Starting phenix.real_space_refine on Sat Mar 7 08:44:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ut4_26754/03_2026/7ut4_26754.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ut4_26754/03_2026/7ut4_26754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ut4_26754/03_2026/7ut4_26754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ut4_26754/03_2026/7ut4_26754.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ut4_26754/03_2026/7ut4_26754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ut4_26754/03_2026/7ut4_26754.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 1.500 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 74 5.16 5 C 12612 2.51 5 N 3206 2.21 5 O 3756 1.98 5 H 20092 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39740 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 19870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1224, 19870 Classifications: {'peptide': 1224} Link IDs: {'PTRANS': 36, 'TRANS': 1187} Chain breaks: 7 Chain: "B" Number of atoms: 19870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1224, 19870 Classifications: {'peptide': 1224} Link IDs: {'PTRANS': 36, 'TRANS': 1187} Chain breaks: 7 Time building chain proxies: 6.90, per 1000 atoms: 0.17 Number of scatterers: 39740 At special positions: 0 Unit cell: (311.168, 153.088, 123.136, 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 74 16.00 O 3756 8.00 N 3206 7.00 C 12612 6.00 H 20092 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.40 Conformation dependent library (CDL) restraints added in 988.3 milliseconds 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4740 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 1 sheets defined 75.2% alpha, 0.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 11 through 26 removed outlier: 3.953A pdb=" N ILE A 15 " --> pdb=" O PRO A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 83 removed outlier: 3.573A pdb=" N PHE A 76 " --> pdb=" O PHE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 107 removed outlier: 3.625A pdb=" N ILE A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 98 " --> pdb=" O SER A 94 " (cutoff:3.500A) Proline residue: A 100 - end of helix removed outlier: 3.558A pdb=" N LEU A 103 " --> pdb=" O GLN A 99 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE A 104 " --> pdb=" O PRO A 100 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 105 " --> pdb=" O PHE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 129 Processing helix chain 'A' and resid 137 through 151 removed outlier: 3.878A pdb=" N HIS A 151 " --> pdb=" O ASN A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 179 removed outlier: 3.822A pdb=" N VAL A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 removed outlier: 3.639A pdb=" N LEU A 185 " --> pdb=" O GLY A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 203 Processing helix chain 'A' and resid 207 through 227 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 329 through 344 removed outlier: 4.318A pdb=" N ARG A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 removed outlier: 4.536A pdb=" N LEU A 349 " --> pdb=" O GLU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 371 removed outlier: 3.685A pdb=" N PHE A 358 " --> pdb=" O SER A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 376 Processing helix chain 'A' and resid 377 through 386 removed outlier: 3.519A pdb=" N THR A 382 " --> pdb=" O PRO A 378 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU A 383 " --> pdb=" O ARG A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 398 Processing helix chain 'A' and resid 401 through 419 Processing helix chain 'A' and resid 423 through 440 removed outlier: 3.509A pdb=" N ASP A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 467 Processing helix chain 'A' and resid 467 through 472 removed outlier: 3.818A pdb=" N THR A 471 " --> pdb=" O SER A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 493 through 505 Processing helix chain 'A' and resid 506 through 511 removed outlier: 3.590A pdb=" N LEU A 511 " --> pdb=" O GLU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 536 removed outlier: 4.077A pdb=" N ILE A 520 " --> pdb=" O SER A 516 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 525 " --> pdb=" O CYS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 546 removed outlier: 3.815A pdb=" N PHE A 544 " --> pdb=" O ASP A 540 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 545 " --> pdb=" O ARG A 541 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG A 546 " --> pdb=" O GLU A 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 540 through 546' Processing helix chain 'A' and resid 551 through 559 removed outlier: 3.568A pdb=" N ASP A 558 " --> pdb=" O LEU A 554 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A 559 " --> pdb=" O LYS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 567 Processing helix chain 'A' and resid 577 through 585 Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 607 through 617 removed outlier: 3.629A pdb=" N ILE A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 628 Processing helix chain 'A' and resid 629 through 631 No H-bonds generated for 'chain 'A' and resid 629 through 631' Processing helix chain 'A' and resid 637 through 647 Processing helix chain 'A' and resid 654 through 657 Processing helix chain 'A' and resid 658 through 673 Processing helix chain 'A' and resid 687 through 691 removed outlier: 3.570A pdb=" N THR A 690 " --> pdb=" O ASP A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 713 removed outlier: 3.685A pdb=" N THR A 710 " --> pdb=" O ILE A 706 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS A 713 " --> pdb=" O ASN A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 727 removed outlier: 3.730A pdb=" N SER A 727 " --> pdb=" O PHE A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 754 removed outlier: 3.723A pdb=" N TYR A 748 " --> pdb=" O LEU A 744 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE A 751 " --> pdb=" O ILE A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 782 removed outlier: 4.207A pdb=" N SER A 779 " --> pdb=" O ASN A 775 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N THR A 780 " --> pdb=" O LEU A 776 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 796 removed outlier: 3.674A pdb=" N ASP A 795 " --> pdb=" O SER A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 828 removed outlier: 3.718A pdb=" N ARG A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ALA A 808 " --> pdb=" O ASN A 804 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE A 809 " --> pdb=" O PHE A 805 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN A 812 " --> pdb=" O ALA A 808 " (cutoff:3.500A) Proline residue: A 815 - end of helix Processing helix chain 'A' and resid 830 through 852 Processing helix chain 'A' and resid 853 through 868 Processing helix chain 'A' and resid 906 through 915 Processing helix chain 'A' and resid 915 through 932 removed outlier: 3.840A pdb=" N GLN A 919 " --> pdb=" O SER A 915 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 920 " --> pdb=" O PHE A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 956 removed outlier: 3.573A pdb=" N ASP A 956 " --> pdb=" O THR A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 972 removed outlier: 3.611A pdb=" N GLN A 968 " --> pdb=" O PHE A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1027 removed outlier: 3.584A pdb=" N ASN A1027 " --> pdb=" O ILE A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1033 removed outlier: 3.537A pdb=" N VAL A1032 " --> pdb=" O ILE A1028 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE A1033 " --> pdb=" O ALA A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1050 Processing helix chain 'A' and resid 1062 through 1081 removed outlier: 3.590A pdb=" N LEU A1067 " --> pdb=" O PHE A1063 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A1068 " --> pdb=" O GLU A1064 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE A1080 " --> pdb=" O ALA A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1100 removed outlier: 3.546A pdb=" N HIS A1100 " --> pdb=" O PHE A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1123 removed outlier: 3.501A pdb=" N VAL A1109 " --> pdb=" O THR A1105 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A1113 " --> pdb=" O VAL A1109 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR A1114 " --> pdb=" O ARG A1110 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR A1115 " --> pdb=" O ARG A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1136 Processing helix chain 'A' and resid 1146 through 1152 Processing helix chain 'A' and resid 1152 through 1165 Processing helix chain 'A' and resid 1171 through 1176 removed outlier: 3.521A pdb=" N LEU A1175 " --> pdb=" O TYR A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1191 removed outlier: 3.553A pdb=" N TRP A1182 " --> pdb=" O ASN A1178 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A1191 " --> pdb=" O LYS A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1209 removed outlier: 3.738A pdb=" N ASP A1209 " --> pdb=" O SER A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1230 removed outlier: 3.634A pdb=" N VAL A1221 " --> pdb=" O ASN A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1275 removed outlier: 4.138A pdb=" N LEU A1264 " --> pdb=" O LYS A1260 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1279 removed outlier: 3.841A pdb=" N ASN A1279 " --> pdb=" O LEU A1276 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1276 through 1279' Processing helix chain 'A' and resid 1283 through 1297 removed outlier: 3.731A pdb=" N ILE A1287 " --> pdb=" O ARG A1283 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE A1288 " --> pdb=" O LYS A1284 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A1289 " --> pdb=" O ASN A1285 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN A1297 " --> pdb=" O ALA A1293 " (cutoff:3.500A) Processing helix chain 