Starting phenix.real_space_refine on Thu Jun 19 19:30:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxq_36709/06_2025/8jxq_36709_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxq_36709/06_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_36709/06_2025/8jxq_36709.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxq_36709/06_2025/8jxq_36709.map" model { file = "/net/cci-nas-00/data/ceres_data/8jxq_36709/06_2025/8jxq_36709_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxq_36709/06_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-5710/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: 10.92, per 1000 atoms: 0.49 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: 6.64 Conformation dependent library (CDL) restraints added in 1.9 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: 2.72 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: 10.50 Time building geometry restraints manager: 7.92 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: 0.910 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: 0.390 Extract box with map and model: 0.850 Check model and map are aligned: 0.180 Set scattering table: 0.200 Process input model: 53.040 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.130 ------------------------------------------------------------------------------- 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 : 2.055 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: 0.4872 time to fit residues: 126.7651 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 : 1.682 ------------------------------------------------------------------------------- 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 = 33)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.046704 restraints weight = 145694.869| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 4.68 r_work: 0.2857 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 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 7.441 15407 Z= 0.359 Chirality : 0.040 0.153 1800 Planarity : 0.005 0.094 1897 Dihedral : 7.991 177.351 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: -1.77 (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 6.32454 ( 1419) SS BOND : bond 0.00039 ( 1) SS BOND : angle 0.57770 ( 2) covalent geometry : bond 0.00508 (11351) covalent geometry : angle 0.65709 (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 : 1.856 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: 0.9259 (OUTLIER) cc_final: 0.9020 (tm-30) REVERT: A 598 MET cc_start: 0.9444 (mmt) cc_final: 0.9063 (tpt) REVERT: A 684 MET cc_start: 0.9300 (mmm) cc_final: 0.9019 (mmm) outliers start: 11 outliers final: 9 residues processed: 119 average time/residue: 0.4586 time to fit residues: 84.5085 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 : 1.953 ------------------------------------------------------------------------------- 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: 8.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 110 optimal weight: 0.6980 chunk 62 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- 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** A1185 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.065366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.046491 restraints weight = 151672.599| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 4.66 r_work: 0.2845 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11352 Z= 0.229 Angle : 0.587 6.909 15407 Z= 0.317 Chirality : 0.039 0.150 1800 Planarity : 0.004 0.048 1897 Dihedral : 7.620 167.850 1576 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.88 % Favored : 98.04 % Rotamer: Outliers : 1.46 % Allowed : 14.80 % Favored : 83.74 % 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: -1.24 (0.17), residues: 914 sheet: 0.23 (0.54), residues: 75 loop : 0.70 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 517 HIS 0.005 0.001 HIS A1428 PHE 0.033 0.001 PHE A1140 TYR 0.009 0.001 TYR A 319 ARG 0.005 0.000 ARG A1392 Details of bonding type rmsd hydrogen bonds : bond 0.04811 ( 499) hydrogen bonds : angle 5.68023 ( 1419) SS BOND : bond 0.00205 ( 1) SS BOND : angle 0.71752 ( 2) covalent geometry : bond 0.00451 (11351) covalent geometry : angle 0.58729 (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 123 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 1.683 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: 0.9282 (OUTLIER) cc_final: 0.9077 (tm-30) REVERT: A 684 MET cc_start: 0.9327 (mmm) cc_final: 0.9037 (mmm) REVERT: A 1069 MET cc_start: 0.9257 (mmm) cc_final: 0.8831 (tpp) outliers start: 18 outliers final: 14 residues processed: 116 average time/residue: 0.4376 time to fit residues: 78.0800 Evaluate side-chains 109 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLN 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 728 LYS 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 Chi-restraints excluded: chain A residue 1454 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 65 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 133 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.065907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.046845 restraints weight = 149132.012| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 4.67 r_work: 0.2859 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11352 Z= 