Starting phenix.real_space_refine on Sat Mar 7 05:29:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7urr_26717/03_2026/7urr_26717.cif Found real_map, /net/cci-nas-00/data/ceres_data/7urr_26717/03_2026/7urr_26717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7urr_26717/03_2026/7urr_26717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7urr_26717/03_2026/7urr_26717.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7urr_26717/03_2026/7urr_26717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7urr_26717/03_2026/7urr_26717.map" } resolution = 4.7 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= -0.064 sd= 1.560 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 72 5.16 5 C 12130 2.51 5 N 3067 2.21 5 O 3568 1.98 5 H 19331 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 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: 38168 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 19748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1216, 19748 Classifications: {'peptide': 1216} Link IDs: {'PTRANS': 36, 'TRANS': 1179} Chain breaks: 8 Chain: "B" Number of atoms: 18420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 18420 Classifications: {'peptide': 1129} Link IDs: {'PTRANS': 34, 'TRANS': 1094} Chain breaks: 13 Time building chain proxies: 5.96, per 1000 atoms: 0.16 Number of scatterers: 38168 At special positions: 0 Unit cell: (307.84, 166.4, 128.128, 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 72 16.00 O 3568 8.00 N 3067 7.00 C 12130 6.00 H 19331 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: 3.22 Conformation dependent library (CDL) restraints added in 1.1 seconds 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4548 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 1 sheets defined 74.1% alpha, 0.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 12 through 17 removed outlier: 4.139A pdb=" N ILE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 24 removed outlier: 3.613A pdb=" N THR A 24 " --> pdb=" O ILE A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 83 removed outlier: 3.810A pdb=" N ILE A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 107 removed outlier: 3.802A pdb=" N ILE A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU A 98 " --> pdb=" O SER A 94 " (cutoff:3.500A) Proline residue: A 100 - end of helix Processing helix chain 'A' and resid 111 through 129 removed outlier: 3.877A pdb=" N THR A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 151 removed outlier: 3.656A pdb=" N HIS A 151 " --> pdb=" O ASN A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 179 removed outlier: 4.198A pdb=" N LEU A 167 " --> pdb=" O ASP A 163 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 186 through 203 Processing helix chain 'A' and resid 207 through 232 removed outlier: 4.115A pdb=" N VAL A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS A 228 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU A 229 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS A 230 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 343 removed outlier: 3.685A pdb=" N ARG A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 370 removed outlier: 3.953A pdb=" N SER A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 376 removed outlier: 3.850A pdb=" N GLN A 375 " --> pdb=" O ASP A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 386 removed outlier: 3.587A pdb=" N PHE A 381 " --> pdb=" O TYR A 377 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A 382 " --> pdb=" O PRO A 378 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LEU A 383 " --> pdb=" O ARG A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 399 Processing helix chain 'A' and resid 401 through 420 Processing helix chain 'A' and resid 424 through 440 Processing helix chain 'A' and resid 456 through 466 Processing helix chain 'A' and resid 467 through 471 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: 3.518A pdb=" N LEU A 511 " --> pdb=" O GLU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 537 removed outlier: 3.881A pdb=" N ILE A 520 " --> pdb=" O SER A 516 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 528 " --> pdb=" O GLY A 524 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A 529 " --> pdb=" O LEU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 547 removed outlier: 3.569A pdb=" N GLN A 547 " --> pdb=" O PHE A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 558 removed outlier: 3.874A pdb=" N LYS A 555 " --> pdb=" O MET A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 567 removed outlier: 3.920A pdb=" N GLU A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N CYS A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 573 Processing helix chain 'A' and resid 578 through 585 removed outlier: 3.567A pdb=" N ILE A 582 " --> pdb=" O ILE A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 602 removed outlier: 3.637A pdb=" N ILE A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU A 597 " --> pdb=" O LYS A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 615 removed outlier: 3.771A pdb=" N ILE A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY A 612 " --> pdb=" O LYS A 608 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU A 613 " --> pdb=" O LYS A 609 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU A 614 " --> pdb=" O THR A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 620 through 631 removed outlier: 3.661A pdb=" N PHE A 631 " --> pdb=" O TYR A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 649 removed outlier: 3.645A pdb=" N LYS A 648 " --> pdb=" O ILE A 644 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE A 649 " --> pdb=" O LEU A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 657 removed outlier: 3.694A pdb=" N GLN A 657 " --> pdb=" O GLU A 654 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 654 through 657' Processing helix chain 'A' and resid 658 through 672 removed outlier: 3.505A pdb=" N ILE A 662 " --> pdb=" O ILE A 658 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA A 664 " --> pdb=" O ARG A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 713 removed outlier: 4.116A pdb=" N HIS A 713 " --> pdb=" O ASN A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 728 removed outlier: 3.812A pdb=" N TYR A 726 " --> pdb=" O SER A 722 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER A 727 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 728 " --> pdb=" O GLU A 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 722 through 728' Processing helix chain 'A' and resid 740 through 754 removed outlier: 3.825A pdb=" N LEU A 744 " --> pdb=" O PRO A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 775 removed outlier: 3.838A pdb=" N ASN A 775 " --> pdb=" O ASP A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 828 removed outlier: 3.975A pdb=" N ARG A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA A 808 " --> pdb=" O ASN A 804 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE A 809 " --> pdb=" O PHE A 805 " (cutoff:3.500A) Proline residue: A 815 - end of helix removed outlier: 3.942A pdb=" N ILE A 824 " --> pdb=" O THR A 820 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 826 " --> pdb=" O PHE A 822 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 827 " --> pdb=" O ASN A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 852 removed outlier: 3.948A pdb=" N THR A 835 " --> pdb=" O ASP