pdb=" C ILE A1040 " ideal model delta sigma weight residual 112.98 109.39 3.59 1.25e+00 6.40e-01 8.26e+00 angle pdb=" N PHE A1084 " pdb=" CA PHE A1084 " pdb=" C PHE A1084 " ideal model delta sigma weight residual 112.26 108.78 3.48 1.32e+00 5.74e-01 6.93e+00 angle pdb=" N PHE A1084 " pdb=" CA PHE A1084 " pdb=" CB PHE A1084 " ideal model delta sigma weight residual 111.17 106.88 4.29 1.64e+00 3.72e-01 6.84e+00 ... (remaining 40715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 9302 17.84 - 35.67: 902 35.67 - 53.51: 231 53.51 - 71.35: 60 71.35 - 89.19: 9 Dihedral angle restraints: 10504 sinusoidal: 5686 harmonic: 4818 Sorted by residual: dihedral pdb=" CB GLU A 647 " pdb=" CG GLU A 647 " pdb=" CD GLU A 647 " pdb=" OE1 GLU A 647 " ideal model delta sinusoidal sigma weight residual 0.00 -89.19 89.19 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU A 614 " pdb=" CG GLU A 614 " pdb=" CD GLU A 614 " pdb=" OE1 GLU A 614 " ideal model delta sinusoidal sigma weight residual 0.00 88.77 -88.77 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CA HIS A 823 " pdb=" C HIS A 823 " pdb=" N PHE A 824 " pdb=" CA PHE A 824 " ideal model delta harmonic sigma weight residual -180.00 -164.55 -15.45 0 5.00e+00 4.00e-02 9.55e+00 ... (remaining 10501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1142 0.028 - 0.055: 423 0.055 - 0.083: 135 0.083 - 0.111: 65 0.111 - 0.139: 19 Chirality restraints: 1784 Sorted by residual: chirality pdb=" CB ILE A 479 " pdb=" CA ILE A 479 " pdb=" CG1 ILE A 479 " pdb=" CG2 ILE A 479 " both_signs ideal model delta sigma weight residual False 2.64 2.78 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE A1524 " pdb=" N ILE A1524 " pdb=" C ILE A1524 " pdb=" CB ILE A1524 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ILE A 759 " pdb=" N ILE A 759 " pdb=" C ILE A 759 " pdb=" CB ILE A 759 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 1781 not shown) Planarity restraints: 3220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 746 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO A 747 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 747 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 747 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A1084 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" C PHE A1084 " 0.033 2.00e-02 2.50e+03 pdb=" O PHE A1084 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA A1085 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A1157 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO A1158 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A1158 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A1158 " -0.021 5.00e-02 4.00e+02 ... (remaining 3217 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1097 2.18 - 2.78: 45268 2.78 - 3.39: 62741 3.39 - 3.99: 77298 3.99 - 4.60: 121616 Nonbonded interactions: 308020 Sorted by model distance: nonbonded pdb=" O PHE A 800 " pdb=" H GLY A 805 " model vdw 1.573 2.450 nonbonded pdb=" OE1 GLN A 707 " pdb=" H GLN A 707 " model vdw 1.581 2.450 nonbonded pdb="HD21 ASN A 712 " pdb=" OE1 GLU A1165 " model vdw 1.590 2.450 nonbonded pdb=" O LEU A1211 " pdb=" H GLY A1215 " model vdw 1.610 2.450 nonbonded pdb=" O ALA A1002 " pdb="HH21 ARG A1023 " model vdw 1.649 2.450 ... (remaining 308015 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.130 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.830 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 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 : 0.003 0.036 11229 Z= 0.140 Angle : 0.551 5.557 15227 Z= 0.320 Chirality : 0.037 0.139 1784 Planarity : 0.003 0.050 1887 Dihedral : 15.961 89.185 4073 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.98 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 20.77 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.23), residues: 1375 helix: -0.21 (0.18), residues: 864 sheet: 0.29 (0.57), residues: 90 loop : -0.41 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 393 TYR 0.010 0.001 TYR A 206 PHE 0.009 0.001 PHE A1240 TRP 0.008 0.001 TRP A 358 HIS 0.002 0.001 HIS A 692 Details of bonding type rmsd covalent geometry : bond 0.00285 (11228) covalent geometry : angle 0.55068 (15225) SS BOND : bond 0.00026 ( 1) SS BOND : angle 0.37120 ( 2) hydrogen bonds : bond 0.25396 ( 638) hydrogen bonds : angle 9.24377 ( 1860) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8349 (mm-30) REVERT: A 362 LEU cc_start: 0.9336 (tp) cc_final: 0.9120 (tt) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.2138 time to fit residues: 78.1568 Evaluate side-chains 177 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 0.6980 overall best weight: 6.