'A' and resid 1298 through 1300 No H-bonds generated for 'chain 'A' and resid 1298 through 1300' Processing helix chain 'A' and resid 1302 through 1320 removed outlier: 3.575A pdb=" N SER A1306 " --> pdb=" O CYS A1302 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL A1311 " --> pdb=" O GLU A1307 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU A1314 " --> pdb=" O VAL A1310 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1338 removed outlier: 4.122A pdb=" N ILE A1335 " --> pdb=" O VAL A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1344 removed outlier: 4.177A pdb=" N LEU A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN A1344 " --> pdb=" O LEU A1340 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1339 through 1344' Processing helix chain 'A' and resid 1349 through 1354 removed outlier: 4.138A pdb=" N GLN A1352 " --> pdb=" O GLN A1349 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A1353 " --> pdb=" O GLU A1350 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE A1354 " --> pdb=" O ASP A1351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1349 through 1354' Processing helix chain 'A' and resid 1355 through 1374 removed outlier: 3.661A pdb=" N ILE A1359 " --> pdb=" O LEU A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1391 removed outlier: 4.413A pdb=" N PHE A1381 " --> pdb=" O SER A1377 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU A1382 " --> pdb=" O ASN A1378 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A1391 " --> pdb=" O ILE A1387 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1402 Processing helix chain 'A' and resid 1403 through 1417 removed outlier: 3.945A pdb=" N ASP A1407 " --> pdb=" O GLN A1403 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY A1416 " --> pdb=" O GLU A1412 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 25 Processing helix chain 'B' and resid 72 through 84 removed outlier: 4.101A pdb=" N PHE B 76 " --> pdb=" O PHE B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 98 removed outlier: 3.846A pdb=" N ILE B 97 " --> pdb=" O ASP B 93 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU B 98 " --> pdb=" O SER B 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 93 through 98' Processing helix chain 'B' and resid 98 through 107 Processing helix chain 'B' and resid 111 through 129 Processing helix chain 'B' and resid 137 through 151 removed outlier: 3.590A pdb=" N HIS B 151 " --> pdb=" O ASN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 179 removed outlier: 3.719A pdb=" N VAL B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 removed outlier: 3.579A pdb=" N LEU B 185 " --> pdb=" O GLY B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 203 Processing helix chain 'B' and resid 207 through 228 removed outlier: 3.674A pdb=" N ILE B 219 " --> pdb=" O GLN B 215 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYS B 228 " --> pdb=" O LYS B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 344 removed outlier: 3.904A pdb=" N GLN B 334 " --> pdb=" O PRO B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 349 removed outlier: 4.506A pdb=" N LEU B 349 " --> pdb=" O GLU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 370 removed outlier: 3.810A pdb=" N SER B 370 " --> pdb=" O ALA B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 376 removed outlier: 3.831A pdb=" N GLN B 375 " --> pdb=" O ASP B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 399 removed outlier: 3.865A pdb=" N LEU B 383 " --> pdb=" O ARG B 379 " (cutoff:3.500A) Proline residue: B 387 - end of helix Processing helix chain 'B' and resid 401 through 419 Processing helix chain 'B' and resid 425 through 440 removed outlier: 3.728A pdb=" N LEU B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP B 440 " --> pdb=" O SER B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 467 removed outlier: 3.842A pdb=" N GLU B 460 " --> pdb=" O SER B 456 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU B 461 " --> pdb=" O ILE B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 472 removed outlier: 3.779A pdb=" N THR B 471 " --> pdb=" O SER B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 484 removed outlier: 3.668A pdb=" N PHE B 484 " --> pdb=" O THR B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 506 removed outlier: 3.946A pdb=" N LEU B 506 " --> pdb=" O THR B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 513 removed outlier: 4.461A pdb=" N THR B 512 " --> pdb=" O GLU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 536 removed outlier: 4.182A pdb=" N ILE B 520 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 529 " --> pdb=" O LEU B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 545 removed outlier: 3.955A pdb=" N PHE B 544 " --> pdb=" O ASP B 540 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY B 545 " --> pdb=" O ARG B 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 540 through 545' Processing helix chain 'B' and resid 551 through 567 removed outlier: 4.203A pdb=" N THR B 561 " --> pdb=" O ARG B 557 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU B 562 " --> pdb=" O ASP B 558 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU B 565 " --> pdb=" O THR B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 585 Processing helix chain 'B' and resid 591 through 602 Processing helix chain 'B' and resid 607 through 616 removed outlier: 3.735A pdb=" N ILE B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 631 removed outlier: 3.964A pdb=" N PHE B 631 " --> pdb=" O TYR B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 647 Processing helix chain 'B' and resid 654 through 672 removed outlier: 3.618A pdb=" N GLU B 659 " --> pdb=" O SER B 655 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG B 660 " --> pdb=" O GLN B 656 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ILE B 661 " --> pdb=" O GLN B 657 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE B 662 " --> pdb=" O ILE B 658 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU B 663 " --> pdb=" O GLU B 659 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA B 664 " --> pdb=" O ARG B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 713 Processing helix chain 'B' and resid 722 through 730 removed outlier: 3.899A pdb=" N GLY B 728 " --> pdb=" O GLU B 724 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN B 729 " --> pdb=" O ASP B 725 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU B 730 " --> pdb=" O TYR B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 754 removed outlier: 3.684A pdb=" N LEU B 744 " --> pdb=" O PRO B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 779 removed outlier: 4.278A pdb=" N SER B 779 " --> pdb=" O ASN B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 796 removed outlier: 3.669A pdb=" N ASP B 795 " --> pdb=" O SER B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 806 Processing helix chain 'B' and resid 806 through 828 removed outlier: 3.619A pdb=" N GLN B 812 " --> pdb=" O ALA B 808 " (cutoff:3.500A) Proline residue: B 815 - end of helix Processing helix chain 'B' and resid 830 through 852 removed outlier: 3.596A pdb=" N SER B 834 " --> pdb=" O ASP B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 868 removed outlier: 3.649A pdb=" N LEU B 861 " --> pdb=" O PHE B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 915 removed outlier: 3.749A pdb=" N SER B 915 " --> pdb=" O ARG B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 931 removed outlier: 3.682A pdb=" N ASN B 921 " --> pdb=" O LYS B 917 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR B 922 " --> pdb=" O GLY B 918 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL B 923 " --> pdb=" O GLN B 919 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 924 " --> pdb=" O LEU B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 956 removed outlier: 3.547A pdb=" N ASP B 956 " --> pdb=" O THR B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 972 removed outlier: 3.598A pdb=" N GLN B 968 " --> pdb=" O PHE B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 1009 through 1027 Processing helix chain 'B' and resid 1028 through 1033 removed outlier: 3.860A pdb=" N PHE B1033 " --> pdb=" O ALA B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1035 through 1039 removed outlier: 3.605A pdb=" N ILE B1039 " --> pdb=" O GLU B1036 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1050 Processing helix chain 'B' and resid 1056 through 1060 removed outlier: 3.864A pdb=" N SER B1060 " --> pdb=" O ALA B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1062 through 1081 removed outlier: 3.852A pdb=" N LEU B1067 " --> pdb=" O PHE B1063 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU B1068 " --> pdb=" O GLU B1064 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE B1080 " --> pdb=" O ALA B1076 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N CYS B1081 " --> pdb=" O LEU B1077 " (cutoff:3.500A) Processing helix chain 'B' and resid 1086 through 1100 Processing helix chain 'B' and resid 1105 through 1123 removed outlier: 3.632A pdb=" N VAL B1109 " --> pdb=" O THR B1105 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B1113 " --> pdb=" O VAL B1109 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR B1114 " --> pdb=" O ARG B1110 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR B1115 " --> pdb=" O ARG B1111 " (cutoff:3.500A) Processing helix chain 'B' and resid 1126 through 1137 Processing helix chain 'B' and resid 1146 through 1151 Processing helix chain 'B' and resid 1152 through 1168 removed outlier: 3.574A pdb=" N LYS B1156 " --> pdb=" O THR B1152 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU B1157 " --> pdb=" O ASN B1153 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR B1166 " --> pdb=" O LEU B1162 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU B1167 " --> pdb=" O PHE B1163 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B1168 " --> pdb=" O SER