0.159 Angle : 0.541 7.129 15407 Z= 0.287 Chirality : 0.038 0.142 1800 Planarity : 0.003 0.045 1897 Dihedral : 7.460 168.532 1576 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.38 % Favored : 98.55 % Rotamer: Outliers : 1.30 % Allowed : 14.88 % 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: -0.78 (0.23), residues: 1380 helix: -0.81 (0.17), residues: 914 sheet: 0.05 (0.55), residues: 75 loop : 0.71 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1254 HIS 0.004 0.001 HIS A 648 PHE 0.012 0.001 PHE A 639 TYR 0.008 0.001 TYR A 319 ARG 0.002 0.000 ARG A1210 Details of bonding type rmsd hydrogen bonds : bond 0.04007 ( 499) hydrogen bonds : angle 5.28799 ( 1419) SS BOND : bond 0.00153 ( 1) SS BOND : angle 0.56491 ( 2) covalent geometry : bond 0.00323 (11351) covalent geometry : angle 0.54056 (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 120 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 1.728 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 684 MET cc_start: 0.9327 (mmm) cc_final: 0.9008 (mmm) REVERT: A 1069 MET cc_start: 0.9225 (mmm) cc_final: 0.8793 (tpp) outliers start: 16 outliers final: 12 residues processed: 114 average time/residue: 0.4199 time to fit residues: 75.1714 Evaluate side-chains 107 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 1.694 ------------------------------------------------------------------------------- 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 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 1117 CYS Chi-restraints excluded: chain A residue 1206 TRP 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: 5.9990 chunk 68 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.064523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.045644 restraints weight = 154086.260| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 4.73 r_work: 0.2833 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11352 Z= 0.235 Angle : 0.570 6.517 15407 Z= 0.305 Chirality : 0.038 0.144 1800 Planarity : 0.003 0.041 1897 Dihedral : 7.331 168.481 1576 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.32 % Favored : 97.61 % Rotamer: Outliers : 1.46 % Allowed : 15.53 % Favored : 83.01 % 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: -0.59 (0.17), residues: 914 sheet: -0.02 (0.57), residues: 73 loop : 0.58 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1206 HIS 0.004 0.001 HIS A1371 PHE 0.010 0.001 PHE A 580 TYR 0.009 0.001 TYR A 319 ARG 0.003 0.000 ARG A1210 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 499) hydrogen bonds : angle 5.32643 ( 1419) SS BOND : bond 0.00288 ( 1) SS BOND : angle 0.70038 ( 2) covalent geometry : bond 0.00466 (11351) covalent geometry : angle 0.56953 (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 112 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 2.344 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 440 MET cc_start: 0.9378 (mmm) cc_final: 0.9131 (mmm) REVERT: A 599 MET cc_start: 0.9287 (ttp) cc_final: 0.9036 (tmm) REVERT: A 1069 MET cc_start: 0.9238 (mmm) cc_final: 0.8810 (tpp) outliers start: 18 outliers final: 13 residues processed: 108 average time/residue: 0.4487 time to fit residues: 75.1818 Evaluate side-chains 100 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR 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 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 771 LEU 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 1371 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 132 optimal weight: 2.9990 chunk 121 optimal weight: 20.0000 chunk 111 optimal weight: 3.9990 chunk 15 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 106 optimal weight: 0.0170 chunk 125 optimal weight: 9.9990 overall best weight: 2.0824 ------------------------------------------------------------------------------- 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 = 0.3603 r_free = 0.3603 target = 0.064876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.045893 restraints weight = 152299.029| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 4.73 r_work: 0.2856 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11352 Z= 0.142 Angle : 0.527 7.194 15407 Z= 0.277 Chirality : 0.037 0.139 1800 Planarity : 0.003 0.041 1897 Dihedral : 7.194 168.665 1575 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.81 % Favored : 98.12 % 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: -0.21 (0.23), residues: 1380 helix: -0.26 (0.18), residues: 913 sheet: -0.11 (0.57), residues: 73 loop : 0.66 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1206 HIS 0.003 0.001 HIS A1371 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 0.03645 ( 499) hydrogen bonds : angle 5.01193 ( 1419) SS BOND : bond 0.00201 ( 1) SS BOND : angle 0.53919 ( 2) covalent geometry : bond 0.00288 (11351) covalent geometry : angle 0.52690 (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 110 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 1.906 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 440 MET cc_start: 0.9369 (mmm) cc_final: 0.9149 (mmm) REVERT: A 599 MET cc_start: 0.9366 (ttp) cc_final: 0.9060 (tmm) REVERT: A 684 MET cc_start: 0.9270 (mmm) cc_final: 0.9030 (mmm) REVERT: A 1069 MET cc_start: 0.9229 (mmm) cc_final: 0.8817 (tpp) outliers start: 16 outliers final: 14 residues processed: 106 average time/residue: 