Starting phenix.real_space_refine on Thu May 22 12:18:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxq_36709/05_2025/8jxq_36709_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxq_36709/05_2025/8jxq_36709.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jxq_36709/05_2025/8jxq_36709.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxq_36709/05_2025/8jxq_36709.map" model { file = "/net/cci-nas-00/data/ceres_data/8jxq_36709/05_2025/8jxq_36709_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxq_36709/05_2025/8jxq_36709_trim.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.045 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 59 5.16 5 C 7228 2.51 5 N 1829 2.21 5 O 1994 1.98 5 H 11287 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 22397 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 22314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1388, 22314 Classifications: {'peptide': 1388} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 1345} Chain breaks: 3 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'CLR': 1, 'FEI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.34, per 1000 atoms: 0.46 Number of scatterers: 22397 At special positions: 0 Unit cell: (94.16, 123.05, 153.01, 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 59 16.00 O 1994 8.00 N 1829 7.00 C 7228 6.00 H 11287 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: 5.67 Conformation dependent library (CDL) restraints added in 1.7 seconds 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2624 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 6 sheets defined 65.6% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 12 through 17 Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 33 through 42 Processing helix chain 'A' and resid 43 through 54 removed outlier: 4.349A pdb=" N VAL A 51 " --> pdb=" O GLN A 47 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A 54 " --> pdb=" O HIS A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 89 removed outlier: 3.783A pdb=" N VAL A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 121 removed outlier: 3.742A pdb=" N TYR A 101 " --> pdb=" O PRO A 97 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN A 103 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Proline residue: A 104 - end of helix removed outlier: 3.509A pdb=" N LEU A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 124 No H-bonds generated for 'chain 'A' and resid 122 through 124' Processing helix chain 'A' and resid 134 through 139 removed outlier: 3.615A pdb=" N LEU A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 156 removed outlier: 3.527A pdb=" N GLN A 148 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR A 149 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE A 151 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN A 156 " --> pdb=" O ARG A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 184 removed outlier: 3.787A pdb=" N ILE A 170 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 176 " --> pdb=" O TYR A 172 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 removed outlier: 3.734A pdb=" N SER A 196 " --> pdb=" O ASN A 193 " (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 217 Processing helix chain 'A' and resid 234 through 257 removed outlier: 3.664A pdb=" N SER A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 257 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 325 through 335 removed outlier: 3.627A pdb=" N VAL A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 341 Processing helix chain 'A' and resid 342 through 352 removed outlier: 3.738A pdb=" N LEU A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 364 removed outlier: 3.661A pdb=" N GLY A 360 " --> pdb=" O TYR A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 375 through 380 removed outlier: 3.808A pdb=" N GLN A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 396 through 405 removed outlier: 3.558A pdb=" N LYS A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 405 " --> pdb=" O TYR A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 407 No H-bonds generated for 'chain 'A' and resid 406 through 407' Processing helix chain 'A' and resid 408 through 412 Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.647A pdb=" N VAL A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 426 removed outlier: 3.676A pdb=" N SER A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 460 removed outlier: 4.287A pdb=" N VAL A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A 458 " --> pdb=" O PHE A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 472 removed outlier: 4.010A pdb=" N GLY A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 490 removed outlier: 3.980A pdb=" N SER A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A 482 " --> pdb=" O ALA A 478 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A 487 " --> pdb=" O LYS A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 507 removed outlier: 3.702A pdb=" N LEU A 499 " --> pdb=" O LYS A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 515 removed outlier: 3.524A pdb=" N PHE A 515 " --> pdb=" O ILE A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 541 removed outlier: 4.161A pdb=" N LYS A 531 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASN A 535 " --> pdb=" O LYS