B1164 " (cutoff:3.500A) Processing helix chain 'B' and resid 1171 through 1178 removed outlier: 3.666A pdb=" N GLY B1177 " --> pdb=" O GLY B1173 " (cutoff:3.500A) Processing helix chain 'B' and resid 1178 through 1190 removed outlier: 3.801A pdb=" N TRP B1182 " --> pdb=" O ASN B1178 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B1190 " --> pdb=" O ARG B1186 " (cutoff:3.500A) Processing helix chain 'B' and resid 1191 through 1193 No H-bonds generated for 'chain 'B' and resid 1191 through 1193' Processing helix chain 'B' and resid 1194 through 1208 removed outlier: 4.126A pdb=" N THR B1208 " --> pdb=" O GLU B1204 " (cutoff:3.500A) Processing helix chain 'B' and resid 1217 through 1230 Processing helix chain 'B' and resid 1261 through 1275 removed outlier: 3.737A pdb=" N SER B1265 " --> pdb=" O SER B1261 " (cutoff:3.500A) Processing helix chain 'B' and resid 1276 through 1278 No H-bonds generated for 'chain 'B' and resid 1276 through 1278' Processing helix chain 'B' and resid 1283 through 1297 removed outlier: 3.583A pdb=" N ILE B1287 " --> pdb=" O ARG B1283 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE B1288 " --> pdb=" O LYS B1284 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN B1297 " --> pdb=" O ALA B1293 " (cutoff:3.500A) Processing helix chain 'B' and resid 1298 through 1300 No H-bonds generated for 'chain 'B' and resid 1298 through 1300' Processing helix chain 'B' and resid 1302 through 1320 removed outlier: 3.863A pdb=" N SER B1306 " --> pdb=" O CYS B1302 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B1311 " --> pdb=" O GLU B1307 " (cutoff:3.500A) Processing helix chain 'B' and resid 1330 through 1339 removed outlier: 3.859A pdb=" N LEU B1339 " --> pdb=" O ILE B1335 " (cutoff:3.500A) Processing helix chain 'B' and resid 1339 through 1344 Processing helix chain 'B' and resid 1349 through 1352 removed outlier: 3.918A pdb=" N GLN B1352 " --> pdb=" O GLN B1349 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1349 through 1352' Processing helix chain 'B' and resid 1353 through 1374 removed outlier: 4.032A pdb=" N SER B1358 " --> pdb=" O ILE B1354 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ILE B1359 " --> pdb=" O LEU B1355 " (cutoff:3.500A) Processing helix chain 'B' and resid 1377 through 1392 removed outlier: 3.692A pdb=" N PHE B1381 " --> pdb=" O SER B1377 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE B1391 " --> pdb=" O ILE B1387 " (cutoff:3.500A) Processing helix chain 'B' and resid 1394 through 1417 removed outlier: 5.694A pdb=" N LEU B1406 " --> pdb=" O GLN B1402 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASP B1407 " --> pdb=" O GLN B1403 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE B1411 " --> pdb=" O ASP B1407 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLU B1412 " --> pdb=" O LYS B1408 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LYS B1413 " --> pdb=" O LYS B1409 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 154 removed outlier: 4.050A pdb=" N PHE A 154 " --> pdb=" O GLY A 258 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 1101 hydrogen bonds defined for protein. 3249 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.05 Time building geometry restraints manager: 4.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 20058 1.03 - 1.23: 47 1.23 - 1.42: 7991 1.42 - 1.62: 11844 1.62 - 1.82: 114 Bond restraints: 40054 Sorted by residual: bond pdb=" CB ILE A 15 " pdb=" CG2 ILE A 15 " ideal model delta sigma weight residual 1.521 1.601 -0.080 3.30e-02 9.18e+02 5.87e+00 bond pdb=" CB ILE B 357 " pdb=" CG2 ILE B 357 " ideal model delta sigma weight residual 1.521 1.598 -0.077 3.30e-02 9.18e+02 5.51e+00 bond pdb=" CB ASP A 842 " pdb=" CG ASP A 842 " ideal model delta sigma weight residual 1.516 1.572 -0.056 2.50e-02 1.60e+03 5.07e+00 bond pdb=" CB ILE A 946 " pdb=" CG2 ILE A 946 " ideal model delta sigma weight residual 1.521 1.592 -0.071 3.30e-02 9.18e+02 4.63e+00 bond pdb=" CB ILE B 864 " pdb=" CG2 ILE B 864 " ideal model delta sigma weight residual 1.521 1.589 -0.068 3.30e-02 9.18e+02 4.29e+00 ... (remaining 40049 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 68762 1.77 - 3.55: 3366 3.55 - 5.32: 485 5.32 - 7.09: 99 7.09 - 8.87: 24 Bond angle restraints: 72736 Sorted by residual: angle pdb=" CA GLN B1194 " pdb=" CB GLN B1194 " pdb=" CG GLN B1194 " ideal model delta sigma weight residual 114.10 122.85 -8.75 2.00e+00 2.50e-01 1.92e+01 angle pdb=" CA GLU B 766 " pdb=" CB GLU B 766 " pdb=" CG GLU B 766 " ideal model delta sigma weight residual 114.10 122.67 -8.57 2.00e+00 2.50e-01 1.84e+01 angle pdb=" CA ARG B1283 " pdb=" CB ARG B1283 " pdb=" CG ARG B1283 " ideal model delta sigma weight residual 114.10 121.64 -7.54 2.00e+00 2.50e-01 1.42e+01 angle pdb=" CB ASP A 842 " pdb=" CG ASP A 842 " pdb=" OD1 ASP A 842 " ideal model delta sigma weight residual 118.40 126.94 -8.54 2.30e+00 1.89e-01 1.38e+01 angle pdb=" CA ASP A 842 " pdb=" CB ASP A 842 " pdb=" CG ASP A 842 " ideal model delta sigma weight residual 112.60 116.31 -3.71 1.00e+00 1.00e+00 1.38e+01 ... (remaining 72731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 15723 17.88 - 35.76: 2118 35.76 - 53.64: 634 53.64 - 71.52: 152 71.52 - 89.39: 37 Dihedral angle restraints: 18664 sinusoidal: 10328 harmonic: 8336 Sorted by residual: dihedral pdb=" CA ASN A 607 " pdb=" C ASN A 607 " pdb=" N LYS A 608 " pdb=" CA LYS A 608 " ideal model delta harmonic sigma weight residual -180.00 -152.14 -27.86 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA LEU B 329 " pdb=" C LEU B 329 " pdb=" N PRO B 330 " pdb=" CA PRO B 330 " ideal model delta harmonic sigma weight residual -180.00 -156.62 -23.38 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA LEU A 329 " pdb=" C LEU A 329 " pdb=" N PRO A 330 " pdb=" CA PRO A 330 " ideal model delta harmonic sigma weight residual -180.00 -157.09 -22.91 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 18661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2458 0.046 - 0.092: 580 0.092 - 0.139: 145 0.139 - 0.185: 17 0.185 - 0.231: 4 Chirality restraints: 3204 Sorted by residual: chirality pdb=" CB THR A 820 " pdb=" CA THR A 820 " pdb=" OG1 THR A 820 " pdb=" CG2 THR A 820 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB ILE B1091 " pdb=" CA ILE B1091 " pdb=" CG1 ILE B1091 " pdb=" CG2 ILE B1091 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CG LEU A1225 " pdb=" CB LEU A1225 " pdb=" CD1 LEU A1225 " pdb=" CD2 LEU A1225 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 3201 not shown) Planarity restraints: 5756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 333 " 0.267 9.50e-02 1.11e+02 8.95e-02 9.53e+00 pdb=" NE ARG B 333 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG B 333 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 333 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 333 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG B 333 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG B 333 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG B 333 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG B 333 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 617 " 0.048 5.00e-02 4.00e+02 7.33e-02 8.61e+00 pdb=" N PRO B 618 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 618 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 618 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 665 " 0.014 2.00e-02 2.50e+03 1.48e-02 6.61e+00 pdb=" CG PHE A 665 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE A 665 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A 665 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE A 665 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 665 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 665 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE A 665 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE A 665 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE A 665 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE A 665 " 0.003 2.00e-02 2.50e+03 pdb=" HZ PHE A 665 " -0.001 2.00e-02 2.50e+03 ... (remaining 5753 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.29: 7798 2.29 - 2.87: 89589 2.87 - 3.45: 102130 3.45 - 4.02: 128247 4.02 - 4.60: 196950 Nonbonded interactions: 524714 Sorted by model distance: nonbonded pdb=" OE1 GLU A 562 " pdb=" H GLU A 562 " model vdw 1.719 2.450 nonbonded pdb=" OE1 GLU A 941 " pdb=" H GLU A 941 " model vdw 1.722 2.450 nonbonded pdb=" OE1 GLU B1286 " pdb=" H GLU B1286 " model vdw 1.731 2.450 nonbonded pdb=" OD1 ASN A1178 " pdb=" H PHE A1181 " model vdw 1.732 2.450 nonbonded pdb=" OD1 ASN B1178 " pdb=" H PHE B1181 " model vdw 1.746 2.450 ... (remaining 524709 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 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: 0.200 Extract box with map and model: 0.510 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 35.490 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 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 0.080 19962 Z= 0.240 Angle : 0.933 8.867 26956 Z= 0.474 Chirality : 0.044 0.231 3204 Planarity : 0.006 0.118 3392 Dihedral : 18.883 89.394 7528 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.05 % Favored : 94.91 % Rotamer: Outliers : 0.53 % Allowed : 32.15 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.16), residues: 2416 helix: 0.33 (0.12), residues: 1538 sheet: None (None), residues: 0 loop : -1.24 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 333 TYR 0.027 0.001 TYR B 181 PHE 0.043 0.002 PHE A 665 TRP 0.020 0.002 TRP A1182 HIS 0.003 0.001 HIS B 617 Details of bonding type rmsd covalent geometry : bond 0.00584 (19962) covalent geometry : angle 0.93300 (26956) hydrogen bonds : bond 0.13279 ( 1101) hydrogen bonds : angle 5.44915 ( 3249) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 669 time to evaluate : 1.033 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 171 PHE cc_start: 0.7099 (m-80) cc_final: 0.6860 (m-80) REVERT: A 665 PHE cc_start: 0.8233 (t80) cc_final: 0.7903 (t80) REVERT: B 770 GLU cc_start: 0.8868 (tt0) cc_final: 0.8117 (mp0) REVERT: B 831 ASP cc_start: 0.7753 (m-30) cc_final: 0.7481 (m-30) REVERT: B 916 PHE cc_start: 0.8142 (t80) cc_final: 0.7835 (t80) REVERT: B 1063 PHE cc_start: 0.9167 (t80) cc_final: 0.8846 (t80) REVERT: B 1166 THR cc_start: 0.8773 (p) cc_final: 0.8439 (m) REVERT: B 1270 GLN cc_start: 0.7109 (mm-40) cc_final: 0.6905 (mm-40) outliers start: 12 outliers final: 9 residues processed: 672 average time/residue: 0.2933 time to fit residues: 318.3850 Evaluate side-chains 657 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 648 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 726 TYR Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 1381 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 639 ASP Chi-restraints excluded: chain B residue 1150 PHE Chi-restraints excluded: chain B residue 1339 LEU Chi-restraints excluded: chain B residue 1376 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.0970 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 235 optimal weight: 0.5980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 617 HIS A 736 HIS A 975 ASN A1352 GLN B 142 HIS B 716 GLN B 919 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.146319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.124003 restraints weight = 110750.