A 831 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG A 836 " --> pdb=" O HIS A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 868 Processing helix chain 'A' and resid 906 through 915 removed outlier: 3.575A pdb=" N ARG A 911 " --> pdb=" O THR A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 931 removed outlier: 3.619A pdb=" N GLN A 919 " --> pdb=" O SER A 915 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL A 923 " --> pdb=" O GLN A 919 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL A 924 " --> pdb=" O LEU A 920 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 929 " --> pdb=" O PHE A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 956 removed outlier: 4.033A pdb=" N ASP A 956 " --> pdb=" O THR A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 971 Processing helix chain 'A' and resid 1011 through 1025 removed outlier: 3.745A pdb=" N SER A1025 " --> pdb=" O GLU A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1033 removed outlier: 4.514A pdb=" N VAL A1032 " --> pdb=" O ILE A1028 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE A1033 " --> pdb=" O ALA A1029 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1028 through 1033' Processing helix chain 'A' and resid 1035 through 1039 removed outlier: 4.237A pdb=" N ASN A1038 " --> pdb=" O ASN A1035 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A1039 " --> pdb=" O GLU A1036 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1035 through 1039' Processing helix chain 'A' and resid 1040 through 1050 Processing helix chain 'A' and resid 1058 through 1061 removed outlier: 3.779A pdb=" N ARG A1061 " --> pdb=" O ASP A1058 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1058 through 1061' Processing helix chain 'A' and resid 1062 through 1081 removed outlier: 3.606A pdb=" N ALA A1076 " --> pdb=" O GLU A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1100 Processing helix chain 'A' and resid 1105 through 1123 removed outlier: 3.508A pdb=" N VAL A1109 " --> pdb=" O THR A1105 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR A1114 " --> pdb=" O ARG A1110 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR A1115 " --> pdb=" O ARG A1111 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A1116 " --> pdb=" O MET A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1136 removed outlier: 3.733A pdb=" N LEU A1130 " --> pdb=" O GLN A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1152 removed outlier: 3.648A pdb=" N THR A1152 " --> pdb=" O LYS A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1165 removed outlier: 3.573A pdb=" N LYS A1156 " --> pdb=" O THR A1152 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A1157 " --> pdb=" O ASN A1153 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A1158 " --> pdb=" O GLN A1154 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE A1163 " --> pdb=" O LEU A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1168 No H-bonds generated for 'chain 'A' and resid 1166 through 1168' Processing helix chain 'A' and resid 1171 through 1178 Processing helix chain 'A' and resid 1179 through 1190 removed outlier: 3.647A pdb=" N ALA A1190 " --> pdb=" O ARG A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1209 removed outlier: 3.711A pdb=" N GLU A1204 " --> pdb=" O GLU A1200 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP A1209 " --> pdb=" O SER A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1231 removed outlier: 3.852A pdb=" N VAL A1221 " --> pdb=" O ASN A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1275 removed outlier: 4.083A pdb=" N LEU A1266 " --> pdb=" O ILE A1262 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LYS A1267 " --> pdb=" O GLU A1263 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER A1268 " --> pdb=" O LEU A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1286 through 1298 removed outlier: 3.941A pdb=" N ILE A1290 " --> pdb=" O GLU A1286 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS A1298 " --> pdb=" O LEU A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1302 through 1320 removed outlier: 4.157A pdb=" N ASN A1319 " --> pdb=" O GLN A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1330 through 1338 removed outlier: 4.020A pdb=" N LEU A1334 " --> pdb=" O SER A1330 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLY A1338 " --> pdb=" O LEU A1334 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1343 removed outlier: 3.833A pdb=" N LEU A1342 " --> pdb=" O GLY A1338 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1338 through 1343' Processing helix chain 'A' and resid 1351 through 1356 Processing helix chain 'A' and resid 1360 through 1374 removed outlier: 4.144A pdb=" N SER A1364 " --> pdb=" O LEU A1360 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU A1368 " --> pdb=" O SER A1364 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N HIS A1369 " --> pdb=" O ASN A1365 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR A1370 " --> pdb=" O VAL A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1388 removed outlier: 3.776A pdb=" N PHE A1381 " --> pdb=" O SER A1377 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU A1382 " --> pdb=" O ASN A1378 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A1386 " --> pdb=" O LEU A1382 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 3.774A pdb=" N LYS A1399 " --> pdb=" O SER A1395 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLN A1402 " --> pdb=" O GLU A1398 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN A1403 " --> pdb=" O LYS A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1415 removed outlier: 3.571A pdb=" N ILE A1411 " --> pdb=" O LYS A1408 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU A1412 " --> pdb=" O LYS A1409 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A1413 " --> pdb=" O SER A1410 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN A1415 " --> pdb=" O GLU A1412 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 24 removed outlier: 3.949A pdb=" N LYS B 17 " --> pdb=" O THR B 13 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR B 24 " --> pdb=" O ILE B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 83 removed outlier: 3.722A pdb=" N PHE B 76 " --> pdb=" O PHE B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 107 removed outlier: 3.723A pdb=" N LEU B 98 " --> pdb=" O SER B 94 " (cutoff:3.500A) Proline residue: B 100 - end of helix Processing helix chain 'B' and resid 111 through 129 removed outlier: 3.503A pdb=" N THR B 115 " --> pdb=" O SER B 111 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B 128 " --> pdb=" O LYS B 124 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B 129 " --> pdb=" O PHE B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 150 removed outlier: 3.895A pdb=" N THR B 150 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 179 removed outlier: 3.598A pdb=" N LEU B 167 " --> pdb=" O ASP B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 188 through 203 removed outlier: 3.645A pdb=" N ASP B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B 201 " --> pdb=" O ILE B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 228 removed outlier: 3.701A pdb=" N LYS B 228 " --> pdb=" O LYS B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 344 Processing helix chain 'B' and resid 345 through 348 Processing helix chain 'B' and resid 352 through 370 removed outlier: 4.124A pdb=" N SER B 370 " --> pdb=" O