0.5149 time to fit residues: 88.0361 Evaluate side-chains 102 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 1.790 ------------------------------------------------------------------------------- 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 434 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain A residue 1206 TRP 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: 20.0000 chunk 115 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.064110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.045225 restraints weight = 154011.928| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 4.69 r_work: 0.2836 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11352 Z= 0.209 Angle : 0.549 6.454 15407 Z= 0.292 Chirality : 0.038 0.134 1800 Planarity : 0.003 0.041 1897 Dihedral : 7.095 169.619 1575 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.14 % Allowed : 15.93 % Favored : 82.93 % 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: -0.12 (0.17), residues: 924 sheet: -0.23 (0.57), residues: 73 loop : 0.63 (0.33), 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 0.003 0.000 ARG A1174 Details of bonding type rmsd hydrogen bonds : bond 0.03538 ( 499) hydrogen bonds : angle 5.06837 ( 1419) SS BOND : bond 0.00312 ( 1) SS BOND : angle 0.72600 ( 2) covalent geometry : bond 0.00416 (11351) covalent geometry : angle 0.54891 (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 105 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 1.873 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 440 MET cc_start: 0.9411 (mmm) cc_final: 0.9182 (mmm) REVERT: A 599 MET cc_start: 0.9299 (ttp) cc_final: 0.9061 (tmm) REVERT: A 662 MET cc_start: 0.9294 (mmm) cc_final: 0.9045 (mmm) REVERT: A 1069 MET cc_start: 0.9251 (mmm) cc_final: 0.8866 (tpp) outliers start: 14 outliers final: 14 residues processed: 102 average time/residue: 0.4463 time to fit residues: 70.9038 Evaluate side-chains 102 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL 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 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 771 LEU 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 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: 3.9990 chunk 116 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3602 r_free = 0.3602 target = 0.064698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.045649 restraints weight = 152786.253| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 4.72 r_work: 0.2854 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11352 Z= 0.122 Angle : 0.519 8.001 15407 Z= 0.269 Chirality : 0.037 0.138 1800 Planarity : 0.003 0.041 1897 Dihedral : 6.977 168.661 1575 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.22 % Allowed : 16.10 % Favored : 82.68 % 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: 0.31 (0.23), residues: 1380 helix: 0.26 (0.18), residues: 927 sheet: -0.28 (0.57), residues: 73 loop : 0.64 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 517 HIS 0.003 0.001 HIS A1371 PHE 0.008 0.001 PHE A 639 TYR 0.009 0.001 TYR A 319 ARG 0.002 0.000 ARG A1308 Details of bonding type rmsd hydrogen bonds : bond 0.03327 ( 499) hydrogen bonds : angle 4.74404 ( 1419) SS BOND : bond 0.00221 ( 1) SS BOND : angle 0.59997 ( 2) covalent geometry : bond 0.00254 (11351) covalent geometry : angle 0.51915 (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 114 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 1.670 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 234 LYS cc_start: 0.9181 (mttt) cc_final: 0.8979 (mmtm) REVERT: A 440 MET cc_start: 0.9405 (mmm) cc_final: 0.9162 (mmm) REVERT: A 599 MET cc_start: 0.9291 (ttp) cc_final: 0.9054 (tmm) REVERT: A 662 MET cc_start: 0.9301 (mmm) cc_final: 0.9065 (mmm) REVERT: A 684 MET cc_start: 0.9448 (mmm) cc_final: 0.9035 (mmm) REVERT: A 1069 MET cc_start: 0.9236 (mmm) cc_final: 0.8873 (tpp) REVERT: A 1083 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7857 (mpt90) REVERT: A 1226 MET cc_start: 0.9499 (mmt) cc_final: 0.9060 (mmm) REVERT: A 1460 LEU cc_start: 0.9698 (OUTLIER) cc_final: 0.9299 (tt) outliers start: 15 outliers final: 13 residues processed: 111 average time/residue: 0.4546 time to fit residues: 77.6288 Evaluate side-chains 104 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL 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 434 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 771 LEU 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 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: 0.9980 chunk 58 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 69 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.3590 r_free = 0.3590 target = 0.064285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.046834 restraints weight = 150360.503| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 4.89 r_work: 0.2844 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3751 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= 0.127 Angle : 0.515 6.216 15407 Z= 0.267 Chirality : 0.037 0.135 1800 Planarity : 0.003 0.042 1897 Dihedral : 6.872 169.927 1575 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.38 % Allowed : 16.26 % Favored : 82.36 % 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: 0.54 (0.23), residues: 1380 helix: 0.49 (0.18), residues: 926 sheet: -0.41 (0.56), residues: 