A 531 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE A 539 " --> pdb=" O ASN A 535 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 552 Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.521A pdb=" N SER A 558 " --> pdb=" O PRO A 554 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 559 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE A 562 " --> pdb=" O SER A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 584 removed outlier: 3.664A pdb=" N PHE A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N THR A 581 " --> pdb=" O GLN A 577 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER A 582 " --> pdb=" O LYS A 578 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR A 584 " --> pdb=" O PHE A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 604 removed outlier: 3.893A pdb=" N LEU A 596 " --> pdb=" O PRO A 592 " (cutoff:3.500A) Proline residue: A 597 - end of helix removed outlier: 3.603A pdb=" N SER A 602 " --> pdb=" O MET A 598 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 617 Processing helix chain 'A' and resid 676 through 685 Processing helix chain 'A' and resid 715 through 721 Processing helix chain 'A' and resid 726 through 737 Processing helix chain 'A' and resid 739 through 746 Processing helix chain 'A' and resid 748 through 751 Processing helix chain 'A' and resid 755 through 759 Processing helix chain 'A' and resid 762 through 778 removed outlier: 3.583A 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 844 through 852 Processing helix chain 'A' and resid 853 through 866 Processing helix chain 'A' and resid 964 through 975 removed outlier: 3.647A pdb=" N GLY A 975 " --> pdb=" O LEU A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 981 removed outlier: 3.889A pdb=" N PHE A 981 " --> pdb=" O PHE A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1001 removed outlier: 3.810A pdb=" N ASN A 989 " --> pdb=" O ALA A 985 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 994 " --> pdb=" O SER A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1009 Processing helix chain 'A' and resid 1016 through 1030 removed outlier: 4.109A pdb=" N MET A1022 " --> pdb=" O SER A1018 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG A1023 " --> pdb=" O GLN A1019 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL A1024 " --> pdb=" O ARG A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1053 removed outlier: 3.798A pdb=" N TRP A1044 " --> pdb=" O ILE A1040 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER A1045 " --> pdb=" O ALA A1041 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS A1051 " --> pdb=" O PHE A1047 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A1052 " --> pdb=" O GLY A1048 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER A1053 " --> pdb=" O PHE A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1065 removed outlier: 3.513A pdb=" N LYS A1058 " --> pdb=" O ASN A1054 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN A1059 " --> pdb=" O ILE A1055 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A1065 " --> pdb=" O LEU A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1075 removed outlier: 3.852A pdb=" N PHE A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1081 removed outlier: 3.801A pdb=" N ILE A1080 " --> pdb=" O PRO A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1089 through 1111 removed outlier: 3.789A pdb=" N ASP A1093 " --> pdb=" O SER A1089 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LEU A1095 " --> pdb=" O VAL A1091 " (cutoff:3.500A) Proline residue: A1096 - end of helix removed outlier: 3.700A pdb=" N SER A1101 " --> pdb=" O GLN A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1120 removed outlier: 3.738A pdb=" N CYS A1117 " --> pdb=" O LEU A1113 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A1119 " --> pdb=" O MET A1115 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR A1120 " --> pdb=" O ILE A1116 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1154 removed outlier: 3.927A pdb=" N ILE A1128 " --> pdb=" O THR A1124 " (cutoff:3.500A) Proline residue: A1129 - end of helix removed outlier: 4.008A pdb=" N GLN A1147 " --> pdb=" O SER A1143 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A1151 " --> pdb=" O GLN A1147 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP A1152 " --> pdb=" O LEU A1148 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER A1153 " --> pdb=" O ARG A1149 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A1154 " --> pdb=" O ARG A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1169 removed outlier: 4.185A pdb=" N TYR A1160 " --> pdb=" O ARG A1156 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A1165 " --> pdb=" O SER A1161 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1177 removed outlier: 3.620A pdb=" N ILE A1173 " --> pdb=" O GLY A1169 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A1176 " --> pdb=" O VAL A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1187 Processing helix chain 'A' and resid 1190 through 1202 removed outlier: 3.540A pdb=" N LYS A1195 " --> pdb=" O ASP A1191 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N CYS A1196 " --> pdb=" O THR A1192 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER A1199 " --> pdb=" O LYS A1195 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP A1200 " --> pdb=" O CYS A1196 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A1202 " --> pdb=" O PHE A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1204 through 1212 removed outlier: 3.746A pdb=" N ARG A1210 " --> pdb=" O TRP A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1222 Processing helix chain 'A' and resid 1234 through 1246 removed outlier: 3.566A pdb=" N VAL A1238 " --> pdb=" O SER A1234 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY A1239 " --> pdb=" O GLY A1235 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASN A1244 " --> pdb=" O PHE A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1265 removed outlier: 3.505A pdb=" N THR A1259 " --> pdb=" O LEU A1255 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER A1260 " --> pdb=" O VAL A1256 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A1262 " --> pdb=" O MET A1258 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU A1263 " --> pdb=" O THR A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1277 removed outlier: 3.600A pdb=" N GLU A1270 " --> pdb=" O ILE A1266 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR A1276 " --> pdb=" O ILE A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1348 removed outlier: 3.652A pdb=" N THR A1344 " --> pdb=" O LYS A1340 " (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 1535 Processing sheet with id=AA1, first strand: chain 'A' and resid 627 through 629 removed outlier: 3.703A pdb=" N GLU A 689 " --> pdb=" O THR A 645 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER A 643 " --> pdb=" O VAL A 691 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY A 693 " --> pdb=" O GLU A 641 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N GLU A 641 " --> pdb=" O GLY A 693 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ILE A 695 " --> pdb=" O PHE A 639 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N PHE A 639 " --> pdb=" O ILE A 695 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE A 697 " --> pdb=" O MET A 637 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N MET A 637 " --> pdb=" O ILE A 697 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET A 637 " --> pdb=" O ILE A 661 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 641 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL A 657 " --> pdb=" O GLU A 641 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N SER A 643 " --> pdb=" O ARG A 655 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG A 655 " --> pdb=" O SER A 643 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.453A pdb=" N TYR A 782 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N VAL A 818 " --> pdb=" O TYR A 782 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU A 784 " --> pdb=" O VAL A 818 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL A 667 " --> pdb=" O LEU A 817 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU A 666 " --> pdb=" O GLU A 830 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N VAL A 832 " --> pdb=" O LEU A 666 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA A 668 " --> pdb=" O VAL A 832 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LEU A 834 " --> pdb=" O ALA A 668 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE A 670 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE A 831 " --> pdb=" O LYS A 842 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LYS A 842 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL A 833 " --> pdb=" O VAL A 840 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 713 through 714 removed outlier: 3.705A pdb=" N GLY A 713 " --> pdb=" O ILE A 754 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1317 through 1324 removed outlier: 7.153A pdb=" N ARG A1318 " --> pdb=" O GLN A1306 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N GLN A1306 " --> pdb=" O ARG A1318 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ILE A1320 " --> pdb=" O ASN A1304 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N PHE A1302 " --> pdb=" O ILE A1359 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ILE A1359 " --> pdb=" O PHE A1302 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ASN A1304 " --> pdb=" O GLN A1357 " (cutoff:3.500A) removed outlier: 4.943A 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: 6.597A pdb=" N LEU A1458 " --> pdb=" O ILE A1489 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ILE A1491 " --> pdb=" O LEU A1458 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU A1460 " --> pdb=" O ILE A1491 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS A1329 " --> pdb=" O LYS A1503 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N MET A1505 " --> pdb=" O LYS A1329 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY A1331 " --> pdb=" O MET A1505 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU A1507 " --> pdb=" O GLY A1331 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL A1333 " --> pdb=" O LEU A1507 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU A1514 " --> pdb=" O VAL A1506 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ASP A1508 " --> pdb=" O ILE A1512 " (cutoff:3.500A) removed outlier: 5.345A 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 499 hydrogen bonds defined for protein. 