ALA B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 376 removed outlier: 3.826A pdb=" N GLN B 375 " --> pdb=" O ASP B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 398 removed outlier: 3.826A pdb=" N PHE B 381 " --> pdb=" O TYR B 377 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP B 386 " --> pdb=" O THR B 382 " (cutoff:3.500A) Proline residue: B 387 - end of helix removed outlier: 3.614A pdb=" N LYS B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER B 391 " --> pdb=" O PRO B 387 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE B 392 " --> pdb=" O ILE B 388 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE B 396 " --> pdb=" O ILE B 392 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLN B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 420 removed outlier: 3.642A pdb=" N LEU B 405 " --> pdb=" O LYS B 401 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B 420 " --> pdb=" O VAL B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 439 removed outlier: 4.017A pdb=" N GLU B 428 " --> pdb=" O GLN B 424 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR B 430 " --> pdb=" O GLN B 426 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE B 434 " --> pdb=" O THR B 430 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 473 removed outlier: 4.273A pdb=" N GLU B 460 " --> pdb=" O SER B 456 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 467 " --> pdb=" O ILE B 463 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ILE B 468 " --> pdb=" O GLU B 464 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TRP B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER B 473 " --> pdb=" O LEU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 484 Processing helix chain 'B' and resid 493 through 506 removed outlier: 3.584A pdb=" N LYS B 503 " --> pdb=" O LYS B 499 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU B 506 " --> pdb=" O THR B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 512 Processing helix chain 'B' and resid 516 through 535 removed outlier: 3.687A pdb=" N ILE B 520 " --> pdb=" O SER B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 545 removed outlier: 3.755A pdb=" N PHE B 544 " --> pdb=" O ASP B 540 " (cutoff:3.500A) removed outlier: 4.018A 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 556 through 571 removed outlier: 3.662A pdb=" N LYS B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLU B 562 " --> pdb=" O ASP B 558 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR B 567 " --> pdb=" O PHE B 563 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA B 569 " --> pdb=" O GLU B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 584 removed outlier: 3.959A pdb=" N MET B 580 " --> pdb=" O LYS B 576 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 583 " --> pdb=" O PRO B 579 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS B 584 " --> pdb=" O MET B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 602 removed outlier: 3.832A pdb=" N ASN B 602 " --> pdb=" O PHE B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 617 Processing helix chain 'B' and resid 620 through 628 removed outlier: 4.158A pdb=" N ILE B 628 " --> pdb=" O LEU B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 631 No H-bonds generated for 'chain 'B' and resid 629 through 631' Processing helix chain 'B' and resid 637 through 649 removed outlier: 4.042A pdb=" N THR B 647 " --> pdb=" O ARG B 643 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS B 648 " --> pdb=" O ILE B 644 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE B 649 " --> pdb=" O LEU B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 668 removed outlier: 4.359A pdb=" N ILE B 661 " --> pdb=" O GLN B 657 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU B 663 " --> pdb=" O GLU B 659 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER B 666 " --> pdb=" O ILE B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 removed outlier: 3.973A pdb=" N ASN B 672 " --> pdb=" O ALA B 668 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN B 673 " --> pdb=" O TYR B 669 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 668 through 673' Processing helix chain 'B' and resid 676 through 680 removed outlier: 4.068A pdb=" N ILE B 680 " --> pdb=" O PRO B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 712 removed outlier: 4.007A pdb=" N MET B 707 " --> pdb=" O TYR B 703 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU B 708 " --> pdb=" O SER B 704 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASN B 709 " --> pdb=" O ILE B 705 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THR B 710 " --> pdb=" O ILE B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 730 removed outlier: 3.592A pdb=" N TYR B 726 " --> pdb=" O SER B 722 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU B 730 " --> pdb=" O TYR B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 752 Processing helix chain 'B' and resid 753 through 755 No H-bonds generated for 'chain 'B' and resid 753 through 755' Processing helix chain 'B' and resid 800 through 806 Processing helix chain 'B' and resid 807 through 822 removed outlier: 4.510A pdb=" N LYS B 811 " --> pdb=" O ARG B 807 " (cutoff:3.500A) removed outlier: 3.615A 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 851 removed outlier: 3.631A pdb=" N ARG B 836 " --> pdb=" O HIS B 832 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 849 " --> pdb=" O SER B 845 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE B 850 " --> pdb=" O TYR B 846 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE B 851 " --> pdb=" O ILE B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 868 removed outlier: 4.364A pdb=" N LEU B 861 " --> pdb=" O PHE B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 915 Processing helix chain 'B' and resid 915 through 932 removed outlier: 3.741A pdb=" N THR B 922 " --> pdb=" O GLY B 918 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL B 923 " --> pdb=" O GLN B 919 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL B 924 " --> pdb=" O LEU B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 956 removed outlier: 3.645A pdb=" N ASN B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE B 949 " --> pdb=" O ASN B 945 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE B 950 " --> pdb=" O ILE B 946 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N THR B 952 " --> pdb=" O ASN B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 972 Processing helix chain 'B' and resid 1009 through 1026 removed outlier: 3.872A pdb=" N ILE B1013 " --> pdb=" O THR B1009 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS B1014 " --> pdb=" O GLU B1010 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER B1015 " --> pdb=" O GLU B1011 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LYS B1018 " --> pdb=" O LYS B1014 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA B1019 " --> pdb=" O SER B1015 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET B1020 " --> pdb=" O SER B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1033 removed outlier: 4.002A pdb=" N VAL B1032 " --> pdb=" O ILE B1028 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE B1033 " --> pdb=" O ALA B1029 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1028 through 1033' Processing helix chain 'B' and resid 1035 through 1039 removed outlier: 3.632A pdb=" N ASN B1038 " --> pdb=" O ASN