75 loop : 0.63 (0.34), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1206 HIS 0.003 0.001 HIS A1371 PHE 0.008 0.001 PHE A1049 TYR 0.006 0.001 TYR A 730 ARG 0.002 0.000 ARG A1308 Details of bonding type rmsd hydrogen bonds : bond 0.03183 ( 499) hydrogen bonds : angle 4.63822 ( 1419) SS BOND : bond 0.00262 ( 1) SS BOND : angle 0.70454 ( 2) covalent geometry : bond 0.00266 (11351) covalent geometry : angle 0.51542 (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 112 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 1.784 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 234 LYS cc_start: 0.9168 (mttt) cc_final: 0.8967 (mmtm) REVERT: A 440 MET cc_start: 0.9410 (mmm) cc_final: 0.9165 (mmm) REVERT: A 599 MET cc_start: 0.9253 (ttp) cc_final: 0.9004 (tmm) REVERT: A 662 MET cc_start: 0.9322 (mmm) cc_final: 0.9095 (mmm) REVERT: A 684 MET cc_start: 0.9466 (mmm) cc_final: 0.9059 (mmm) REVERT: A 1069 MET cc_start: 0.9252 (mmm) cc_final: 0.8886 (tpp) REVERT: A 1083 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7958 (mpt90) REVERT: A 1226 MET cc_start: 0.9440 (mmt) cc_final: 0.8995 (mmm) REVERT: A 1460 LEU cc_start: 0.9689 (OUTLIER) cc_final: 0.9276 (tt) outliers start: 17 outliers final: 13 residues processed: 107 average time/residue: 0.4621 time to fit residues: 75.8284 Evaluate side-chains 105 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL 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 512 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 994 ILE 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 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: 3.9990 chunk 129 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 72 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1193 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.063841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.046339 restraints weight = 153392.794| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 4.98 r_work: 0.2834 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11352 Z= 0.155 Angle : 0.530 6.944 15407 Z= 0.276 Chirality : 0.038 0.133 1800 Planarity : 0.003 0.041 1897 Dihedral : 6.784 169.403 1575 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.22 % Allowed : 16.34 % Favored : 82.44 % 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: 0.62 (0.23), residues: 1380 helix: 0.57 (0.18), residues: 926 sheet: -0.47 (0.56), residues: 75 loop : 0.60 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1206 HIS 0.003 0.001 HIS A1371 PHE 0.008 0.001 PHE A1049 TYR 0.007 0.001 TYR A 319 ARG 0.002 0.000 ARG A1308 Details of bonding type rmsd hydrogen bonds : bond 0.03151 ( 499) hydrogen bonds : angle 4.64666 ( 1419) SS BOND : bond 0.00285 ( 1) SS BOND : angle 0.79575 ( 2) covalent geometry : bond 0.00316 (11351) covalent geometry : angle 0.52955 (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 108 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 1.621 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 234 LYS cc_start: 0.9173 (mttt) cc_final: 0.8972 (mmtm) REVERT: A 440 MET cc_start: 0.9415 (mmm) cc_final: 0.9178 (mmm) REVERT: A 599 MET cc_start: 0.9254 (ttp) cc_final: 0.9004 (tmm) REVERT: A 662 MET cc_start: 0.9308 (mmm) cc_final: 0.9084 (mmm) REVERT: A 684 MET cc_start: 0.9463 (mmm) cc_final: 0.9057 (mmm) REVERT: A 1083 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7968 (mpt90) REVERT: A 1226 MET cc_start: 0.9467 (mmt) cc_final: 0.9029 (mmm) REVERT: A 1460 LEU cc_start: 0.9691 (OUTLIER) cc_final: 0.9273 (tt) REVERT: A 1528 PHE cc_start: 0.9452 (t80) cc_final: 0.9162 (t80) outliers start: 15 outliers final: 12 residues processed: 104 average time/residue: 0.4655 time to fit residues: 74.4635 Evaluate side-chains 105 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL 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 608 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 994 ILE 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 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: 9.9990 chunk 12 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 95 optimal weight: 0.8980 chunk 132 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.064071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.046752 restraints weight = 152660.709| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 4.96 r_work: 0.2848 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11352 Z= 0.118 Angle : 0.519 9.244 15407 Z= 0.266 Chirality : 0.037 0.135 1800 Planarity : 0.003 0.041 1897 Dihedral : 6.735 169.124 1575 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.22 % Allowed : 16.26 % Favored : 82.52 % 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 (0.23), residues: 1380 helix: 0.74 (0.18), residues: 926 sheet: -0.46 (0.55), residues: 75 loop : 0.63 (0.34), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 517 HIS 0.003 0.001 HIS A1371 PHE 0.008 0.001 PHE A 521 TYR 0.007 0.001 TYR A 319 ARG 0.002 0.000 ARG A1070 Details of bonding type rmsd hydrogen bonds : bond 0.03067 ( 499) hydrogen bonds : angle 4.48757 ( 1419) SS BOND : bond 0.00273 ( 1) SS BOND : angle 0.76388 ( 2) covalent geometry : bond 0.00249 (11351) covalent geometry : angle 0.51933 (15405) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10381.37 seconds wall clock time: 179 minutes 4.25 seconds (10744.25 seconds total)