1419 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: 9.06 Time building geometry restraints manager: 6.77 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: 11269 1.03 - 1.23: 99 1.23 - 1.43: 4579 1.43 - 1.62: 6595 1.62 - 1.82: 96 Bond restraints: 22638 Sorted by residual: bond pdb=" C32 FEI A1602 " pdb=" C33 FEI A1602 " ideal model delta sigma weight residual 1.332 1.529 -0.197 2.00e-02 2.50e+03 9.71e+01 bond pdb=" C53 FEI A1602 " pdb=" C54 FEI A1602 " ideal model delta sigma weight residual 1.336 1.528 -0.192 2.00e-02 2.50e+03 9.20e+01 bond pdb=" C28 FEI A1602 " pdb=" O29 FEI A1602 " ideal model delta sigma weight residual 1.220 1.400 -0.180 2.00e-02 2.50e+03 8.08e+01 bond pdb=" C24 FEI A1602 " pdb=" C25 FEI A1602 " ideal model delta sigma weight residual 1.349 1.528 -0.179 2.00e-02 2.50e+03 7.97e+01 bond pdb=" C50 FEI A1602 " pdb=" O51 FEI A1602 " ideal model delta sigma weight residual 1.221 1.396 -0.175 2.00e-02 2.50e+03 7.64e+01 ... (remaining 22633 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.73: 40936 3.73 - 7.45: 27 7.45 - 11.18: 12 11.18 - 14.91: 1 14.91 - 18.64: 3 Bond angle restraints: 40979 Sorted by residual: angle pdb=" C22 FEI A1602 " pdb=" C24 FEI A1602 " pdb=" C25 FEI A1602 " ideal model delta sigma weight residual 127.47 108.83 18.64 3.00e+00 1.11e-01 3.86e+01 angle pdb=" C03 FEI A1602 " pdb=" C46 FEI A1602 " pdb=" C47 FEI A1602 " ideal model delta sigma weight residual 129.40 112.53 16.87 3.00e+00 1.11e-01 3.16e+01 angle pdb=" C49 FEI A1602 " pdb=" C53 FEI A1602 " pdb=" C54 FEI A1602 " ideal model delta sigma weight residual 127.31 111.98 15.33 3.00e+00 1.11e-01 2.61e+01 angle pdb=" C26 FEI A1602 " pdb=" C32 FEI A1602 " pdb=" C33 FEI A1602 " ideal model delta sigma weight residual 125.80 113.41 12.39 3.00e+00 1.11e-01 1.70e+01 angle pdb=" N ILE A 396 " pdb=" CA ILE A 396 " pdb=" C ILE A 396 " ideal model delta sigma weight residual 111.90 108.77 3.13 8.10e-01 1.52e+00 1.49e+01 ... (remaining 40974 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.94: 10367 34.94 - 69.88: 251 69.88 - 104.82: 13 104.82 - 139.76: 0 139.76 - 174.70: 1 Dihedral angle restraints: 10632 sinusoidal: 5795 harmonic: 4837 Sorted by residual: dihedral pdb=" C09 FEI A1602 " pdb=" C12 FEI A1602 " pdb=" N11 FEI A1602 " pdb=" C13 FEI A1602 " ideal model delta sinusoidal sigma weight residual -80.60 94.10 -174.70 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CB CYS A 6 " pdb=" SG CYS A 6 " pdb=" SG CYS A 26 " pdb=" CB CYS A 26 " ideal model delta sinusoidal sigma weight residual 93.00 55.31 37.69 1 1.00e+01 1.00e-02 2.00e+01 dihedral pdb=" CA SER A 185 " pdb=" C SER A 185 " pdb=" N GLU A 186 " pdb=" CA GLU A 186 " ideal model delta harmonic sigma weight residual 180.00 159.85 20.15 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 10629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1131 0.029 - 0.057: 477 0.057 - 0.086: 115 0.086 - 0.115: 61 0.115 - 0.143: 16 Chirality restraints: 1800 Sorted by residual: chirality pdb=" CA ILE A1491 " pdb=" N ILE A1491 " pdb=" C ILE A1491 " pdb=" CB ILE A1491 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE A1380 " pdb=" N ILE A1380 " pdb=" C ILE A1380 " pdb=" CB ILE A1380 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-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 -0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 1797 not shown) Planarity restraints: 3239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C03 FEI A1602 " 0.562 2.00e-02 2.50e+03 2.32e-01 1.35e+03 pdb=" C46 FEI A1602 " -0.320 2.00e-02 2.50e+03 pdb=" C47 FEI A1602 " -0.175 2.00e-02 2.50e+03 pdb=" C48 FEI A1602 " -0.118 2.00e-02 2.50e+03 pdb=" C49 FEI A1602 " 0.015 2.00e-02 2.50e+03 pdb=" C50 FEI A1602 " 0.035 2.00e-02 2.50e+03 pdb=" C53 FEI A1602 " 0.118 2.00e-02 2.50e+03 pdb=" C55 FEI A1602 " -0.181 2.00e-02 2.50e+03 pdb=" N52 FEI A1602 " -0.083 2.00e-02 2.50e+03 pdb=" O51 FEI A1602 " 0.149 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 FEI A1602 " -0.538 2.00e-02 2.50e+03 2.32e-01 1.35e+03 pdb=" C24 FEI A1602 " 0.343 2.00e-02 2.50e+03 pdb=" C25 FEI A1602 " 0.199 2.00e-02 2.50e+03 pdb=" C26 FEI A1602 " 0.047 2.00e-02 2.50e+03 pdb=" C27 FEI A1602 " -0.052 2.00e-02 2.50e+03 pdb=" C28 FEI A1602 " 0.043 2.00e-02 2.50e+03 pdb=" C31 FEI A1602 " -0.223 2.00e-02 2.50e+03 pdb=" C32 FEI A1602 " -0.001 2.00e-02 2.50e+03 pdb=" N30 FEI A1602 " 0.193 2.00e-02 2.50e+03 pdb=" O29 FEI A1602 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A1128 " -0.031 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO A1129 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A1129 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1129 " -0.027 5.00e-02 4.00e+02 ... (remaining 3236 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 835 2.17 - 2.78: 44798 2.78 - 3.38: 61646 3.38 - 3.99: 79707 3.99 - 4.60: 126076 Nonbonded interactions: 313062 Sorted by model distance: nonbonded pdb=" O PHE A 800 " pdb=" H GLY A 805 " model vdw 1.559 2.450 nonbonded pdb=" O LEU A 720 " pdb=" HG1 THR A 723 " model vdw 1.611 2.450 nonbonded pdb=" HG1 THR A 235 " pdb=" OD1 ASP A1191 " model vdw 1.615 2.450 nonbonded pdb=" HG SER A 139 " pdb=" OE1 GLN A 175 " model vdw 1.623 2.450 nonbonded pdb=" O GLN A1097 " pdb="HE21 GLN A1097 " model vdw 1.628 2.450 ... (remaining 313057 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 0.400 Extract box with map and model: 0.870 