B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1044 through 1051 Processing helix chain 'B' and resid 1056 through 1060 Processing helix chain 'B' and resid 1062 through 1079 removed outlier: 3.777A pdb=" N LEU B1079 " --> pdb=" O ILE B1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1099 Processing helix chain 'B' and resid 1105 through 1112 Processing helix chain 'B' and resid 1115 through 1122 removed outlier: 4.212A pdb=" N LEU B1119 " --> pdb=" O TYR B1115 " (cutoff:3.500A) Processing helix chain 'B' and resid 1146 through 1152 removed outlier: 3.746A pdb=" N PHE B1150 " --> pdb=" O THR B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1152 through 1168 removed outlier: 3.840A pdb=" N LEU B1165 " --> pdb=" O ARG B1161 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THR B1166 " --> pdb=" O LEU B1162 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU B1167 " --> pdb=" O PHE B1163 " (cutoff:3.500A) Processing helix chain 'B' and resid 1169 through 1171 No H-bonds generated for 'chain 'B' and resid 1169 through 1171' Processing helix chain 'B' and resid 1172 through 1177 removed outlier: 4.016A pdb=" N LEU B1176 " --> pdb=" O ARG B1172 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY B1177 " --> pdb=" O GLY B1173 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1172 through 1177' Processing helix chain 'B' and resid 1178 through 1191 removed outlier: 3.943A pdb=" N TRP B1182 " --> pdb=" O ASN B1178 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET B1191 " --> pdb=" O LYS B1187 " (cutoff:3.500A) Processing helix chain 'B' and resid 1194 through 1209 removed outlier: 3.979A pdb=" N THR B1208 " --> pdb=" O GLU B1204 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP B1209 " --> pdb=" O SER B1205 " (cutoff:3.500A) Processing helix chain 'B' and resid 1217 through 1230 removed outlier: 3.631A pdb=" N VAL B1221 " --> pdb=" O ASN B1217 " (cutoff:3.500A) Processing helix chain 'B' and resid 1260 through 1279 removed outlier: 3.858A pdb=" N LEU B1264 " --> pdb=" O LYS B1260 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN B1270 " --> pdb=" O LEU B1266 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU B1276 " --> pdb=" O THR B1272 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU B1277 " --> pdb=" O SER B1273 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN B1279 " --> pdb=" O LEU B1275 " (cutoff:3.500A) Processing helix chain 'B' and resid 1283 through 1297 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 1319 removed outlier: 3.605A pdb=" N PHE B1308 " --> pdb=" O GLN B1304 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE B1318 " --> pdb=" O GLU B1314 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASN B1319 " --> pdb=" O GLN B1315 " (cutoff:3.500A) Processing helix chain 'B' and resid 1332 through 1338 removed outlier: 4.241A pdb=" N GLU B1336 " --> pdb=" O GLU B1332 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY B1337 " --> pdb=" O GLU B1333 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY B1338 " --> pdb=" O LEU B1334 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1332 through 1338' Processing helix chain 'B' and resid 1338 through 1344 removed outlier: 3.636A pdb=" N LEU B1342 " --> pdb=" O GLY B1338 " (cutoff:3.500A) Processing helix chain 'B' and resid 1355 through 1373 removed outlier: 4.134A pdb=" N ILE B1359 " --> pdb=" O LEU B1355 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B1363 " --> pdb=" O ILE B1359 " (cutoff:3.500A) Processing helix chain 'B' and resid 1378 through 1389 removed outlier: 3.874A pdb=" N LEU B1382 " --> pdb=" O ASN B1378 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS B1383 " --> pdb=" O GLU B1379 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER B1386 " --> pdb=" O LEU B1382 " (cutoff:3.500A) Processing helix chain 'B' and resid 1390 through 1392 No H-bonds generated for 'chain 'B' and resid 1390 through 1392' Processing helix chain 'B' and resid 1396 through 1412 removed outlier: 4.017A pdb=" N LEU B1401 " --> pdb=" O ILE B1397 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN B1402 " --> pdb=" O GLU B1398 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU B1412 " --> pdb=" O LYS B1408 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 241 through 242 removed outlier: 3.593A pdb=" N TYR A 241 " --> pdb=" O THR A 784 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A 784 " --> pdb=" O TYR A 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 943 hydrogen bonds defined for protein. 2754 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: 8.78 Time building geometry restraints manager: 4.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 19297 1.03 - 1.23: 167 1.23 - 1.43: 7528 1.43 - 1.63: 11365 1.63 - 1.82: 110 Bond restraints: 38467 Sorted by residual: bond pdb=" CB ASN A 84 " pdb=" CG ASN A 84 " ideal model delta sigma weight residual 1.516 1.574 -0.058 2.50e-02 1.60e+03 5.30e+00 bond pdb=" CB GLU B1193 " pdb=" CG GLU B1193 " ideal model delta sigma weight residual 1.520 1.587 -0.067 3.00e-02 1.11e+03 5.05e+00 bond pdb=" CB ILE A 357 " pdb=" CG2 ILE A 357 " ideal model delta sigma weight residual 1.521 1.590 -0.069 3.30e-02 9.18e+02 4.36e+00 bond pdb=" CG1 ILE A 392 " pdb=" CD1 ILE A 392 " ideal model delta sigma weight residual 1.513 1.432 0.081 3.90e-02 6.57e+02 4.35e+00 bond pdb=" C ILE A 578 " pdb=" N PRO A 579 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.19e-02 7.06e+03 4.21e+00 ... (remaining 38462 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 66565 1.92 - 3.84: 2846 3.84 - 5.77: 373 5.77 - 7.69: 76 7.69 - 9.61: 9 Bond angle restraints: 69869 Sorted by residual: angle pdb=" CA GLU B1012 " pdb=" CB GLU B1012 " pdb=" CG GLU B1012 " ideal model delta sigma weight residual 114.10 123.61 -9.51 2.00e+00 2.50e-01 2.26e+01 angle pdb=" CA GLN B 410 " pdb=" CB GLN B 410 " pdb=" CG GLN B 410 " ideal model delta sigma weight residual 114.10 123.60 -9.50 2.00e+00 2.50e-01 2.26e+01 angle pdb=" CA GLU B 565 " pdb=" CB GLU B 565 " pdb=" CG GLU B 565 " ideal model delta sigma weight residual 114.10 122.92 -8.82 2.00e+00 2.50e-01 1.94e+01 angle pdb=" C SER B1026 " pdb=" N ASN B1027 " pdb=" CA ASN B1027 " ideal model delta sigma weight residual 121.54 129.86 -8.32 1.91e+00 2.74e-01 1.90e+01 angle pdb=" CA ASN A 84 " pdb=" CB ASN A 84 " pdb=" CG ASN A 84 " ideal model delta sigma weight residual 112.60 116.52 -3.92 1.00e+00 1.00e+00 1.54e+01 ... (remaining 69864 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 15136 17.95 - 35.90: 2069 35.90 - 53.85: 537 53.85 - 71.79: 129 71.79 - 89.74: 38 Dihedral angle restraints: 17909 sinusoidal: 9901 harmonic: 8008 Sorted by residual: dihedral pdb=" CA TYR B1062 " pdb=" C TYR B1062 " pdb=" N PHE B1063 " pdb=" CA PHE B1063 " ideal model delta harmonic sigma weight residual 180.00 -151.93 -28.07 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA ASP A 676 " pdb=" C ASP A 676 " pdb=" N PRO A 677 " pdb=" CA PRO A 677 " ideal model delta harmonic sigma weight residual -180.00 -154.02 -25.98 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA THR A1009 " pdb=" C THR A1009 " pdb=" N GLU A1010 " pdb=" CA GLU A1010 " ideal model delta harmonic sigma weight residual 180.00 -155.37 -24.63 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 17906 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2644 0.061 - 0.121: 397 0.121 - 0.182: 34 0.182 - 0.242: 4 0.242 - 0.303: 3 