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.128956 restraints weight = 46043.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.132096 restraints weight = 25511.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.134111 restraints weight = 16679.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.135429 restraints weight = 12276.049| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19962 Z= 0.152 Angle : 0.548 6.556 26956 Z= 0.297 Chirality : 0.034 0.136 3204 Planarity : 0.004 0.058 3392 Dihedral : 5.338 57.947 2589 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.30 % Favored : 94.62 % Rotamer: Outliers : 3.52 % Allowed : 30.47 % Favored : 66.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.17), residues: 2416 helix: 1.07 (0.13), residues: 1584 sheet: None (None), residues: 0 loop : -0.98 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 333 TYR 0.010 0.001 TYR B1171 PHE 0.014 0.001 PHE B1288 TRP 0.009 0.001 TRP A1182 HIS 0.004 0.001 HIS B 617 Details of bonding type rmsd covalent geometry : bond 0.00338 (19962) covalent geometry : angle 0.54838 (26956) hydrogen bonds : bond 0.04105 ( 1101) hydrogen bonds : angle 4.40773 ( 3249) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 671 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLN cc_start: 0.7940 (mt0) cc_final: 0.7690 (mt0) REVERT: A 381 PHE cc_start: 0.7897 (t80) cc_final: 0.7486 (t80) REVERT: A 426 GLN cc_start: 0.9040 (mp10) cc_final: 0.8789 (mp10) REVERT: A 665 PHE cc_start: 0.8687 (t80) cc_final: 0.8354 (t80) REVERT: A 678 SER cc_start: 0.4839 (OUTLIER) cc_final: 0.4231 (p) REVERT: A 801 GLU cc_start: 0.9304 (pm20) cc_final: 0.8943 (pm20) REVERT: A 1005 ASP cc_start: 0.2798 (OUTLIER) cc_final: -0.0782 (p0) REVERT: B 208 GLU cc_start: 0.7874 (tp30) cc_final: 0.7514 (tp30) REVERT: B 465 GLN cc_start: 0.8630 (mm-40) cc_final: 0.8395 (mm-40) REVERT: B 554 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.8659 (tt) REVERT: B 753 ASP cc_start: 0.7011 (OUTLIER) cc_final: 0.6655 (t70) REVERT: B 770 GLU cc_start: 0.8936 (tt0) cc_final: 0.8438 (mp0) REVERT: B 1286 GLU cc_start: 0.8680 (mp0) cc_final: 0.8251 (mp0) outliers start: 80 outliers final: 59 residues processed: 703 average time/residue: 0.2908 time to fit residues: 331.4720 Evaluate side-chains 722 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 659 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 726 TYR Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 763 HIS Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1005 ASP Chi-restraints excluded: chain A residue 1016 SER Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1265 SER Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1381 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 639 ASP Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 742 TRP Chi-restraints excluded: chain B residue 753 ASP Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 820 THR Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 966 ASP Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain B residue 1032 VAL Chi-restraints excluded: chain B residue 1073 LEU Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain B residue 1150 PHE Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain B residue 1221 VAL Chi-restraints excluded: chain B residue 1339 LEU Chi-restraints excluded: chain B residue 1358 SER Chi-restraints excluded: chain B residue 1362 ILE Chi-restraints excluded: chain B residue 1363 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 200 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 178 optimal weight: 0.7980 chunk 152 optimal weight: 0.2980 chunk 55 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 219 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 212 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.152197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.130944 restraints weight = 112611.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.135632 restraints weight = 51043.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.138620 restraints weight = 29524.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.140551 restraints weight = 19798.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.141815 restraints weight = 14790.533| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19962 Z= 0.136 Angle : 0.525 5.690 26956 Z= 0.283 Chirality : 0.034 0.136 3204 Planarity : 0.004 0.057 3392 Dihedral : 5.179 58.986 2587 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.59 % Favored : 94.33 % Rotamer: Outliers : 3.91 % Allowed : 30.78 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.17), residues: 2416 helix: 1.33 (0.13), residues: 1574 sheet: None (None), residues: 0 loop : -0.91 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 333 TYR 0.009 0.001 TYR B 327 PHE 0.016 0.001 PHE A 850 TRP 0.008 0.001 TRP A1182 HIS 0.004 0.001 HIS B 617 Details of bonding type rmsd covalent geometry : bond 0.00296 (19962) covalent geometry : angle 0.52524 (26956) hydrogen bonds : bond 0.03819 ( 1101) hydrogen bonds : angle 4.23594 ( 3249) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 674 time to evaluate : 1.030 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: A 381 PHE cc_start: 0.8044 (t80) cc_final: 0.7501 (t80) REVERT: A 426 GLN cc_start: 0.8999 (mp10) cc_final: 0.8742 (mp10) REVERT: A 678 SER cc_start: 0.4823 (OUTLIER) cc_final: 0.4223 (p) REVERT: A 939 SER cc_start: 0.8575 (OUTLIER) cc_final: 0.8338 (t) REVERT: A 971 LEU cc_start: 0.9471 (mt) cc_final: 0.9230 (mt) REVERT: A 1005 ASP cc_start: 0.2865 (OUTLIER) cc_final: 0.0639 (m-30) REVERT: A 1011 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6589 (mp0) REVERT: B 208 GLU cc_start: 0.7903 (tp30) cc_final: 0.7556 (tp30) REVERT: B 465 GLN cc_start: 0.8692 (mm-40) cc_final: 0.8398 (mm-40) REVERT: B 554 LEU cc_start: 0.9508 (mm) cc_final: 0.8703 (tt) REVERT: B 753 ASP cc_start: 0.7282 (OUTLIER) cc_final: 0.6913 (t0) REVERT: B 770 GLU cc_start: 0.8918 (tt0) cc_final: 0.8442 (mp0) REVERT: B 917 LYS cc_start: 0.9127 (mmmm) cc_final: 0.8884 (mmmm) REVERT: B 1011 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: B 1222 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8319 (mp) REVERT: B 1286 GLU cc_start: 0.8690 (mp0) cc_final: 0.8330 (mp0) outliers start: 89 outliers final: 70 residues processed: 712 average time/residue: 0.2725 time to fit residues: 315.5974 Evaluate side-chains 735 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 658 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 726 TYR Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 763 HIS Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 987 LYS Chi-restraints excluded: chain A residue 1005 ASP Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1016 SER Chi-restraints excluded: chain A residue 1022 CYS Chi-restraints excluded: chain A residue 1091 ILE Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1265 SER Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1363 ILE Chi-restraints excluded: chain A residue 1381 PHE Chi-restraints excluded: chain A residue 1398 GLU Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 639 ASP Chi-restraints excluded: chain B residue 742 TRP Chi-restraints excluded: chain B residue 753 ASP Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 820 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 966 ASP Chi-restraints excluded: chain B residue 968 GLN Chi-restraints excluded: chain B residue 1011 GLU Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain B residue 1032 VAL Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain B residue 1070 ILE Chi-restraints excluded: chain B residue 1073 LEU Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1100 HIS Chi-restraints excluded: chain B residue 1150 PHE Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain B residue 1221 VAL Chi-restraints excluded: chain B residue 1222 LEU Chi-restraints excluded: chain B residue 1339 LEU Chi-restraints excluded: chain B residue 1362 ILE Chi-restraints excluded: chain B residue 1363 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 156 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 177 optimal weight: 0.0970 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 241 optimal weight: 0.7980 chunk 114 optimal weight: 0.2980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN A 968 GLN A 975 ASN B1154 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.144712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.122511 restraints weight = 112058.