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 GLN A 767 GLN A1097 GLN A1247 ASN A1303 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.052845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.038930 restraints weight = 188290.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.040781 restraints weight = 78432.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.042005 restraints weight = 44349.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.042836 restraints weight = 29790.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.043394 restraints weight = 22528.053| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11229 Z= 0.283 Angle : 0.690 6.286 15227 Z= 0.385 Chirality : 0.040 0.139 1784 Planarity : 0.005 0.048 1887 Dihedral : 3.932 15.213 1474 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.71 % Favored : 96.22 % Rotamer: Outliers : 2.93 % Allowed : 21.25 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.22), residues: 1375 helix: -0.17 (0.16), residues: 880 sheet: 0.07 (0.59), residues: 80 loop : -0.49 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1174 TYR 0.011 0.001 TYR A 776 PHE 0.016 0.002 PHE A 337 TRP 0.011 0.001 TRP A 41 HIS 0.003 0.001 HIS A 648 Details of bonding type rmsd covalent geometry : bond 0.00532 (11228) covalent geometry : angle 0.69049 (15225) SS BOND : bond 0.00161 ( 1) SS BOND : angle 0.24948 ( 2) hydrogen bonds : bond 0.06798 ( 638) hydrogen bonds : angle 6.12493 ( 1860) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 GLU cc_start: 0.9373 (mm-30) cc_final: 0.8969 (mm-30) REVERT: A 362 LEU cc_start: 0.9615 (tp) cc_final: 0.9369 (tt) REVERT: A 438 MET cc_start: 0.9358 (ppp) cc_final: 0.9137 (tmm) REVERT: A 513 LYS cc_start: 0.9908 (mmmt) cc_final: 0.9647 (tttt) REVERT: A 1093 ASP cc_start: 0.9176 (m-30) cc_final: 0.8831 (m-30) outliers start: 36 outliers final: 21 residues processed: 195 average time/residue: 0.1820 time to fit residues: 54.3680 Evaluate side-chains 179 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1157 SER Chi-restraints excluded: chain A residue 1445 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 16 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 131 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 136 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.052935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.039049 restraints weight = 193932.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.040860 restraints weight = 79905.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.042063 restraints weight = 45282.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.042892 restraints weight = 30649.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.043421 restraints weight = 23274.617| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11229 Z= 0.294 Angle : 0.652 8.803 15227 Z= 0.364 Chirality : 0.039 0.205 1784 Planarity : 0.004 0.044 1887 Dihedral : 3.964 15.633 1474 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.78 % Favored : 96.15 % Rotamer: Outliers : 2.93 % Allowed : 22.07 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.21), residues: 1375 helix: -0.18 (0.16), residues: 881 sheet: -0.20 (0.57), residues: 80 loop : -0.81 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1083 TYR 0.011 0.001 TYR A 776 PHE 0.013 0.001 PHE A 200 TRP 0.011 0.001 TRP A 41 HIS 0.003 0.001 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00546 (11228) covalent geometry : angle 0.65211 (15225) SS BOND : bond 0.00362 ( 1) SS BOND : angle 0.36660 ( 2) hydrogen bonds : bond 0.05640 ( 638) hydrogen bonds : angle 5.79618 ( 1860) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.9731 (OUTLIER) cc_final: 0.9360 (m-10) REVERT: A 387 LYS cc_start: 0.9151 (mtpt) cc_final: 0.8876 (mtpp) REVERT: A 438 MET cc_start: 0.9389 (ppp) cc_final: 0.9163 (tmm) REVERT: A 1093 ASP cc_start: 0.9136 (m-30) cc_final: 0.8792 (m-30) REVERT: A 1443 GLN cc_start: 0.9561 (tp40) cc_final: 0.9274 (tm-30) outliers start: 36 outliers final: 26 residues processed: 177 average time/residue: 0.1929 time to fit residues: 53.1050 Evaluate side-chains 171 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1134 TYR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1157 SER Chi-restraints excluded: chain A residue 1270 GLU Chi-restraints excluded: chain A residue 1372 ASP Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1445 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 122 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.052973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.038903 restraints weight = 191743.