Chirality restraints: 3082 Sorted by residual: chirality pdb=" CB ILE A 860 " pdb=" CA ILE A 860 " pdb=" CG1 ILE A 860 " pdb=" CG2 ILE A 860 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB THR A 222 " pdb=" CA THR A 222 " pdb=" OG1 THR A 222 " pdb=" CG2 THR A 222 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CB ILE B 418 " pdb=" CA ILE B 418 " pdb=" CG1 ILE B 418 " pdb=" CG2 ILE B 418 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 3079 not shown) Planarity restraints: 5489 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 506 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO A 507 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO A 507 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 507 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1340 " -0.062 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO A1341 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO A1341 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A1341 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 739 " 0.021 2.00e-02 2.50e+03 1.80e-02 9.76e+00 pdb=" CG PHE A 739 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE A 739 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 739 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE A 739 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 739 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 739 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE A 739 " -0.003 2.00e-02 2.50e+03 pdb=" HD2 PHE A 739 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 PHE A 739 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE A 739 " 0.003 2.00e-02 2.50e+03 pdb=" HZ PHE A 739 " -0.001 2.00e-02 2.50e+03 ... (remaining 5486 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 6706 2.28 - 2.86: 84904 2.86 - 3.44: 97573 3.44 - 4.02: 120356 4.02 - 4.60: 183939 Nonbonded interactions: 493478 Sorted by model distance: nonbonded pdb=" OE1 GLU B 562 " pdb=" H GLU B 562 " model vdw 1.700 2.450 nonbonded pdb=" OE1 GLU A 543 " pdb=" H GLU A 543 " model vdw 1.706 2.450 nonbonded pdb=" OE1 GLU B 801 " pdb=" H GLU B 801 " model vdw 1.707 2.450 nonbonded pdb=" H CYS B 734 " pdb=" O LYS B 737 " model vdw 1.734 2.450 nonbonded pdb=" O ASN B 858 " pdb="HD21 ASN B 862 " model vdw 1.739 2.450 ... (remaining 493473 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 154 or (resid 162 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name OD2 or name HA or name H \ B2 or name HB3)) or resid 163 through 230 or (resid 329 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD1 or name CD2 or name HA or n \ ame HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD \ 21 or name HD22 or name HD23)) or resid 330 through 545 or (resid 554 and (name \ N or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 o \ r name HA or name HB2 or name HB3 or name HG or name HD11 or name HD12 or name H \ D13 or name HD21 or name HD22 or name HD23)) or resid 555 through 758 or (resid \ 765 and (name N or name CA or name C or name O or name CB or name CG or name OD1 \ or name ND2 or name HA or name HB2 or name HB3 or name HD21 or name HD22)) or r \ esid 766 through 779 or resid 799 through 871 or resid 889 through 986 or (resid \ 1007 and (name N or name CA or name C or name O or name CB or name CG or name C \ D or name OE1 or name OE2 or name HA or name HB2 or name HB3 or name HG2 or name \ HG3)) or resid 1008 through 1344 or (resid 1352 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name NE2 or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HE21 or name HE22)) or r \ esid 1353 through 1392 or (resid 1395 and (name N or name CA or name C or name O \ or name CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resid \ 1396 through 1415)) 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: 1.790 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: 0.230 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 32.330 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 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 0.081 19136 Z= 0.246 Angle : 0.962 9.611 25829 Z= 0.496 Chirality : 0.044 0.303 3082 Planarity : 0.006 0.104 3232 Dihedral : 18.749 89.742 7202 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.87 % Favored : 94.00 % Rotamer: Outliers : 0.23 % Allowed : 32.89 % Favored : 66.88 % 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: -1.06 (0.17), residues: 2299 helix: -0.31 (0.13), residues: 1421 sheet: None (None), residues: 0 loop : -1.19 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B1186 TYR 0.030 0.001 TYR A1367 PHE 0.054 0.002 PHE A 739 TRP 0.018 0.002 TRP B 943 HIS 0.017 0.001 HIS A1369 Details of bonding type rmsd covalent geometry : bond 0.00566 (19136) covalent geometry : angle 0.96184 (25829) hydrogen bonds : bond 0.15487 ( 943) hydrogen bonds : angle 5.83574 ( 2754) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 644 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.8721 (mm) cc_final: 0.8480 (mm) REVERT: A 84 ASN cc_start: 0.8473 (t0) cc_final: 0.8208 (m110) REVERT: A 372 ASP cc_start: 0.7692 (p0) cc_final: 0.7445 (p0) REVERT: A 376 LEU cc_start: 0.9185 (mp) cc_final: 0.8951 (mp) REVERT: A 560 LYS cc_start: 0.9350 (mmmm) cc_final: 0.9023 (mmmm) REVERT: A 562 GLU cc_start: 0.7689 (mt-10) cc_final: 0.6953 (mm-30) REVERT: A 567 THR cc_start: 0.8121 (m) cc_final: 0.7709 (p) REVERT: A 663 GLU cc_start: 0.6249 (tm-30) cc_final: 0.5635 (mt-10) REVERT: A 723 PHE cc_start: 0.8034 (t80) cc_final: 0.7628 (t80) REVERT: A 758 MET cc_start: 0.6494 (ptm) cc_final: 0.5732 (ptm) REVERT: A 832 HIS cc_start: 0.8795 (m-70) cc_final: 0.8569 (m170) REVERT: A 837 MET cc_start: 0.9270 (mmm) cc_final: 0.8739 (mmm) REVERT: A 911 ARG cc_start: 0.7155 (mmt180) cc_final: 0.6744 (mpt180) REVERT: A 973 LEU cc_start: 0.9100 (tp) cc_final: 0.8872 (tp) REVERT: A 1036 GLU cc_start: 0.7546 (mp0) cc_final: 0.7255 (mp0) REVERT: A 1157 GLU cc_start: 0.8532 (tp30) cc_final: 0.8167 (tp30) REVERT: B 361 GLU cc_start: 0.8022 (mp0) cc_final: 0.7713 (mp0) REVERT: B 379 ARG cc_start: 0.7649 (tpt90) cc_final: 0.7339 (tpt90) REVERT: B 616 CYS cc_start: 0.8665 (m) cc_final: 0.8393 (m) REVERT: B 729 ASN cc_start: 0.6720 (t0) cc_final: 0.6424 (m110) REVERT: B 812 GLN cc_start: 0.8124 (tp-100) cc_final: 0.7527 (mp10) REVERT: B 1062 TYR cc_start: 0.6896 (m-10) cc_final: 0.6490 (m-10) outliers start: 5 outliers final: 3 residues processed: 646 average time/residue: 0.2675 time to fit residues: 276.1293 Evaluate side-chains 596 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 593 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 GLN A 483 ASN A 571 ASN A 617 HIS A 672 ASN A 729 ASN A 762 HIS A 945 ASN A1365 ASN B 215 GLN B 398 ASN B 410 GLN B 422 ASN B 604 ASN B 862 ASN B1135 ASN B1180 ASN B1203 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.165431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.140283 restraints weight = 119781.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.145918 restraints weight = 57609.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.149542 restraints weight = 33821.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.151888 restraints weight = 22565.