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.127344 restraints weight = 48450.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.130449 restraints weight = 27434.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.132432 restraints weight = 18195.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.133725 restraints weight = 13510.235| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19962 Z= 0.120 Angle : 0.511 6.130 26956 Z= 0.274 Chirality : 0.034 0.176 3204 Planarity : 0.003 0.052 3392 Dihedral : 5.063 58.068 2587 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.30 % Favored : 94.62 % Rotamer: Outliers : 4.35 % Allowed : 31.35 % Favored : 64.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.17), residues: 2416 helix: 1.42 (0.13), residues: 1586 sheet: None (None), residues: 0 loop : -0.94 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1110 TYR 0.009 0.001 TYR B 327 PHE 0.017 0.001 PHE A 850 TRP 0.008 0.001 TRP A1182 HIS 0.003 0.001 HIS B 617 Details of bonding type rmsd covalent geometry : bond 0.00269 (19962) covalent geometry : angle 0.51112 (26956) hydrogen bonds : bond 0.03489 ( 1101) hydrogen bonds : angle 4.13571 ( 3249) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 681 time to evaluate : 1.291 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: A 327 TYR cc_start: 0.7104 (t80) cc_final: 0.6886 (t80) REVERT: A 381 PHE cc_start: 0.8071 (t80) cc_final: 0.7546 (t80) REVERT: A 426 GLN cc_start: 0.9002 (mp10) cc_final: 0.8762 (mp10) REVERT: A 532 MET cc_start: 0.8328 (mmm) cc_final: 0.8122 (tpp) REVERT: A 626 GLU cc_start: 0.8265 (tp30) cc_final: 0.6617 (tt0) REVERT: A 678 SER cc_start: 0.4842 (OUTLIER) cc_final: 0.4231 (p) REVERT: A 971 LEU cc_start: 0.9474 (mt) cc_final: 0.9227 (mt) REVERT: A 1005 ASP cc_start: 0.2971 (OUTLIER) cc_final: 0.0701 (m-30) REVERT: A 1011 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6582 (mp0) REVERT: B 82 MET cc_start: 0.8303 (ttm) cc_final: 0.7988 (ttm) REVERT: B 88 ASN cc_start: 0.9425 (OUTLIER) cc_final: 0.9183 (p0) REVERT: B 208 GLU cc_start: 0.7887 (tp30) cc_final: 0.7542 (tp30) REVERT: B 465 GLN cc_start: 0.8626 (mm-40) cc_final: 0.8297 (mm-40) REVERT: B 554 LEU cc_start: 0.9505 (mm) cc_final: 0.8703 (tt) REVERT: B 753 ASP cc_start: 0.7295 (OUTLIER) cc_final: 0.6899 (t0) REVERT: B 770 GLU cc_start: 0.8929 (tt0) cc_final: 0.8496 (mp0) REVERT: B 917 LYS cc_start: 0.9137 (mmmm) cc_final: 0.8828 (mmmm) REVERT: B 1011 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: B 1222 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8474 (mp) REVERT: B 1283 ARG cc_start: 0.6905 (tpt170) cc_final: 0.6595 (tpt90) REVERT: B 1286 GLU cc_start: 0.8683 (mp0) cc_final: 0.8443 (mp0) outliers start: 99 outliers final: 76 residues processed: 722 average time/residue: 0.2683 time to fit residues: 315.5755 Evaluate side-chains 744 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 661 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 726 TYR Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 832 HIS Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 987 LYS Chi-restraints excluded: chain A residue 1005 ASP Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1016 SER Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1265 SER Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1363 ILE Chi-restraints excluded: chain A residue 1381 PHE Chi-restraints excluded: chain A residue 1398 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 742 TRP Chi-restraints excluded: chain B residue 753 ASP Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 806 ASP Chi-restraints excluded: chain B residue 820 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 858 ASN Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 957 LEU Chi-restraints excluded: chain B residue 966 ASP Chi-restraints excluded: chain B residue 968 GLN Chi-restraints excluded: chain B residue 1011 GLU Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain B residue 1032 VAL Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1100 HIS Chi-restraints excluded: chain B residue 1150 PHE Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain B residue 1221 VAL Chi-restraints excluded: chain B residue 1222 LEU Chi-restraints excluded: chain B residue 1339 LEU Chi-restraints excluded: chain B residue 1358 SER Chi-restraints excluded: chain B residue 1362 ILE Chi-restraints excluded: chain B residue 1363 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 161 optimal weight: 0.4980 chunk 187 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 192 optimal weight: 0.0370 chunk 85 optimal weight: 1.9990 chunk 202 optimal weight: 0.9990 chunk 227 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 HIS A 968 GLN A 975 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.150692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.128879 restraints weight = 112751.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.133823 restraints weight = 48478.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.136961 restraints weight = 27149.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.138976 restraints weight = 17821.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.140298 restraints weight = 13128.599| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19962 Z= 0.151 Angle : 0.528 6.770 26956 Z= 0.285 Chirality : 0.035 0.166 3204 Planarity : 0.003 0.051 3392 Dihedral : 5.039 58.513 2585 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.92 % Favored : 94.00 % Rotamer: Outliers : 5.01 % Allowed : 31.31 % Favored : 63.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.17), residues: 2416 helix: 1.40 (0.13), residues: 1588 sheet: None (None), residues: 0 loop : -1.00 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 637 TYR 0.008 0.001 TYR B 327 PHE 0.020 0.001 PHE A 850 TRP 0.008 0.001 TRP A1182 HIS 0.005 0.001 HIS B 617 Details of bonding type rmsd covalent geometry : bond 0.00337 (19962) covalent geometry : angle 0.52795 (26956) hydrogen bonds : bond 0.03534 ( 1101) hydrogen bonds : angle 4.19828 ( 3249) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 677 time to evaluate : 1.048 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 381 PHE cc_start: 0.8168 (t80) cc_final: 0.7554 (t80) REVERT: A 426 GLN cc_start: 0.9144 (mp10) cc_final: 0.8858 (mp10) REVERT: A 626 GLU cc_start: 0.8313 (tp30) cc_final: 0.6688 (tt0) REVERT: A 678 SER cc_start: 0.5828 (OUTLIER) cc_final: 0.5405 (p) REVERT: A 745 ASP cc_start: 0.7409 (m-30) cc_final: 0.7011 (m-30) REVERT: A 971 LEU cc_start: 0.9476 (mt) cc_final: 0.9245 (mt) REVERT: A 1005 ASP cc_start: 0.2701 (OUTLIER) cc_final: 0.0365 (m-30) REVERT: A 1011 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6783 (mp0) REVERT: B 82 MET cc_start: 0.8313 (ttm) cc_final: 0.7979 (ttm) REVERT: B 88 ASN cc_start: 0.9441 (OUTLIER) cc_final: 0.9201 (p0) REVERT: B 208 GLU cc_start: 0.7864 (tp30) cc_final: 0.7657 (tp30) REVERT: B 327 TYR cc_start: 0.7715 (OUTLIER) cc_final: 0.7302 (t80) REVERT: B 465 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8305 (mm-40) REVERT: B 554 LEU cc_start: 0.9503 (mm) cc_final: 0.8716 (tt) REVERT: B 753 ASP cc_start: 0.7398 (OUTLIER) cc_final: 0.6993 (t0) REVERT: B 770 GLU cc_start: 0.8931 (tt0) cc_final: 0.8502 (mp0) REVERT: B 775 ASN cc_start: 0.8728 (m-40) cc_final: 0.8469 (m-40) REVERT: B 917 LYS cc_start: 0.9125 (mmmm) cc_final: 0.8769 (mmmm) REVERT: B 1011 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7591 (mp0) REVERT: B 1119 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8995 (mm) REVERT: B 1207 LYS cc_start: 0.8440 (mmmt) cc_final: 0.8103 (mmtp) REVERT: B 1286 GLU cc_start: 0.8737 (mp0) cc_final: 0.8465 (mp0) REVERT: B 1412 GLU cc_start: 0.5733 (OUTLIER) cc_final: 0.5450 (pp20) outliers start: 114 outliers final: 93 residues processed: 730 average time/residue: 0.2782 time to fit residues: 330.2750 Evaluate side-chains 764 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 662 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 726 TYR Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 763 HIS Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 832 HIS Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 987 LYS Chi-restraints excluded: chain A residue 1005 ASP Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1016 SER Chi-restraints excluded: chain A residue 1022 CYS Chi-restraints excluded: chain A residue 1081 CYS Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1265 SER Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1363 ILE Chi-restraints excluded: chain A residue 1381 PHE Chi-restraints excluded: chain A residue 1398 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 327 TYR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 639 ASP Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 742 TRP Chi-restraints excluded: chain B residue 753 ASP Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 806 ASP Chi-restraints excluded: chain B residue 810 PHE Chi-restraints excluded: chain B residue 820 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 858 ASN Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 957 LEU Chi-restraints excluded: chain B residue 966 ASP Chi-restraints excluded: chain B residue 968 GLN Chi-restraints excluded: chain B residue 987 LYS Chi-restraints excluded: chain B residue 1011 GLU Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain B residue 1070 ILE Chi-restraints excluded: chain B residue 1100 HIS Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1150 PHE Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain B residue 1221 VAL Chi-restraints excluded: chain B residue 1328 MET Chi-restraints excluded: chain B residue 1356 ILE Chi-restraints excluded: chain B residue 1358 SER Chi-restraints excluded: chain B residue 1362 ILE Chi-restraints excluded: chain B residue 1363 ILE Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1412 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 0.1980 chunk 120 optimal weight: 0.9990 chunk 222 optimal weight: 0.9980 chunk 195 optimal weight: 0.9990 chunk 170 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3645 r_free = 0.3645 target = 0.147993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.126200 restraints weight = 113190.