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.040765 restraints weight = 77881.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.041980 restraints weight = 44023.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.042813 restraints weight = 29721.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.043310 restraints weight = 22574.497| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11229 Z= 0.195 Angle : 0.601 8.014 15227 Z= 0.320 Chirality : 0.038 0.137 1784 Planarity : 0.004 0.042 1887 Dihedral : 3.851 15.842 1474 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.71 % Favored : 96.22 % Rotamer: Outliers : 2.69 % Allowed : 21.91 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.22), residues: 1375 helix: 0.26 (0.16), residues: 886 sheet: -0.36 (0.58), residues: 80 loop : -0.75 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1083 TYR 0.012 0.001 TYR A 101 PHE 0.010 0.001 PHE A 337 TRP 0.009 0.001 TRP A 709 HIS 0.002 0.001 HIS A1428 Details of bonding type rmsd covalent geometry : bond 0.00378 (11228) covalent geometry : angle 0.60132 (15225) SS BOND : bond 0.00267 ( 1) SS BOND : angle 0.30601 ( 2) hydrogen bonds : bond 0.05022 ( 638) hydrogen bonds : angle 5.31695 ( 1860) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.9729 (OUTLIER) cc_final: 0.9374 (m-10) REVERT: A 387 LYS cc_start: 0.9153 (mtpt) cc_final: 0.8875 (mtpp) REVERT: A 438 MET cc_start: 0.9403 (ppp) cc_final: 0.9162 (tmm) REVERT: A 440 MET cc_start: 0.9211 (mmm) cc_final: 0.8948 (mmm) outliers start: 33 outliers final: 25 residues processed: 169 average time/residue: 0.1817 time to fit residues: 48.2839 Evaluate side-chains 171 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1134 TYR Chi-restraints excluded: chain A residue 1157 SER Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1445 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 137 optimal weight: 4.9990 chunk 121 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 114 optimal weight: 0.0980 chunk 86 optimal weight: 9.9990 overall best weight: 4.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.052288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.038310 restraints weight = 194617.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.040148 restraints weight = 80125.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.041356 restraints weight = 45493.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.042164 restraints weight = 30782.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.042744 restraints weight = 23459.084| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11229 Z= 0.214 Angle : 0.592 6.755 15227 Z= 0.320 Chirality : 0.038 0.155 1784 Planarity : 0.004 0.049 1887 Dihedral : 3.820 16.525 1474 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.85 % Favored : 96.07 % Rotamer: Outliers : 2.93 % Allowed : 21.91 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.22), residues: 1375 helix: 0.47 (0.16), residues: 886 sheet: -0.32 (0.54), residues: 90 loop : -0.72 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 498 TYR 0.011 0.001 TYR A 776 PHE 0.012 0.001 PHE A 337 TRP 0.010 0.001 TRP A 709 HIS 0.003 0.001 HIS A1057 Details of bonding type rmsd covalent geometry : bond 0.00410 (11228) covalent geometry : angle 0.59165 (15225) SS BOND : bond 0.00290 ( 1) SS BOND : angle 0.41874 ( 2) hydrogen bonds : bond 0.04706 ( 638) hydrogen bonds : angle 5.26654 ( 1860) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.9704 (OUTLIER) cc_final: 0.9347 (m-10) REVERT: A 387 LYS cc_start: 0.9185 (mtpt) cc_final: 0.8910 (mtpp) REVERT: A 438 MET cc_start: 0.9393 (ppp) cc_final: 0.9159 (tmm) REVERT: A 440 MET cc_start: 0.9157 (mmm) cc_final: 0.8947 (mmm) REVERT: A 607 SER cc_start: 0.9590 (OUTLIER) cc_final: 0.9359 (p) outliers start: 36 outliers final: 28 residues processed: 165 average time/residue: 0.1795 time to fit residues: 47.2429 Evaluate side-chains 175 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1134 TYR Chi-restraints excluded: chain A residue 1157 SER Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1445 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 119 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 137 optimal weight: 30.0000 chunk 96 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 chunk 57 optimal weight: 0.0870 overall best weight: 2.