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 47.470 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 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 : 0.006 0.197 11352 Z= 0.310 Angle : 0.684 18.637 15407 Z= 0.361 Chirality : 0.037 0.143 1800 Planarity : 0.008 0.232 1897 Dihedral : 15.067 174.705 4174 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.45 % Favored : 98.48 % Rotamer: Outliers : 0.41 % Allowed : 11.95 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.23), residues: 1380 helix: -2.05 (0.17), residues: 885 sheet: 1.42 (0.56), residues: 75 loop : 0.53 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1206 HIS 0.010 0.001 HIS A1428 PHE 0.009 0.001 PHE A 986 TYR 0.017 0.001 TYR A 101 ARG 0.013 0.000 ARG A1392 Details of bonding type rmsd hydrogen bonds : bond 0.28786 ( 499) hydrogen bonds : angle 10.72024 ( 1419) SS BOND : bond 0.00091 ( 1) SS BOND : angle 0.54558 ( 2) covalent geometry : bond 0.00622 (11351) covalent geometry : angle 0.68384 (15405) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 174 time to evaluate : 1.704 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 outliers start: 5 outliers final: 2 residues processed: 177 average time/residue: 0.4711 time to fit residues: 121.2673 Evaluate side-chains 116 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 1053 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.065656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.046724 restraints weight = 145693.078| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 4.59 r_work: 0.2861 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11352 Z= 0.256 Angle : 0.657 7.439 15407 Z= 0.359 Chirality : 0.040 0.153 1800 Planarity : 0.005 0.094 1897 Dihedral : 7.991 177.347 1579 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.45 % Favored : 98.48 % Rotamer: Outliers : 0.89 % Allowed : 14.88 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.22), residues: 1380 helix: -1.76 (0.16), residues: 907 sheet: 0.94 (0.52), residues: 80 loop : 0.66 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1206 HIS 0.006 0.001 HIS A1042 PHE 0.017 0.002 PHE A 639 TYR 0.011 0.001 TYR A1141 ARG 0.006 0.001 ARG A1149 Details of bonding type rmsd hydrogen bonds : bond 0.06161 ( 499) hydrogen bonds : angle 6.32423 ( 1419) SS BOND : bond 0.00039 ( 1) SS BOND : angle 0.57778 ( 2) covalent geometry : bond 0.00508 (11351) covalent geometry : angle 0.65702 (15405) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 1.892 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: A 429 GLN cc_start: 0.9260 (OUTLIER) cc_final: 0.9020 (tm-30) REVERT: A 598 MET cc_start: 0.9444 (mmt) cc_final: 0.9061 (tpt) REVERT: A 684 MET cc_start: 0.9297 (mmm) cc_final: 0.9015 (mmm) outliers start: 11 outliers final: 9 residues processed: 119 average time/residue: 0.4518 time to fit residues: 82.8880 Evaluate side-chains 116 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 429 GLN Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1206 TRP Chi-restraints excluded: chain A residue 1261 GLU Chi-restraints excluded: chain A residue 1371 HIS Chi-restraints excluded: chain A residue 1377 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 136 optimal weight: 20.0000 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 0.0170 chunk 70 optimal weight: 9.9990 chunk 110 optimal weight: 0.7980 chunk 62 optimal weight: 8.9990 chunk 97 optimal weight: 0.5980 chunk 74 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 overall best weight: 2.4822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.066384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.047334 restraints weight = 147455.633| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 4.65 r_work: 0.2871 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11352 Z= 0.166 Angle : 0.556 7.122 15407 Z= 0.298 Chirality : 0.038 0.147 1800 Planarity : 0.004 0.048 1897 Dihedral : 7.677 170.453 1576 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.52 % Favored : 98.41 % Rotamer: Outliers : 1.06 % Allowed : 15.12 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.23), residues: 1380 helix: -1.28 (0.17), residues: 910 sheet: 0.40 (0.54), residues: 75 loop : 0.77 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 517 HIS 0.005 0.001 HIS A1428 PHE 0.028 0.001 PHE A1140 TYR 0.008 0.001 TYR A 319 ARG 0.005 0.000 ARG A1392 Details of bonding type rmsd hydrogen bonds : bond 0.04948 ( 499) hydrogen bonds : angle 5.62982 ( 1419) SS BOND : bond 0.00086 ( 1) SS BOND : angle 0.60942 ( 2) covalent geometry : bond 0.00333 (11351) covalent geometry : angle 0.55633 (15405) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 1.703 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: A 429 GLN cc_start: 0.9266 (OUTLIER) cc_final: 0.9059 (tm-30) REVERT: A 684 MET cc_start: 0.9280 (mmm) cc_final: 0.8967 (mmm) outliers start: 13 outliers final: 10 residues processed: 114 average time/residue: 0.4058 time to fit residues: 72.4778 Evaluate side-chains 112 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 429 GLN Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1206 TRP Chi-restraints excluded: chain A residue 1371 HIS Chi-restraints excluded: chain A residue 1377 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 65 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 