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.131078 restraints weight = 48821.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.134186 restraints weight = 27452.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.136207 restraints weight = 18101.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.137511 restraints weight = 13323.083| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19962 Z= 0.167 Angle : 0.543 5.953 26956 Z= 0.294 Chirality : 0.035 0.156 3204 Planarity : 0.003 0.050 3392 Dihedral : 5.058 59.764 2583 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.21 % Favored : 93.75 % Rotamer: Outliers : 5.50 % Allowed : 32.06 % Favored : 62.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.17), residues: 2416 helix: 1.33 (0.13), residues: 1598 sheet: None (None), residues: 0 loop : -1.10 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 333 TYR 0.008 0.001 TYR B 327 PHE 0.021 0.001 PHE A 850 TRP 0.008 0.001 TRP A1182 HIS 0.006 0.001 HIS B 617 Details of bonding type rmsd covalent geometry : bond 0.00372 (19962) covalent geometry : angle 0.54263 (26956) hydrogen bonds : bond 0.03605 ( 1101) hydrogen bonds : angle 4.25187 ( 3249) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 663 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 PHE cc_start: 0.8168 (t80) cc_final: 0.7529 (t80) REVERT: A 426 GLN cc_start: 0.9194 (mp10) cc_final: 0.8867 (mp10) REVERT: A 472 ARG cc_start: 0.8264 (tpp-160) cc_final: 0.8001 (tpp-160) REVERT: A 678 SER cc_start: 0.5802 (OUTLIER) cc_final: 0.5394 (p) REVERT: A 741 PHE cc_start: 0.7040 (m-10) cc_final: 0.6832 (m-10) REVERT: A 745 ASP cc_start: 0.7548 (m-30) cc_final: 0.7114 (m-30) REVERT: A 747 ILE cc_start: 0.9056 (tp) cc_final: 0.8822 (tp) REVERT: A 941 GLU cc_start: 0.8062 (mp0) cc_final: 0.7798 (mp0) REVERT: A 971 LEU cc_start: 0.9472 (mt) cc_final: 0.9227 (mt) REVERT: A 1005 ASP cc_start: 0.2878 (OUTLIER) cc_final: 0.1489 (t70) REVERT: A 1011 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6817 (mp0) REVERT: B 88 ASN cc_start: 0.9557 (OUTLIER) cc_final: 0.9202 (p0) REVERT: B 208 GLU cc_start: 0.7878 (tp30) cc_final: 0.7646 (tp30) REVERT: B 327 TYR cc_start: 0.7594 (OUTLIER) cc_final: 0.7170 (t80) REVERT: B 459 LYS cc_start: 0.9393 (mttm) cc_final: 0.9163 (mttm) REVERT: B 465 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8417 (mm-40) REVERT: B 753 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7213 (t0) REVERT: B 770 GLU cc_start: 0.8956 (tt0) cc_final: 0.8480 (mp0) REVERT: B 917 LYS cc_start: 0.9023 (mmmm) cc_final: 0.8624 (mmmm) REVERT: B 1011 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: B 1100 HIS cc_start: 0.8605 (OUTLIER) cc_final: 0.8243 (t-90) REVERT: B 1119 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9086 (mm) REVERT: B 1207 LYS cc_start: 0.8442 (mmmt) cc_final: 0.8062 (mmtp) REVERT: B 1222 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8518 (mp) REVERT: B 1412 GLU cc_start: 0.5696 (OUTLIER) cc_final: 0.5444 (pp20) outliers start: 125 outliers final: 96 residues processed: 726 average time/residue: 0.2866 time to fit residues: 336.9860 Evaluate side-chains 762 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 655 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 726 TYR Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 763 HIS Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 832 HIS Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 987 LYS Chi-restraints excluded: chain A residue 1005 ASP Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1016 SER Chi-restraints excluded: chain A residue 1022 CYS Chi-restraints excluded: chain A residue 1081 CYS Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1214 THR Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1265 SER Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1348 THR Chi-restraints excluded: chain A residue 1363 ILE Chi-restraints excluded: chain A residue 1381 PHE Chi-restraints excluded: chain A residue 1398 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 327 TYR Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 639 ASP Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 742 TRP Chi-restraints excluded: chain B residue 753 ASP Chi-restraints excluded: chain B residue 779 SER Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 806 ASP Chi-restraints excluded: chain B residue 810 PHE Chi-restraints excluded: chain B residue 820 THR Chi-restraints excluded: chain B residue 824 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 858 ASN Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 957 LEU Chi-restraints excluded: chain B residue 966 ASP Chi-restraints excluded: chain B residue 968 GLN Chi-restraints excluded: chain B residue 987 LYS Chi-restraints excluded: chain B residue 1011 GLU Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain B residue 1070 ILE Chi-restraints excluded: chain B residue 1100 HIS Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain B residue 1221 VAL Chi-restraints excluded: chain B residue 1222 LEU Chi-restraints excluded: chain B residue 1328 MET Chi-restraints excluded: chain B residue 1356 ILE Chi-restraints excluded: chain B residue 1358 SER Chi-restraints excluded: chain B residue 1362 ILE Chi-restraints excluded: chain B residue 1363 ILE Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1412 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 92 optimal weight: 0.4980 chunk 180 optimal weight: 2.9990 chunk 238 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 217 optimal weight: 0.5980 chunk 187 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 147 optimal weight: 0.6980 chunk 225 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.145742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.124129 restraints weight = 111152.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.128908 restraints weight = 47813.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.131971 restraints weight = 26868.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.133942 restraints weight = 17709.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.135240 restraints weight = 13064.760| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19962 Z= 0.136 Angle : 0.531 6.466 26956 Z= 0.285 Chirality : 0.035 0.176 3204 Planarity : 0.003 0.047 3392 Dihedral : 4.890 59.509 2581 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.92 % Favored : 94.04 % Rotamer: Outliers : 4.84 % Allowed : 32.50 % Favored : 62.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.17), residues: 2416 helix: 1.38 (0.13), residues: 1600 sheet: None (None), residues: 0 loop : -1.10 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1283 TYR 0.008 0.001 TYR B 327 PHE 0.020 0.001 PHE A 850 TRP 0.008 0.001 TRP A1182 HIS 0.004 0.001 HIS B 713 Details of bonding type rmsd covalent geometry : bond 0.00308 (19962) covalent geometry : angle 0.53068 (26956) hydrogen bonds : bond 0.03478 ( 1101) hydrogen bonds : angle 4.16248 ( 3249) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 666 time to evaluate : 1.045 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: A 381 PHE cc_start: 0.8025 (t80) cc_final: 0.7368 (t80) REVERT: A 410 GLN cc_start: 0.7900 (tp40) cc_final: 0.7456 (tp-100) REVERT: A 426 GLN cc_start: 0.9178 (mp10) cc_final: 0.8855 (mp10) REVERT: A 472 ARG cc_start: 0.8259 (tpp-160) cc_final: 0.8009 (tpp-160) REVERT: A 678 SER cc_start: 0.5782 (OUTLIER) cc_final: 0.5373 (p) REVERT: A 745 ASP cc_start: 0.7556 (m-30) cc_final: 0.7103 (m-30) REVERT: A 747 ILE cc_start: 0.9077 (tp) cc_final: 0.8852 (tp) REVERT: A 944 LEU cc_start: 0.8848 (mp) cc_final: 0.8625 (mp) REVERT: A 971 LEU cc_start: 0.9468 (mt) cc_final: 0.9230 (mt) REVERT: A 1005 ASP cc_start: 0.2887 (OUTLIER) cc_final: 0.1498 (t70) REVERT: A 1011 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6797 (mp0) REVERT: B 88 ASN cc_start: 0.9551 (OUTLIER) cc_final: 0.9195 (p0) REVERT: B 208 GLU cc_start: 0.7838 (tp30) cc_final: 0.7609 (tp30) REVERT: B 459 LYS cc_start: 0.9398 (mttm) cc_final: 0.9165 (mttm) REVERT: B 465 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8380 (mm-40) REVERT: B 753 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7199 (t0) REVERT: B 770 GLU cc_start: 0.8951 (tt0) cc_final: 0.8480 (mp0) REVERT: B 917 LYS cc_start: 0.8972 (mmmm) cc_final: 0.8536 (mmmm) REVERT: B 1011 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: B 1100 HIS cc_start: 0.8606 (OUTLIER) cc_final: 0.8264 (t-90) REVERT: B 1119 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9087 (mm) REVERT: B 1207 LYS cc_start: 0.8439 (mmmt) cc_final: 0.8053 (mmtp) REVERT: B 1222 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8522 (mp) REVERT: B 1412 GLU cc_start: 0.5680 (OUTLIER) cc_final: 0.5451 (pp20) outliers start: 110 outliers final: 92 residues processed: 718 average time/residue: 0.2921 time to fit residues: 340.7476 Evaluate side-chains 751 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 649 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 670 CYS Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 726 TYR Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 832 HIS Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 987 LYS Chi-restraints excluded: chain A residue 1005 ASP Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1016 SER Chi-restraints excluded: chain A residue 1022 CYS Chi-restraints excluded: chain A residue 1081 CYS Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1214 THR Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1265 SER Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1348 THR Chi-restraints excluded: chain A residue 1363 ILE Chi-restraints excluded: chain A residue 1381 PHE Chi-restraints excluded: chain A residue 1398 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 639 ASP Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 742 TRP Chi-restraints excluded: chain B residue 753 ASP Chi-restraints excluded: chain B residue 779 SER Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 806 ASP Chi-restraints excluded: chain B residue 810 PHE Chi-restraints excluded: chain B residue 820 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 858 ASN Chi-restraints excluded: chain B residue 966 ASP Chi-restraints excluded: chain B residue 968 GLN Chi-restraints excluded: chain B residue 987 LYS Chi-restraints excluded: chain B residue 1011 GLU Chi-restraints excluded: chain B residue 1016 SER Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain B residue 1070 ILE Chi-restraints excluded: chain B residue 1100 HIS Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain B residue 1221 VAL Chi-restraints excluded: chain B residue 1222 LEU Chi-restraints excluded: chain B residue 1328 MET Chi-restraints excluded: chain B residue 1339 LEU Chi-restraints excluded: chain B residue 1356 ILE Chi-restraints excluded: chain B residue 1358 SER Chi-restraints excluded: chain B residue 1362 ILE Chi-restraints excluded: chain B residue 1363 ILE Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1412 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 165 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 178 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 163 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 122 optimal weight: 0.0570 chunk 77 optimal weight: 0.0970 chunk 128 optimal weight: 0.2980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 968 GLN A 975 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.151316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.129428 restraints weight = 112290.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.134460 restraints weight = 47903.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.137652 restraints weight = 26615.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.139711 restraints weight = 17344.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.141040 restraints weight = 12646.146| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19962 Z= 0.117 Angle : 0.521 5.832 26956 Z= 0.278 Chirality : 0.034 0.146 3204 Planarity : 0.003 0.047 3392 Dihedral : 4.827 59.670 2581 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.84 % Favored : 94.12 % Rotamer: Outliers : 4.66 % Allowed : 32.59 % Favored : 62.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.18), residues: 2416 helix: 1.48 (0.13), residues: 1600 sheet: None (None), residues: 0 loop : -1.04 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 629 TYR 0.008 0.001 TYR B 327 PHE 0.026 0.001 PHE B 850 TRP 0.008 0.001 TRP A1182 HIS 0.004 0.001 HIS B 713 Details of bonding type rmsd covalent geometry : bond 0.00270 (19962) covalent geometry : angle 0.52115 (26956) hydrogen bonds : bond 0.03327 ( 1101) hydrogen bonds : angle 4.05982 ( 3249) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 664 time to evaluate : 0.918 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: A 410 GLN cc_start: 0.7906 (tp40) cc_final: 0.7473 (tp-100) REVERT: A 426 GLN cc_start: 0.9183 (mp10) cc_final: 0.8910 (mp10) REVERT: A 472 ARG cc_start: 0.8318 (tpp-160) cc_final: 0.8113 (tpp-160) REVERT: A 626 GLU cc_start: 0.8420 (tp30) cc_final: 0.7142 (tt0) REVERT: A 678 SER cc_start: 0.5826 (OUTLIER) cc_final: 0.5403 (p) REVERT: A 725 ASP cc_start: 0.2143 (OUTLIER) cc_final: 0.1896 (m-30) REVERT: A 745 ASP cc_start: 0.7427 (m-30) cc_final: 0.6984 (m-30) REVERT: A 747 ILE cc_start: 0.9101 (tp) cc_final: 0.8878 (tp) REVERT: A 941 GLU cc_start: 0.8023 (mp0) cc_final: 0.7788 (mp0) REVERT: A 944 LEU cc_start: 0.8991 (mp) cc_final: 0.8779 (mp) REVERT: A 971 LEU cc_start: 0.9477 (mt) cc_final: 0.9237 (mt) REVERT: A 1005 ASP cc_start: 0.3006 (OUTLIER) cc_final: 0.1585 (t70) REVERT: A 1011 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6721 (mp0) REVERT: B 82 MET cc_start: 0.8289 (ttm) cc_final: 0.7940 (ttm) REVERT: B 88 ASN cc_start: 0.9506 (OUTLIER) cc_final: 0.9160 (p0) REVERT: B 208 GLU cc_start: 0.7799 (tp30) cc_final: 0.7578 (tp30) REVERT: B 459 LYS cc_start: 0.9451 (mttm) cc_final: 0.9208 (mttm) REVERT: B 465 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8395 (mm-40) REVERT: B 753 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.7177 (t0) REVERT: B 770 GLU cc_start: 0.8911 (tt0) cc_final: 0.8540 (mp0) REVERT: B 917 LYS cc_start: 0.9053 (mmmm) cc_final: 0.8573 (mmmm) REVERT: B 1011 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: B 1100 HIS cc_start: 0.8517 (OUTLIER) cc_final: 0.8198 (t-90) REVERT: B 1119 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9121 (mm) REVERT: B 1207 LYS cc_start: 0.8395 (mmmt) cc_final: 0.8038 (mmtp) REVERT: B 1222 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8567 (mp) REVERT: B 1412 GLU cc_start: 0.5749 (OUTLIER) cc_final: 0.5027 (tm-30) outliers start: 106 outliers final: 84 residues processed: 711 average time/residue: 0.2944 time to fit residues: 339.3238 Evaluate side-chains 748 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 653 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain A residue 726 TYR Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 832 HIS Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 987 LYS Chi-restraints excluded: chain A residue 1005 ASP Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1022 CYS Chi-restraints excluded: chain A residue 1081 CYS Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1214 THR Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1265 SER Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1348 THR Chi-restraints excluded: chain A residue 1363 ILE Chi-restraints excluded: chain A residue 1381 PHE Chi-restraints excluded: chain A residue 1398 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 639 ASP Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 742 TRP Chi-restraints excluded: chain B residue 753 ASP Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 806 ASP Chi-restraints excluded: chain B residue 810 PHE Chi-restraints excluded: chain B residue 820 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 966 ASP Chi-restraints excluded: chain B residue 987 LYS Chi-restraints excluded: chain B residue 1011 GLU Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain B residue 1070 ILE Chi-restraints excluded: chain B residue 1100 HIS Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain B residue 1221 VAL Chi-restraints excluded: chain B residue 1222 LEU Chi-restraints excluded: chain B residue 1328 MET Chi-restraints excluded: chain B residue 1339 LEU Chi-restraints excluded: chain B residue 1342 LEU Chi-restraints excluded: chain B residue 1356 ILE Chi-restraints excluded: chain B residue 1358 SER Chi-restraints excluded: chain B residue 1362 ILE Chi-restraints excluded: chain B residue 1363 ILE Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1412 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 3 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 155 optimal weight: 0.5980 chunk 137 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 133 optimal weight: 0.5980 chunk 202 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.147534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.125693 restraints weight = 113010.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.130639 restraints weight = 47942.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.133796 restraints weight = 26614.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.135837 restraints weight = 17324.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.137156 restraints weight = 12636.014| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19962 Z= 0.157 Angle : 0.548 6.985 26956 Z= 0.295 Chirality : 0.035 0.156 3204 Planarity : 0.004 0.070 3392 Dihedral : 4.890 59.607 2581 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.25 % Favored : 93.71 % Rotamer: Outliers : 4.53 % Allowed : 33.11 % Favored : 62.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.17), residues: 2416 helix: 1.40 (0.13), residues: 1598 sheet: None (None), residues: 0 loop : -1.15 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 541 TYR 0.009 0.001 TYR B 327 PHE 0.026 0.001 PHE B 916 TRP 0.008 0.001 TRP A1182 HIS 0.009 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00354 (19962) covalent geometry : angle 0.54757 (26956) hydrogen bonds : bond 0.03456 ( 1101) hydrogen bonds : angle 4.22358 ( 3249) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 656 time to evaluate : 1.099 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: A 410 GLN cc_start: 0.7941 (tp40) cc_final: 0.7519 (tp-100) REVERT: A 426 GLN cc_start: 0.9230 (mp10) cc_final: 0.8919 (mp10) REVERT: A 472 ARG cc_start: 0.8350 (tpp-160) cc_final: 0.8108 (tpp-160) REVERT: A 626 GLU cc_start: 0.8320 (tp30) cc_final: 0.6882 (tt0) REVERT: A 678 SER cc_start: 0.5867 (OUTLIER) cc_final: 0.5438 (p) REVERT: A 725 ASP cc_start: 0.2270 (OUTLIER) cc_final: 0.2012 (m-30) REVERT: A 745 ASP cc_start: 0.7590 (m-30) cc_final: 0.7102 (m-30) REVERT: A 941 GLU cc_start: 0.8060 (mp0) cc_final: 0.7795 (mp0) REVERT: A 971 LEU cc_start: 0.9481 (mt) cc_final: 0.9244 (mt) REVERT: A 1005 ASP cc_start: 0.2744 (OUTLIER) cc_final: 0.1353 (t70) REVERT: A 1011 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6813 (mp0) REVERT: A 1412 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.5687 (tm-30) REVERT: B 88 ASN cc_start: 0.9524 (OUTLIER) cc_final: 0.9163 (p0) REVERT: B 208 GLU cc_start: 0.7854 (tp30) cc_final: 0.7629 (tp30) REVERT: B 459 LYS cc_start: 0.9453 (mttm) cc_final: 0.9206 (mttm) REVERT: B 465 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8396 (mm-40) REVERT: B 753 