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.052648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.038976 restraints weight = 190008.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.040809 restraints weight = 76687.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.042009 restraints weight = 42849.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.042813 restraints weight = 28669.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.043391 restraints weight = 21627.075| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11229 Z= 0.148 Angle : 0.575 7.337 15227 Z= 0.300 Chirality : 0.038 0.181 1784 Planarity : 0.004 0.046 1887 Dihedral : 3.737 16.079 1474 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.64 % Favored : 96.29 % Rotamer: Outliers : 2.52 % Allowed : 22.48 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.22), residues: 1375 helix: 0.91 (0.17), residues: 886 sheet: -0.23 (0.55), residues: 90 loop : -0.56 (0.33), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 498 TYR 0.011 0.001 TYR A 101 PHE 0.011 0.001 PHE A 337 TRP 0.009 0.001 TRP A 709 HIS 0.002 0.001 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00302 (11228) covalent geometry : angle 0.57520 (15225) SS BOND : bond 0.00163 ( 1) SS BOND : angle 0.26975 ( 2) hydrogen bonds : bond 0.04541 ( 638) hydrogen bonds : angle 4.95848 ( 1860) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.9690 (OUTLIER) cc_final: 0.9372 (m-10) REVERT: A 387 LYS cc_start: 0.9148 (mtpt) cc_final: 0.8872 (mtpp) REVERT: A 438 MET cc_start: 0.9382 (ppp) cc_final: 0.9142 (tmm) REVERT: A 440 MET cc_start: 0.9179 (mmm) cc_final: 0.8978 (mmm) REVERT: A 502 MET cc_start: 0.9613 (ttp) cc_final: 0.9056 (ttp) REVERT: A 607 SER cc_start: 0.9569 (t) cc_final: 0.9318 (p) REVERT: A 1226 MET cc_start: 0.9620 (mmt) cc_final: 0.9406 (mmm) outliers start: 31 outliers final: 28 residues processed: 168 average time/residue: 0.1767 time to fit residues: 47.1494 Evaluate side-chains 175 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1134 TYR Chi-restraints excluded: chain A residue 1157 SER Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1445 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 121 optimal weight: 7.9990 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.053055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.039112 restraints weight = 194277.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.040961 restraints weight = 78391.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.042167 restraints weight = 44056.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.042982 restraints weight = 29598.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.043500 restraints weight = 22496.770| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11229 Z= 0.198 Angle : 0.590 7.492 15227 Z= 0.316 Chirality : 0.038 0.160 1784 Planarity : 0.004 0.046 1887 Dihedral : 3.710 16.475 1474 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.15 % Favored : 95.78 % Rotamer: Outliers : 3.09 % Allowed : 22.72 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.23), residues: 1375 helix: 0.92 (0.17), residues: 889 sheet: -0.19 (0.55), residues: 90 loop : -0.50 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 498 TYR 0.011 0.001 TYR A 101 PHE 0.029 0.001 PHE A1084 TRP 0.010 0.001 TRP A 709 HIS 0.002 0.001 HIS A1057 Details of bonding type rmsd covalent geometry : bond 0.00384 (11228) covalent geometry : angle 0.58992 (15225) SS BOND : bond 0.00164 ( 1) SS BOND : angle 0.30458 ( 2) hydrogen bonds : bond 0.04371 ( 638) hydrogen bonds : angle 5.04233 ( 1860) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 LYS cc_start: 0.9193 (mtpt) cc_final: 0.8840 (mtpp) REVERT: A 438 MET cc_start: 0.9382 (ppp) cc_final: 0.9150 (tmm) REVERT: A 440 MET cc_start: 0.9113 (mmm) cc_final: 0.8846 (mmm) REVERT: A 607 SER cc_start: 0.9579 (OUTLIER) cc_final: 0.9340 (p) REVERT: A 1258 MET cc_start: 0.9359 (mmt) cc_final: 0.9141 (mmp) REVERT: A 1261 GLU cc_start: 0.8774 (mp0) cc_final: 0.8534 (mp0) outliers start: 38 outliers final: 30 residues processed: 165 average time/residue: 0.1912 time to fit residues: 50.6262 Evaluate side-chains 171 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1134 TYR Chi-restraints excluded: chain A residue 1157 SER Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1445 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 81 optimal weight: 0.9990 chunk 109 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 88 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.053306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.039386 restraints weight = 191645.