133 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 0.0050 chunk 88 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A1185 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.065965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.046970 restraints weight = 150031.072| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 4.64 r_work: 0.2860 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11352 Z= 0.186 Angle : 0.544 6.789 15407 Z= 0.291 Chirality : 0.038 0.142 1800 Planarity : 0.003 0.042 1897 Dihedral : 7.440 168.783 1576 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.52 % Favored : 98.41 % Rotamer: Outliers : 1.14 % Allowed : 15.04 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.23), residues: 1380 helix: -0.85 (0.17), residues: 914 sheet: 0.03 (0.54), residues: 75 loop : 0.71 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1254 HIS 0.004 0.001 HIS A1428 PHE 0.011 0.001 PHE A 639 TYR 0.007 0.001 TYR A 319 ARG 0.003 0.000 ARG A1210 Details of bonding type rmsd hydrogen bonds : bond 0.04056 ( 499) hydrogen bonds : angle 5.32671 ( 1419) SS BOND : bond 0.00136 ( 1) SS BOND : angle 0.62811 ( 2) covalent geometry : bond 0.00372 (11351) covalent geometry : angle 0.54421 (15405) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 1.742 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: A 429 GLN cc_start: 0.9276 (OUTLIER) cc_final: 0.8761 (tm-30) REVERT: A 684 MET cc_start: 0.9322 (mmm) cc_final: 0.9014 (mmm) REVERT: A 1069 MET cc_start: 0.9226 (mmm) cc_final: 0.8794 (tpp) outliers start: 14 outliers final: 12 residues processed: 115 average time/residue: 0.4468 time to fit residues: 78.2318 Evaluate side-chains 111 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 429 GLN Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1206 TRP Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain A residue 1371 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 56 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 121 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3577 r_free = 0.3577 target = 0.063743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.046160 restraints weight = 156190.522| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 5.06 r_work: 0.2820 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 11352 Z= 0.297 Angle : 0.607 6.150 15407 Z= 0.330 Chirality : 0.040 0.132 1800 Planarity : 0.004 0.040 1897 Dihedral : 7.330 168.184 1576 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.54 % Favored : 97.39 % Rotamer: Outliers : 1.46 % Allowed : 15.12 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.22), residues: 1380 helix: -0.73 (0.17), residues: 914 sheet: -0.36 (0.54), residues: 75 loop : 0.46 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1206 HIS 0.004 0.001 HIS A 692 PHE 0.011 0.001 PHE A 580 TYR 0.009 0.001 TYR A 319 ARG 0.004 0.000 ARG A1210 Details of bonding type rmsd hydrogen bonds : bond 0.03996 ( 499) hydrogen bonds : angle 5.48548 ( 1419) SS BOND : bond 0.00337 ( 1) SS BOND : angle 0.75960 ( 2) covalent geometry : bond 0.00582 (11351) covalent geometry : angle 0.60730 (15405) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 1.612 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: A 369 THR cc_start: 0.9532 (OUTLIER) cc_final: 0.9265 (t) REVERT: A 429 GLN cc_start: 0.9290 (OUTLIER) cc_final: 0.8792 (tm-30) REVERT: A 599 MET cc_start: 0.9297 (ttp) cc_final: 0.9037 (tmm) REVERT: A 1069 MET cc_start: 0.9241 (mmm) cc_final: 0.8831 (tpp) outliers start: 18 outliers final: 12 residues processed: 113 average time/residue: 0.4844 time to fit residues: 82.9451 Evaluate side-chains 106 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 429 GLN Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain A residue 1206 TRP Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain A residue 1371 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 132 optimal weight: 0.7980 chunk 121 optimal weight: 20.0000 chunk 111 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 106 optimal weight: 0.8980 chunk 125 optimal weight: 10.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 = 0.3593 r_free = 0.3593 target = 0.064409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.045555 restraints weight = 153145.618| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 4.59 r_work: 0.2847 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11352 Z= 0.171 Angle : 0.541 7.132 15407 Z= 0.286 Chirality : 0.038 0.138 1800 Planarity : 0.003 0.042 1897 Dihedral : 7.194 168.283 1575 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.88 % Favored : 98.04 % Rotamer: Outliers : 1.30 % Allowed : 15.53 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.23), residues: 1380 helix: -0.36 (0.17), residues: 915 sheet: -0.37 (0.55), residues: 75 loop : 0.49 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1206 HIS 0.004 0.001 HIS A 648 PHE 0.016 0.001 PHE A 639 TYR 0.009 0.001 TYR A 319 ARG 0.002 0.000 ARG A1210 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 499) hydrogen bonds : angle 5.10040 ( 1419) SS BOND : bond 0.00246 ( 1) SS BOND : angle 0.56854 ( 2) covalent geometry : bond 0.00345 (11351) covalent geometry : angle 0.54117 (15405) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 1.744 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: A 429 GLN cc_start: 0.9250 (OUTLIER) cc_final: 0.8777 (tm-30) REVERT: A 599 MET cc_start: 0.9371 (ttp) cc_final: 0.9057 (tmm) REVERT: A 684 MET cc_start: 0.9248 (mmm) cc_final: 0.8994 (mmm) REVERT: A 1069 MET cc_start: 0.9213 (mmm) cc_final: 0.8795 (tpp) outliers start: 16 outliers final: 13 residues processed: 109 average time/residue: 0.4696 time to fit residues: 78.5424 Evaluate side-chains 104 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 429 GLN Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1206 TRP Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1371 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 78 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.064396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.045569 restraints weight = 152496.824| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 4.56 r_work: 0.2849 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11352 Z= 0.170 Angle : 0.540 11.328 15407 Z= 0.281 Chirality : 0.038 0.136 1800 Planarity : 0.003 0.042 1897 Dihedral : 7.085 169.689 1575 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.14 % Allowed : 15.69 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.23), residues: 1380 helix: -0.06 (0.17), residues: 922 sheet: -0.47 (0.54), residues: 75 loop : 0.48 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1206 HIS 0.003 0.001 HIS A1371 PHE 0.010 0.001 PHE A 639 TYR 0.008 0.001 TYR A 319 ARG 0.002 0.000 ARG A1174 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 499) hydrogen bonds : angle 4.95601 ( 1419) SS BOND : bond 0.00265 ( 1) SS BOND : angle 0.65419 ( 2) covalent geometry : bond 0.00342 (11351) covalent geometry : angle 0.54001 (15405) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 1.736 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: A 429 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.8767 (tm-30) REVERT: A 440 MET cc_start: 0.9341 (mmm) cc_final: 0.9014 (mmm) REVERT: A 599 MET cc_start: 0.9357 (ttp) cc_final: 0.9058 (tmm) REVERT: A 662 MET cc_start: 0.9302 (mmm) cc_final: 0.9053 (mmm) REVERT: A 684 MET cc_start: 0.9289 (mmm) cc_final: 0.9036 (mmm) REVERT: A 688 MET cc_start: 0.9506 (mmm) cc_final: 0.9152 (mmm) REVERT: A 1069 MET cc_start: 0.9233 (mmm) cc_final: 0.8838 (tpp) REVERT: A 1225 MET cc_start: 0.9244 (mmt) cc_final: 0.9035 (mmm) outliers start: 14 outliers final: 11 residues processed: 106 average time/residue: 0.4648 time to fit residues: 75.1165 Evaluate side-chains 103 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 429 GLN Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1206 TRP Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1371 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 106 optimal weight: 0.6980 chunk 116 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 54 optimal weight: 0.0570 chunk 114 optimal weight: 6.9990 overall best weight: 1.2700 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.065219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.046320 restraints weight = 153154.969| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 4.71 r_work: 0.2866 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11352 Z= 0.103 Angle : 0.512 8.281 15407 Z= 0.262 Chirality : 0.037 0.139 1800 Planarity : 0.003 0.042 1897 Dihedral : 6.951 168.733 1575 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.22 % Allowed : 15.93 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.23), residues: 1380 helix: 0.33 (0.18), residues: 927 sheet: -0.48 (0.54), residues: 75 loop : 0.54 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 517 HIS 0.003 0.001 HIS A1371 PHE 0.010 0.001 PHE A 639 TYR 0.008 0.001 TYR A 319 ARG 0.002 0.000 ARG A1308 Details of bonding type rmsd hydrogen bonds : bond 0.03252 ( 499) hydrogen bonds : angle 4.63858 ( 1419) SS BOND : bond 0.00197 ( 1) SS BOND : angle 0.59875 ( 2) covalent geometry : bond 0.00222 (11351) covalent geometry : angle 0.51214 (15405) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 1.688 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: A 429 GLN cc_start: 0.9220 (OUTLIER) cc_final: 0.8792 (tm-30) REVERT: A 440 MET cc_start: 0.9369 (mmm) cc_final: 0.9031 (mmm) REVERT: A 599 MET cc_start: 0.9288 (ttp) cc_final: 0.9037 (tmm) REVERT: A 662 MET cc_start: 0.9298 (mmm) cc_final: 0.9060 (mmm) REVERT: A 684 MET cc_start: 0.9310 (mmm) cc_final: 0.9097 (mmm) REVERT: A 688 MET cc_start: 0.9496 (mmm) cc_final: 0.9134 (mmm) REVERT: A 1069 MET cc_start: 0.9226 (mmm) cc_final: 0.8854 (tpp) REVERT: A 1226 MET cc_start: 0.9503 (mmt) cc_final: 0.9068 (mmm) REVERT: A 1460 LEU cc_start: 0.9702 (OUTLIER) cc_final: 0.9297 (tt) outliers start: 15 outliers final: 13 residues processed: 112 average time/residue: 0.4503 time to fit residues: 76.4724 Evaluate side-chains 111 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 429 GLN Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1083 ARG Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1206 TRP Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1371 HIS 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 24 optimal weight: 0.6980 chunk 58 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1193 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.064781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.046056 restraints weight = 