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.153403 restraints weight = 16636.346| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 19136 Z= 0.186 Angle : 0.612 6.960 25829 Z= 0.336 Chirality : 0.036 0.143 3082 Planarity : 0.005 0.072 3232 Dihedral : 5.250 33.436 2457 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.87 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 2299 helix: 0.23 (0.13), residues: 1446 sheet: None (None), residues: 0 loop : -1.27 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 472 TYR 0.020 0.002 TYR B1115 PHE 0.031 0.002 PHE A 171 TRP 0.023 0.002 TRP B 470 HIS 0.004 0.001 HIS B 351 Details of bonding type rmsd covalent geometry : bond 0.00412 (19136) covalent geometry : angle 0.61227 (25829) hydrogen bonds : bond 0.04977 ( 943) hydrogen bonds : angle 4.87545 ( 2754) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 688 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.8709 (mm) cc_final: 0.8148 (mm) REVERT: A 81 LEU cc_start: 0.8900 (mm) cc_final: 0.8598 (mm) REVERT: A 107 THR cc_start: 0.8839 (m) cc_final: 0.8623 (m) REVERT: A 129 ASN cc_start: 0.8873 (t0) cc_final: 0.8598 (t0) REVERT: A 372 ASP cc_start: 0.7650 (p0) cc_final: 0.7265 (p0) REVERT: A 481 PHE cc_start: 0.9059 (t80) cc_final: 0.8795 (t80) REVERT: A 487 ASN cc_start: 0.8702 (m-40) cc_final: 0.8203 (m-40) REVERT: A 495 ILE cc_start: 0.8481 (mm) cc_final: 0.8191 (mm) REVERT: A 531 ASP cc_start: 0.8199 (m-30) cc_final: 0.7885 (m-30) REVERT: A 532 MET cc_start: 0.8777 (ttm) cc_final: 0.8365 (mtp) REVERT: A 670 CYS cc_start: 0.7695 (m) cc_final: 0.7299 (t) REVERT: A 785 GLU cc_start: 0.6600 (pm20) cc_final: 0.6175 (tm-30) REVERT: A 795 ASP cc_start: 0.7253 (m-30) cc_final: 0.6923 (m-30) REVERT: A 889 MET cc_start: 0.7768 (pmm) cc_final: 0.7517 (pmm) REVERT: A 936 LYS cc_start: 0.8824 (mtpp) cc_final: 0.8458 (mtmm) REVERT: A 1012 GLU cc_start: 0.8357 (mp0) cc_final: 0.8050 (mp0) REVERT: A 1036 GLU cc_start: 0.7675 (mp0) cc_final: 0.6866 (mp0) REVERT: A 1157 GLU cc_start: 0.8276 (tp30) cc_final: 0.8020 (tp30) REVERT: B 13 THR cc_start: 0.7680 (m) cc_final: 0.6570 (m) REVERT: B 163 ASP cc_start: 0.8846 (m-30) cc_final: 0.8610 (m-30) REVERT: B 208 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7965 (mt-10) REVERT: B 361 GLU cc_start: 0.7592 (mp0) cc_final: 0.7216 (mp0) REVERT: B 466 ILE cc_start: 0.9067 (mm) cc_final: 0.8850 (tp) REVERT: B 523 GLU cc_start: 0.8881 (tp30) cc_final: 0.8555 (mm-30) REVERT: B 580 MET cc_start: 0.7146 (mtp) cc_final: 0.6287 (mtt) REVERT: B 729 ASN cc_start: 0.6799 (t0) cc_final: 0.6533 (m110) REVERT: B 758 MET cc_start: 0.0598 (ptt) cc_final: 0.0305 (ppp) REVERT: B 812 GLN cc_start: 0.8041 (tp-100) cc_final: 0.7519 (mp10) REVERT: B 921 ASN cc_start: 0.8980 (m-40) cc_final: 0.8337 (m-40) REVERT: B 938 PHE cc_start: 0.8505 (m-10) cc_final: 0.8094 (m-10) REVERT: B 1021 GLU cc_start: 0.8040 (tp30) cc_final: 0.7758 (tp30) REVERT: B 1036 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7573 (mm-30) REVERT: B 1056 ASN cc_start: 0.8635 (t0) cc_final: 0.8407 (t0) REVERT: B 1058 ASP cc_start: 0.9005 (p0) cc_final: 0.8782 (p0) REVERT: B 1062 TYR cc_start: 0.6470 (m-10) cc_final: 0.6208 (m-10) REVERT: B 1180 ASN cc_start: 0.9165 (m110) cc_final: 0.8882 (m110) REVERT: B 1286 GLU cc_start: 0.8213 (mp0) cc_final: 0.7897 (mp0) outliers start: 0 outliers final: 0 residues processed: 688 average time/residue: 0.2771 time to fit residues: 301.4981 Evaluate side-chains 605 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 605 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 43 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 65 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 145 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 190 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN A 465 GLN A 762 HIS A1147 GLN A1326 ASN B 212 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.164015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.137777 restraints weight = 126552.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.143485 restraints weight = 63906.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.147107 restraints weight = 38386.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.149424 restraints weight = 26174.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.151004 restraints weight = 19809.228| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19136 Z= 0.143 Angle : 0.545 6.546 25829 Z= 0.297 Chirality : 0.035 0.135 3082 Planarity : 0.004 0.065 3232 Dihedral : 5.003 30.814 2457 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.26 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.28 (0.17), residues: 2299 helix: 0.47 (0.13), residues: 1462 sheet: None (None), residues: 0 loop : -1.28 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 373 TYR 0.018 0.001 TYR B1115 PHE 0.020 0.001 PHE B 101 TRP 0.021 0.002 TRP B 470 HIS 0.003 0.001 HIS A 720 Details of bonding type rmsd covalent geometry : bond 0.00312 (19136) covalent geometry : angle 0.54469 (25829) hydrogen bonds : bond 0.04342 ( 943) hydrogen bonds : angle 4.57792 ( 2754) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 665 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.8417 (mm) cc_final: 0.8071 (mm) REVERT: A 194 LEU cc_start: 0.8979 (mp) cc_final: 0.8604 (mp) REVERT: A 358 PHE cc_start: 0.8324 (t80) cc_final: 0.7985 (t80) REVERT: A 372 ASP cc_start: 0.7618 (p0) cc_final: 0.7380 (p0) REVERT: A 393 LEU cc_start: 0.9223 (tp) cc_final: 0.8940 (tp) REVERT: A 481 PHE cc_start: 0.9108 (t80) cc_final: 0.8822 (t80) REVERT: A 487 ASN cc_start: 0.8449 (m-40) cc_final: 0.7999 (m-40) REVERT: A 495 ILE cc_start: 0.8807 (mm) cc_final: 0.8526 (mm) REVERT: A 597 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8356 (tm-30) REVERT: A 670 CYS cc_start: 0.7671 (m) cc_final: 0.7302 (t) REVERT: A 785 GLU cc_start: 0.6707 (pm20) cc_final: 0.6170 (tm-30) REVERT: A 795 ASP cc_start: 0.7798 (m-30) cc_final: 0.7349 (m-30) REVERT: A 832 HIS cc_start: 0.9353 (m-70) cc_final: 0.8850 (m170) REVERT: A 837 MET cc_start: 0.9431 (mmm) cc_final: 0.8803 (mmm) REVERT: A 936 LYS cc_start: 0.8930 (mtpp) cc_final: 0.8569 (mtmm) REVERT: A 1012 GLU cc_start: 0.8533 (mp0) cc_final: 0.8192 (mp0) REVERT: A 1036 GLU cc_start: 0.7941 (mp0) cc_final: 0.7105 (mp0) REVERT: B 342 LEU cc_start: 0.9110 (tp) cc_final: 0.8901 (tp) REVERT: B 566 CYS cc_start: 0.7763 (p) cc_final: 0.7504 (p) REVERT: B 580 MET cc_start: 0.7030 (mtp) cc_final: 0.6482 (mtt) REVERT: B 729 ASN cc_start: 0.7278 (t0) cc_final: 0.6760 (m110) REVERT: B 758 MET cc_start: 0.0437 (ptt) cc_final: 0.0042 (ppp) REVERT: B 812 GLN cc_start: 0.7910 (tp-100) cc_final: 0.7425 (mp10) REVERT: B 844 CYS cc_start: 0.9163 (m) cc_final: 0.8913 (m) REVERT: B 966 ASP cc_start: 0.7469 (t70) cc_final: 0.7210 (t70) REVERT: B 1021 GLU cc_start: 0.8049 (tp30) cc_final: 0.7789 (tp30) REVERT: B 1036 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7572 (mm-30) REVERT: B 1056 ASN cc_start: 0.8488 (t0) cc_final: 0.8179 (t0) REVERT: B 1058 ASP cc_start: 0.9207 (p0) cc_final: 0.9000 (p0) REVERT: B 1062 TYR cc_start: 0.6402 (m-10) cc_final: 0.6062 (m-10) outliers start: 0 outliers final: 0 residues processed: 665 average time/residue: 0.2662 time to fit residues: 284.2711 Evaluate side-chains 589 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 589 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 134 optimal weight: 0.9990 chunk 221 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 148 optimal weight: 0.7980 chunk 225 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1038 ASN B 212 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 713 HIS B 862 ASN B1154 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.161974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.138065 restraints weight = 120556.