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.041260 restraints weight = 77725.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.042508 restraints weight = 43656.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.043316 restraints weight = 29222.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.043885 restraints weight = 22221.735| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11229 Z= 0.139 Angle : 0.572 7.730 15227 Z= 0.297 Chirality : 0.038 0.150 1784 Planarity : 0.003 0.047 1887 Dihedral : 3.664 16.277 1474 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.27 % Favored : 96.65 % Rotamer: Outliers : 3.01 % Allowed : 23.21 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.23), residues: 1375 helix: 1.15 (0.17), residues: 893 sheet: -0.15 (0.55), residues: 90 loop : -0.36 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 498 TYR 0.010 0.001 TYR A 101 PHE 0.013 0.001 PHE A 562 TRP 0.009 0.001 TRP A 709 HIS 0.002 0.001 HIS A1057 Details of bonding type rmsd covalent geometry : bond 0.00287 (11228) covalent geometry : angle 0.57207 (15225) SS BOND : bond 0.00023 ( 1) SS BOND : angle 0.06473 ( 2) hydrogen bonds : bond 0.04307 ( 638) hydrogen bonds : angle 4.83176 ( 1860) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.9647 (OUTLIER) cc_final: 0.9335 (m-10) REVERT: A 387 LYS cc_start: 0.9192 (mtpt) cc_final: 0.8843 (mtpp) REVERT: A 438 MET cc_start: 0.9373 (ppp) cc_final: 0.9135 (tmm) REVERT: A 440 MET cc_start: 0.9064 (mmm) cc_final: 0.8795 (mmm) REVERT: A 513 LYS cc_start: 0.9915 (mmmt) cc_final: 0.9657 (mtmm) REVERT: A 607 SER cc_start: 0.9572 (t) cc_final: 0.9307 (p) REVERT: A 1460 LEU cc_start: 0.9731 (OUTLIER) cc_final: 0.9321 (tt) outliers start: 37 outliers final: 30 residues processed: 173 average time/residue: 0.1847 time to fit residues: 51.0932 Evaluate side-chains 175 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1134 TYR Chi-restraints excluded: chain A residue 1157 SER Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1445 LEU Chi-restraints excluded: chain A residue 1460 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 97 optimal weight: 0.0670 overall best weight: 3.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.053547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.039694 restraints weight = 192784.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.041532 restraints weight = 78913.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.042735 restraints weight = 44586.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.043525 restraints weight = 30044.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.044084 restraints weight = 22875.203| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11229 Z= 0.166 Angle : 0.578 8.062 15227 Z= 0.305 Chirality : 0.038 0.152 1784 Planarity : 0.003 0.047 1887 Dihedral : 3.637 16.252 1474 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.56 % Favored : 96.36 % Rotamer: Outliers : 2.77 % Allowed : 23.94 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.23), residues: 1375 helix: 1.17 (0.17), residues: 888 sheet: -0.09 (0.55), residues: 90 loop : -0.38 (0.33), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 498 TYR 0.010 0.001 TYR A 101 PHE 0.010 0.001 PHE A 580 TRP 0.009 0.001 TRP A 709 HIS 0.002 0.001 HIS A1057 Details of bonding type rmsd covalent geometry : bond 0.00331 (11228) covalent geometry : angle 0.57806 (15225) SS BOND : bond 0.00008 ( 1) SS BOND : angle 0.15238 ( 2) hydrogen bonds : bond 0.04196 ( 638) hydrogen bonds : angle 4.86542 ( 1860) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 LYS cc_start: 0.9173 (mtpt) cc_final: 0.8831 (mtpp) REVERT: A 438 MET cc_start: 0.9382 (ppp) cc_final: 0.9139 (tmm) REVERT: A 440 MET cc_start: 0.9109 (mmm) cc_final: 0.8854 (mmm) REVERT: A 607 SER cc_start: 0.9536 (t) cc_final: 0.9291 (p) REVERT: A 1460 LEU cc_start: 0.9734 (OUTLIER) cc_final: 0.9332 (tt) outliers start: 34 outliers final: 29 residues processed: 165 average time/residue: 0.1968 time to fit residues: 52.1150 Evaluate side-chains 173 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1134 TYR Chi-restraints excluded: chain A residue 1157 SER Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1445 LEU Chi-restraints excluded: chain A residue 1460 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 87 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 108 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.052948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.039283 restraints weight = 189781.