148854.973| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 4.64 r_work: 0.2869 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11352 Z= 0.094 Angle : 0.511 8.353 15407 Z= 0.258 Chirality : 0.037 0.142 1800 Planarity : 0.003 0.042 1897 Dihedral : 6.840 169.895 1575 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.14 % Allowed : 16.10 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.23), residues: 1380 helix: 0.61 (0.18), residues: 927 sheet: -0.44 (0.55), residues: 75 loop : 0.58 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 517 HIS 0.003 0.001 HIS A1371 PHE 0.008 0.001 PHE A 639 TYR 0.006 0.001 TYR A 730 ARG 0.002 0.000 ARG A1318 Details of bonding type rmsd hydrogen bonds : bond 0.03059 ( 499) hydrogen bonds : angle 4.49790 ( 1419) SS BOND : bond 0.00211 ( 1) SS BOND : angle 0.68144 ( 2) covalent geometry : bond 0.00209 (11351) covalent geometry : angle 0.51144 (15405) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 1.651 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: A 429 GLN cc_start: 0.9227 (OUTLIER) cc_final: 0.8810 (tm-30) REVERT: A 440 MET cc_start: 0.9385 (mmm) cc_final: 0.9180 (mmp) REVERT: A 599 MET cc_start: 0.9275 (ttp) cc_final: 0.9032 (tmm) REVERT: A 1069 MET cc_start: 0.9249 (mmm) cc_final: 0.8864 (tpp) REVERT: A 1083 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7940 (mpt90) REVERT: A 1226 MET cc_start: 0.9452 (mmt) cc_final: 0.9013 (mmm) REVERT: A 1460 LEU cc_start: 0.9686 (OUTLIER) cc_final: 0.9266 (tt) outliers start: 14 outliers final: 8 residues processed: 107 average time/residue: 0.4576 time to fit residues: 74.2116 Evaluate side-chains 101 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 429 GLN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1083 ARG Chi-restraints excluded: chain A residue 1206 TRP Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1371 HIS 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 18 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 87 optimal weight: 0.4980 chunk 72 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.063718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.046311 restraints weight = 153942.809| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 4.87 r_work: 0.2834 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11352 Z= 0.193 Angle : 0.548 7.304 15407 Z= 0.286 Chirality : 0.038 0.154 1800 Planarity : 0.003 0.041 1897 Dihedral : 6.748 169.133 1575 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.06 % Allowed : 16.10 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.23), residues: 1380 helix: 0.58 (0.18), residues: 927 sheet: -0.50 (0.54), residues: 75 loop : 0.51 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1206 HIS 0.003 0.001 HIS A1371 PHE 0.010 0.001 PHE A1049 TYR 0.008 0.001 TYR A 319 ARG 0.002 0.000 ARG A1210 Details of bonding type rmsd hydrogen bonds : bond 0.03125 ( 499) hydrogen bonds : angle 4.69235 ( 1419) SS BOND : bond 0.00312 ( 1) SS BOND : angle 0.87172 ( 2) covalent geometry : bond 0.00388 (11351) covalent geometry : angle 0.54789 (15405) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 1.778 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: A 429 GLN cc_start: 0.9243 (OUTLIER) cc_final: 0.8814 (tm-30) REVERT: A 599 MET cc_start: 0.9278 (ttp) cc_final: 0.9037 (tmm) REVERT: A 684 MET cc_start: 0.9435 (mmm) cc_final: 0.9070 (mmm) REVERT: A 688 MET cc_start: 0.9473 (mmm) cc_final: 0.9082 (mmm) REVERT: A 1069 MET cc_start: 0.9235 (mmm) cc_final: 0.8888 (tpp) REVERT: A 1226 MET cc_start: 0.9452 (mmt) cc_final: 0.9211 (mmm) REVERT: A 1460 LEU cc_start: 0.9688 (OUTLIER) cc_final: 0.9264 (tt) REVERT: A 1528 PHE cc_start: 0.9314 (t80) cc_final: 0.9060 (t80) outliers start: 13 outliers final: 11 residues processed: 101 average time/residue: 0.4785 time to fit residues: 72.5868 Evaluate side-chains 103 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 429 GLN Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1083 ARG Chi-restraints excluded: chain A residue 1206 TRP Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1371 HIS 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 134 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.063455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.046118 restraints weight = 153896.965| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 4.93 r_work: 0.2829 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11352 Z= 0.185 Angle : 0.548 9.269 15407 Z= 0.286 Chirality : 0.038 0.158 1800 Planarity : 0.003 0.041 1897 Dihedral : 6.705 168.533 1575 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.22 % Allowed : 16.18 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.23), residues: 1380 helix: 0.58 (0.17), residues: 933 sheet: -0.51 (0.55), residues: 75 loop : 0.45 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1206 HIS 0.004 0.001 HIS A1371 PHE 0.008 0.001 PHE A1049 TYR 0.008 0.001 TYR A 319 ARG 0.002 0.000 ARG A1308 Details of bonding type rmsd hydrogen bonds : bond 0.03193 ( 499) hydrogen bonds : angle 4.67034 ( 1419) SS BOND : bond 0.00328 ( 1) SS BOND : angle 0.90446 ( 2) covalent geometry : bond 0.00372 (11351) covalent geometry : angle 0.54778 (15405) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10116.29 seconds wall clock time: 174 minutes 11.98 seconds (10451.98 seconds total)