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7424 (t0) REVERT: B 770 GLU cc_start: 0.8911 (tt0) cc_final: 0.8536 (mp0) REVERT: B 917 LYS cc_start: 0.9059 (mmmm) cc_final: 0.8555 (mmmm) REVERT: B 1011 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: B 1100 HIS cc_start: 0.8532 (OUTLIER) cc_final: 0.8239 (t-90) REVERT: B 1119 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9130 (mm) REVERT: B 1207 LYS cc_start: 0.8340 (mmmt) cc_final: 0.8049 (mmtp) REVERT: B 1222 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8419 (mp) REVERT: B 1412 GLU cc_start: 0.5804 (OUTLIER) cc_final: 0.5557 (pp20) outliers start: 103 outliers final: 86 residues processed: 705 average time/residue: 0.2918 time to fit residues: 334.5775 Evaluate side-chains 747 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 649 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 670 CYS Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain A residue 726 TYR Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 832 HIS Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 987 LYS Chi-restraints excluded: chain A residue 1005 ASP Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1022 CYS Chi-restraints excluded: chain A residue 1081 CYS Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1214 THR Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1265 SER Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1348 THR Chi-restraints excluded: chain A residue 1363 ILE Chi-restraints excluded: chain A residue 1381 PHE Chi-restraints excluded: chain A residue 1398 GLU Chi-restraints excluded: chain A residue 1412 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 639 ASP Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 742 TRP Chi-restraints excluded: chain B residue 753 ASP Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 806 ASP Chi-restraints excluded: chain B residue 810 PHE Chi-restraints excluded: chain B residue 820 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 858 ASN Chi-restraints excluded: chain B residue 966 ASP Chi-restraints excluded: chain B residue 987 LYS Chi-restraints excluded: chain B residue 1011 GLU Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain B residue 1070 ILE Chi-restraints excluded: chain B residue 1100 HIS Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain B residue 1221 VAL Chi-restraints excluded: chain B residue 1222 LEU Chi-restraints excluded: chain B residue 1328 MET Chi-restraints excluded: chain B residue 1342 LEU Chi-restraints excluded: chain B residue 1356 ILE Chi-restraints excluded: chain B residue 1358 SER Chi-restraints excluded: chain B residue 1362 ILE Chi-restraints excluded: chain B residue 1363 ILE Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1412 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 106 optimal weight: 0.0970 chunk 173 optimal weight: 0.2980 chunk 111 optimal weight: 0.2980 chunk 55 optimal weight: 0.0770 chunk 78 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 235 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 overall best weight: 0.2936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 602 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.143163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.120898 restraints weight = 111249.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.125884 restraints weight = 47018.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.129089 restraints weight = 26120.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.131157 restraints weight = 17067.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.132507 restraints weight = 12494.769| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19962 Z= 0.107 Angle : 0.528 7.624 26956 Z= 0.279 Chirality : 0.034 0.150 3204 Planarity : 0.003 0.053 3392 Dihedral : 4.777 59.273 2581 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.01 % Favored : 94.95 % Rotamer: Outliers : 3.69 % Allowed : 33.86 % Favored : 62.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.18), residues: 2416 helix: 1.56 (0.13), residues: 1602 sheet: None (None), residues: 0 loop : -1.00 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 541 TYR 0.008 0.001 TYR B 327 PHE 0.027 0.001 PHE B 916 TRP 0.009 0.001 TRP A1182 HIS 0.004 0.001 HIS B 720 Details of bonding type rmsd covalent geometry : bond 0.00250 (19962) covalent geometry : angle 0.52824 (26956) hydrogen bonds : bond 0.03207 ( 1101) hydrogen bonds : angle 4.01102 ( 3249) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 668 time to evaluate : 1.023 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: A 410 GLN cc_start: 0.7842 (tp40) cc_final: 0.7401 (tp-100) REVERT: A 426 GLN cc_start: 0.9139 (mp10) cc_final: 0.8858 (mp10) REVERT: A 472 ARG cc_start: 0.8268 (tpp-160) cc_final: 0.8048 (tpp-160) REVERT: A 626 GLU cc_start: 0.8524 (tp30) cc_final: 0.7146 (tt0) REVERT: A 673 GLN cc_start: 0.7554 (mm110) cc_final: 0.7251 (tp40) REVERT: A 678 SER cc_start: 0.5743 (OUTLIER) cc_final: 0.5133 (p) REVERT: A 745 ASP cc_start: 0.7033 (m-30) cc_final: 0.6592 (m-30) REVERT: A 801 GLU cc_start: 0.9296 (pm20) cc_final: 0.8991 (pm20) REVERT: A 941 GLU cc_start: 0.7990 (mp0) cc_final: 0.7762 (mp0) REVERT: A 971 LEU cc_start: 0.9492 (mt) cc_final: 0.9272 (mt) REVERT: A 1011 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6655 (mp0) REVERT: B 82 MET cc_start: 0.8290 (ttm) cc_final: 0.7943 (ttm) REVERT: B 88 ASN cc_start: 0.9535 (OUTLIER) cc_final: 0.9179 (p0) REVERT: B 208 GLU cc_start: 0.7783 (tp30) cc_final: 0.7556 (tp30) REVERT: B 459 LYS cc_start: 0.9408 (mttm) cc_final: 0.9176 (mttm) REVERT: B 465 GLN cc_start: 0.8610 (mm-40) cc_final: 0.8354 (mm-40) REVERT: B 753 ASP cc_start: 0.7443 (OUTLIER) cc_final: 0.7099 (t0) REVERT: B 770 GLU cc_start: 0.8912 (tt0) cc_final: 0.8510 (mp0) REVERT: B 831 ASP cc_start: 0.8122 (m-30) cc_final: 0.7598 (m-30) REVERT: B 917 LYS cc_start: 0.9007 (mmmm) cc_final: 0.8514 (mmmm) REVERT: B 1011 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: B 1100 HIS cc_start: 0.8540 (OUTLIER) cc_final: 0.8265 (t-90) REVERT: B 1207 LYS cc_start: 0.8385 (mmmt) cc_final: 0.8063 (mmtp) REVERT: B 1222 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8613 (mp) REVERT: B 1412 GLU cc_start: 0.5645 (OUTLIER) cc_final: 0.4961 (tm-30) outliers start: 84 outliers final: 74 residues processed: 703 average time/residue: 0.2952 time to fit residues: 337.4573 Evaluate side-chains 736 residues out of total 2274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 654 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 670 CYS Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 726 TYR Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1016 SER Chi-restraints excluded: chain A residue 1022 CYS Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1214 THR Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1265 SER Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1363 ILE Chi-restraints excluded: chain A residue 1381 PHE Chi-restraints excluded: chain A residue 1398 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 639 ASP Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 742 TRP Chi-restraints excluded: chain B residue 753 ASP Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 806 ASP Chi-restraints excluded: chain B residue 810 PHE Chi-restraints excluded: chain B residue 820 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 830 ASP Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 858 ASN Chi-restraints excluded: chain B residue 966 ASP Chi-restraints excluded: chain B residue 1011 GLU Chi-restraints excluded: chain B residue 1070 ILE Chi-restraints excluded: chain B residue 1073 LEU Chi-restraints excluded: chain B residue 1100 HIS Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain B residue 1221 VAL Chi-restraints excluded: chain B residue 1222 LEU Chi-restraints excluded: chain B residue 1342 LEU Chi-restraints excluded: chain B residue 1362 ILE Chi-restraints excluded: chain B residue 1363 ILE Chi-restraints excluded: chain B residue 1380 THR Chi-restraints excluded: chain B residue 1412 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 113 optimal weight: 0.0270 chunk 118 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 55 optimal weight: 0.0010 chunk 103 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 241 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 226 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 overall best weight: 0.3444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.150859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.130154 restraints weight = 112224.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.134816 restraints weight = 50359.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.137790 restraints weight = 28712.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.139703 restraints weight = 18994.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.140952 restraints weight = 14034.393| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19962 Z= 0.111 Angle : 0.525 7.097 26956 Z= 0.278 Chirality : 0.034 0.148 3204 Planarity : 0.003 0.053 3392 Dihedral : 4.736 59.049 2581 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.55 % Favored : 94.41 % Rotamer: Outliers : 3.65 % Allowed : 34.04 % Favored : 62.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.18), residues: 2416 helix: 1.57 (0.13), residues: 1602 sheet: None (None), residues: 0 loop : -0.97 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 541 TYR 0.009 0.001 TYR B 327 PHE 0.028 0.001 PHE B 916 TRP 0.008 0.001 TRP A1182 HIS 0.004 0.001 HIS B 720 Details of bonding type rmsd covalent geometry : bond 0.00258 (19962) covalent geometry : angle 0.52550 (26956) hydrogen bonds : bond 0.03190 ( 1101) hydrogen bonds : angle 4.00465 ( 3249) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8193.60 seconds wall clock time: 140 minutes 16.80 seconds (8416.80 seconds total)