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.041169 restraints weight = 78283.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.042408 restraints weight = 43974.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.043220 restraints weight = 29348.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.043779 restraints weight = 22112.719| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11229 Z= 0.122 Angle : 0.585 8.432 15227 Z= 0.297 Chirality : 0.039 0.175 1784 Planarity : 0.003 0.048 1887 Dihedral : 3.588 15.557 1474 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.05 % Favored : 96.87 % Rotamer: Outliers : 2.44 % Allowed : 24.27 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.23), residues: 1375 helix: 1.38 (0.17), residues: 888 sheet: -0.12 (0.55), residues: 90 loop : -0.26 (0.34), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 498 TYR 0.010 0.001 TYR A 319 PHE 0.008 0.001 PHE A 337 TRP 0.008 0.001 TRP A 709 HIS 0.002 0.001 HIS A1162 Details of bonding type rmsd covalent geometry : bond 0.00267 (11228) covalent geometry : angle 0.58468 (15225) SS BOND : bond 0.00076 ( 1) SS BOND : angle 0.19087 ( 2) hydrogen bonds : bond 0.04116 ( 638) hydrogen bonds : angle 4.65624 ( 1860) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.9745 (pt0) cc_final: 0.9491 (tm-30) REVERT: A 107 TYR cc_start: 0.9627 (OUTLIER) cc_final: 0.9330 (m-10) REVERT: A 387 LYS cc_start: 0.9181 (mtpt) cc_final: 0.8833 (mtpp) REVERT: A 438 MET cc_start: 0.9356 (ppp) cc_final: 0.9126 (tmm) REVERT: A 440 MET cc_start: 0.9105 (mmm) cc_final: 0.8845 (mmm) REVERT: A 502 MET cc_start: 0.9586 (ttp) cc_final: 0.8967 (ttp) REVERT: A 607 SER cc_start: 0.9544 (t) cc_final: 0.9306 (p) REVERT: A 1460 LEU cc_start: 0.9722 (OUTLIER) cc_final: 0.9323 (tt) REVERT: A 1505 MET cc_start: 0.9111 (mmt) cc_final: 0.8866 (mmt) outliers start: 30 outliers final: 26 residues processed: 173 average time/residue: 0.1779 time to fit residues: 49.6093 Evaluate side-chains 178 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TRP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1134 TYR Chi-restraints excluded: chain A residue 1157 SER Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1445 LEU Chi-restraints excluded: chain A residue 1460 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 8 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 3 optimal weight: 0.0770 chunk 125 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.053353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.039454 restraints weight = 194272.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.041304 restraints weight = 77729.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.042516 restraints weight = 43404.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.043330 restraints weight = 29095.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.043850 restraints weight = 22115.233| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11229 Z= 0.158 Angle : 0.583 8.478 15227 Z= 0.305 Chirality : 0.038 0.155 1784 Planarity : 0.003 0.047 1887 Dihedral : 3.558 15.854 1474 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.56 % Favored : 96.36 % Rotamer: Outliers : 2.12 % Allowed : 24.76 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.23), residues: 1375 helix: 1.37 (0.17), residues: 888 sheet: -0.17 (0.55), residues: 90 loop : -0.30 (0.34), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 498 TYR 0.010 0.001 TYR A 101 PHE 0.011 0.001 PHE A1163 TRP 0.009 0.001 TRP A 709 HIS 0.002 0.001 HIS A1057 Details of bonding type rmsd covalent geometry : bond 0.00318 (11228) covalent geometry : angle 0.58345 (15225) SS BOND : bond 0.00011 ( 1) SS BOND : angle 0.12374 ( 2) hydrogen bonds : bond 0.04034 ( 638) hydrogen bonds : angle 4.76389 ( 1860) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3620.58 seconds wall clock time: 62 minutes 44.52 seconds (3764.52 seconds total)