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.143499 restraints weight = 58042.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.146899 restraints weight = 34055.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.149122 restraints weight = 22823.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.150411 restraints weight = 16904.272| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19136 Z= 0.182 Angle : 0.567 6.197 25829 Z= 0.310 Chirality : 0.035 0.138 3082 Planarity : 0.004 0.061 3232 Dihedral : 4.997 28.494 2457 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.39 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % 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: -0.36 (0.17), residues: 2299 helix: 0.47 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -1.43 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 650 TYR 0.023 0.002 TYR B1115 PHE 0.021 0.002 PHE B 101 TRP 0.018 0.002 TRP B 470 HIS 0.005 0.001 HIS A 720 Details of bonding type rmsd covalent geometry : bond 0.00402 (19136) covalent geometry : angle 0.56655 (25829) hydrogen bonds : bond 0.04184 ( 943) hydrogen bonds : angle 4.68520 ( 2754) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 659 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 LEU cc_start: 0.8921 (mp) cc_final: 0.8485 (mp) REVERT: A 208 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7178 (mm-30) REVERT: A 223 VAL cc_start: 0.8649 (t) cc_final: 0.8363 (t) REVERT: A 393 LEU cc_start: 0.9319 (tp) cc_final: 0.9019 (tp) REVERT: A 435 PHE cc_start: 0.8080 (m-10) cc_final: 0.7696 (m-80) REVERT: A 481 PHE cc_start: 0.8977 (t80) cc_final: 0.8753 (t80) REVERT: A 487 ASN cc_start: 0.8421 (m-40) cc_final: 0.8096 (m-40) REVERT: A 495 ILE cc_start: 0.8967 (mm) cc_final: 0.8691 (mm) REVERT: A 531 ASP cc_start: 0.8093 (m-30) cc_final: 0.7893 (m-30) REVERT: A 551 MET cc_start: 0.6419 (mpp) cc_final: 0.5907 (mpp) REVERT: A 597 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8359 (tm-30) REVERT: A 611 ILE cc_start: 0.8796 (mm) cc_final: 0.8440 (mm) REVERT: A 718 LYS cc_start: 0.7209 (pptt) cc_final: 0.6861 (tptm) REVERT: A 785 GLU cc_start: 0.6768 (pm20) cc_final: 0.6103 (tm-30) REVERT: A 795 ASP cc_start: 0.7247 (m-30) cc_final: 0.6901 (m-30) REVERT: A 837 MET cc_start: 0.9391 (mmm) cc_final: 0.9114 (mmm) REVERT: A 936 LYS cc_start: 0.9011 (mtpp) cc_final: 0.8665 (mtmm) REVERT: A 1012 GLU cc_start: 0.8642 (mp0) cc_final: 0.8331 (mp0) REVERT: A 1036 GLU cc_start: 0.7897 (mp0) cc_final: 0.7261 (mp0) REVERT: A 1113 LEU cc_start: 0.9142 (tt) cc_final: 0.8888 (tt) REVERT: A 1297 GLN cc_start: 0.8611 (mm-40) cc_final: 0.7994 (mm-40) REVERT: B 222 THR cc_start: 0.8382 (m) cc_final: 0.8120 (m) REVERT: B 335 TYR cc_start: 0.8874 (t80) cc_final: 0.8547 (t80) REVERT: B 342 LEU cc_start: 0.9116 (tp) cc_final: 0.8903 (tp) REVERT: B 464 GLU cc_start: 0.8521 (tp30) cc_final: 0.8261 (tp30) REVERT: B 580 MET cc_start: 0.7108 (mtp) cc_final: 0.6574 (mtt) REVERT: B 729 ASN cc_start: 0.7308 (t0) cc_final: 0.6680 (m110) REVERT: B 746 ARG cc_start: 0.2343 (mmt180) cc_final: 0.1667 (mtm-85) REVERT: B 856 LEU cc_start: 0.9194 (tp) cc_final: 0.8936 (tt) REVERT: B 921 ASN cc_start: 0.9006 (m-40) cc_final: 0.8098 (m110) REVERT: B 1021 GLU cc_start: 0.8094 (tp30) cc_final: 0.7830 (tp30) REVERT: B 1227 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7788 (mt-10) outliers start: 0 outliers final: 0 residues processed: 659 average time/residue: 0.2616 time to fit residues: 279.4804 Evaluate side-chains 589 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 589 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 202 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 221 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1038 ASN A1369 HIS B 212 ASN B 375 GLN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 862 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.160861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.136950 restraints weight = 120470.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.142355 restraints weight = 57942.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.145804 restraints weight = 33970.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.148008 restraints weight = 22731.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.149367 restraints weight = 16854.801| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 19136 Z= 0.171 Angle : 0.549 6.404 25829 Z= 0.301 Chirality : 0.035 0.205 3082 Planarity : 0.004 0.059 3232 Dihedral : 4.943 26.459 2457 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.18 % Favored : 93.69 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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: -0.30 (0.17), residues: 2299 helix: 0.52 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -1.43 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 472 TYR 0.016 0.002 TYR B1115 PHE 0.028 0.002 PHE A 72 TRP 0.016 0.002 TRP B 470 HIS 0.005 0.001 HIS A 720 Details of bonding type rmsd covalent geometry : bond 0.00377 (19136) covalent geometry : angle 0.54933 (25829) hydrogen bonds : bond 0.04058 ( 943) hydrogen bonds : angle 4.61059 ( 2754) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 662 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 PHE cc_start: 0.7864 (t80) cc_final: 0.7603 (t80) REVERT: A 208 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7396 (mm-30) REVERT: A 372 ASP cc_start: 0.7763 (p0) cc_final: 0.7527 (p0) REVERT: A 393 LEU cc_start: 0.9329 (tp) cc_final: 0.9004 (tp) REVERT: A 435 PHE cc_start: 0.8163 (m-10) cc_final: 0.7779 (m-80) REVERT: A 487 ASN cc_start: 0.7985 (m-40) cc_final: 0.7777 (m-40) REVERT: A 495 ILE cc_start: 0.9045 (mm) cc_final: 0.8803 (mm) REVERT: A 531 ASP cc_start: 0.7740 (m-30) cc_final: 0.7531 (m-30) REVERT: A 597 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8315 (tm-30) REVERT: A 611 ILE cc_start: 0.8699 (mm) cc_final: 0.8404 (mm) REVERT: A 718 LYS cc_start: 0.7333 (pptt) cc_final: 0.6920 (tptm) REVERT: A 796 LYS cc_start: 0.9369 (ttmm) cc_final: 0.9108 (ttpt) REVERT: A 806 ASP cc_start: 0.8758 (m-30) cc_final: 0.8438 (m-30) REVERT: A 837 MET cc_start: 0.9437 (mmm) cc_final: 0.9104 (mmm) REVERT: A 936 LYS cc_start: 0.9109 (mtpp) cc_final: 0.8763 (mtmm) REVERT: A 1036 GLU cc_start: 0.7879 (mp0) cc_final: 0.7333 (mp0) REVERT: A 1163 PHE cc_start: 0.8351 (m-80) cc_final: 0.8127 (m-80) REVERT: A 1297 GLN cc_start: 0.8896 (mm-40) cc_final: 0.8210 (mm-40) REVERT: B 163 ASP cc_start: 0.8932 (m-30) cc_final: 0.8527 (m-30) REVERT: B 372 ASP cc_start: 0.8124 (t0) cc_final: 0.7723 (t0) REVERT: B 812 GLN cc_start: 0.8133 (tp-100) cc_final: 0.7914 (tp-100) REVERT: B 844 CYS cc_start: 0.9092 (m) cc_final: 0.8859 (m) REVERT: B 856 LEU cc_start: 0.9167 (tp) cc_final: 0.8946 (tt) REVERT: B 921 ASN cc_start: 0.8817 (m-40) cc_final: 0.8053 (m110) REVERT: B 975 ASN cc_start: 0.8363 (m-40) cc_final: 0.7872 (m-40) REVERT: B 1056 ASN cc_start: 0.8582 (t0) cc_final: 0.8380 (t0) REVERT: B 1227 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8220 (mt-10) REVERT: B 1286 GLU cc_start: 0.8553 (mp0) cc_final: 0.8231 (mp0) REVERT: B 1300 ASN cc_start: 0.7376 (t0) cc_final: 0.7135 (t0) outliers start: 0 outliers final: 0 residues processed: 662 average time/residue: 0.2633 time to fit residues: 282.3592 Evaluate side-chains 587 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 587 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 31 optimal weight: 0.8980 chunk 224 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 150 optimal weight: 0.1980 chunk 93 optimal weight: 0.7980 chunk 128 optimal weight: 0.0870 chunk 27 optimal weight: 0.3980 chunk 218 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 223 optimal weight: 0.7980 chunk 210 optimal weight: 0.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1369 HIS B 212 ASN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 862 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.162270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.138101 restraints weight = 119999.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.143631 restraints weight = 58011.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.147032 restraints weight = 33934.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.149340 restraints weight = 22863.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.150798 restraints weight = 16829.312| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19136 Z= 0.119 Angle : 0.520 7.400 25829 Z= 0.280 Chirality : 0.034 0.138 3082 Planarity : 0.004 0.062 3232 Dihedral : 4.800 25.338 2457 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.61 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % 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: -0.11 (0.17), residues: 2299 helix: 0.67 (0.13), residues: 1461 sheet: None (None), residues: 0 loop : -1.34 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 559 TYR 0.016 0.001 TYR A1062 PHE 0.017 0.001 PHE A 358 TRP 0.013 0.001 TRP B 470 HIS 0.005 0.001 HIS A1369 Details of bonding type rmsd covalent geometry : bond 0.00268 (19136) covalent geometry : angle 0.52041 (25829) hydrogen bonds : bond 0.03766 ( 943) hydrogen bonds : angle 4.38510 ( 2754) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 656 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 PHE cc_start: 0.7872 (t80) cc_final: 0.7621 (t80) REVERT: A 208 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7551 (mm-30) REVERT: A 333 ARG cc_start: 0.7659 (ttm-80) cc_final: 0.7369 (ttm-80) REVERT: A 372 ASP cc_start: 0.7803 (p0) cc_final: 0.7551 (p0) REVERT: A 393 LEU cc_start: 0.9313 (tp) cc_final: 0.8985 (tp) REVERT: A 435 PHE cc_start: 0.8209 (m-10) cc_final: 0.7814 (m-80) REVERT: A 487 ASN cc_start: 0.8371 (m-40) cc_final: 0.8107 (m-40) REVERT: A 495 ILE cc_start: 0.9106 (mm) cc_final: 0.8820 (mm) REVERT: A 597 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8392 (tm-30) REVERT: A 611 ILE cc_start: 0.8687 (mm) cc_final: 0.8381 (mm) REVERT: A 718 LYS cc_start: 0.7875 (pptt) cc_final: 0.7428 (tptm) REVERT: A 796 LYS cc_start: 0.9379 (ttmm) cc_final: 0.9130 (ttpt) REVERT: A 837 MET cc_start: 0.9468 (mmm) cc_final: 0.9102 (mmm) REVERT: A 936 LYS cc_start: 0.9112 (mtpp) cc_final: 0.8763 (mtmm) REVERT: A 1012 GLU cc_start: 0.8630 (mp0) cc_final: 0.8222 (mp0) REVERT: A 1036 GLU cc_start: 0.7864 (mp0) cc_final: 0.7208 (mp0) REVERT: A 1297 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8179 (mm-40) REVERT: B 218 MET cc_start: 0.8290 (tpp) cc_final: 0.7947 (tpp) REVERT: B 222 THR cc_start: 0.8379 (m) cc_final: 0.7670 (m) REVERT: B 342 LEU cc_start: 0.9124 (tp) cc_final: 0.8873 (tp) REVERT: B 372 ASP cc_start: 0.8156 (t0) cc_final: 0.7715 (t0) REVERT: B 542 GLU cc_start: 0.9196 (mp0) cc_final: 0.8847 (mm-30) REVERT: B 729 ASN cc_start: 0.7574 (t0) cc_final: 0.7315 (t0) REVERT: B 812 GLN cc_start: 0.8093 (tp-100) cc_final: 0.7891 (tp-100) REVERT: B 921 ASN cc_start: 0.8818 (m-40) cc_final: 0.8027 (m110) REVERT: B 975 ASN cc_start: 0.8398 (m-40) cc_final: 0.7880 (m-40) REVERT: B 1016 SER cc_start: 0.8387 (p) cc_final: 0.8171 (p) REVERT: B 1056 ASN cc_start: 0.8563 (t0) cc_final: 0.8071 (t0) REVERT: B 1058 ASP cc_start: 0.9160 (p0) cc_final: 0.8882 (p0) REVERT: B 1193 GLU cc_start: 0.7552 (mp0) cc_final: 0.7232 (mp0) REVERT: B 1227 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7743 (mt-10) REVERT: B 1286 GLU cc_start: 0.8515 (mp0) cc_final: 0.8194 (mp0) REVERT: B 1300 ASN cc_start: 0.7507 (t0) cc_final: 0.7273 (t0) outliers start: 0 outliers final: 0 residues processed: 656 average time/residue: 0.2653 time to fit residues: 282.1454 Evaluate side-chains 586 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 586 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 143 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 9 optimal weight: 0.0980 chunk 62 optimal weight: 0.0070 chunk 106 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 overall best weight: 0.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1038 ASN A1369 HIS B 212 ASN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 862 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.157037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.132412 restraints weight = 117667.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.137869 restraints weight = 56625.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.141375 restraints weight = 33277.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.143607 restraints weight = 22302.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.145105 restraints weight = 16629.113| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19136 Z= 0.123 Angle : 0.522 7.736 25829 Z= 0.281 Chirality : 0.034 0.134 3082 Planarity : 0.004 0.060 3232 Dihedral : 4.716 25.513 2457 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.61 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % 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: -0.13 (0.17), residues: 2299 helix: 0.65 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -1.36 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 379 TYR 0.018 0.001 TYR A1062 PHE 0.026 0.001 PHE A 805 TRP 0.013 0.001 TRP B 773 HIS 0.004 0.001 HIS A1369 Details of bonding type rmsd covalent geometry : bond 0.00277 (19136) covalent geometry : angle 0.52246 (25829) hydrogen bonds : bond 0.03738 ( 943) hydrogen bonds : angle 4.35152 ( 2754) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 660 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 PHE cc_start: 0.8021 (t80) cc_final: 0.7820 (t80) REVERT: A 208 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7749 (mm-30) REVERT: A 228 LYS cc_start: 0.9360 (mmmt) cc_final: 0.8981 (mttp) REVERT: A 356 ARG cc_start: 0.8128 (mtm180) cc_final: 0.7901 (mtp85) REVERT: A 372 ASP cc_start: 0.7831 (p0) cc_final: 0.7505 (p0) REVERT: A 393 LEU cc_start: 0.9332 (tp) cc_final: 0.8976 (tp) REVERT: A 435 PHE cc_start: 0.8235 (m-10) cc_final: 0.7872 (m-80) REVERT: A 531 ASP cc_start: 0.7670 (m-30) cc_final: 0.7419 (m-30) REVERT: A 597 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8392 (tm-30) REVERT: A 611 ILE cc_start: 0.8731 (mm) cc_final: 0.8420 (mm) REVERT: A 718 LYS cc_start: 0.7899 (pptt) cc_final: 0.7422 (tptm) REVERT: A 837 MET cc_start: 0.9394 (mmm) cc_final: 0.9083 (mmm) REVERT: A 936 LYS cc_start: 0.9148 (mtpp) cc_final: 0.8758 (mtmm) REVERT: A 1012 GLU cc_start: 0.8609 (mp0) cc_final: 0.8234 (mp0) REVERT: A 1036 GLU cc_start: 0.7852 (mp0) cc_final: 0.7183 (mp0) REVERT: B 342 LEU cc_start: 0.9074 (tp) cc_final: 0.8866 (tp) REVERT: B 459 LYS cc_start: 0.8688 (mtpp) cc_final: 0.8486 (mttp) REVERT: B 812 GLN cc_start: 0.8131 (tp-100) cc_final: 0.7914 (tp-100) REVERT: B 921 ASN cc_start: 0.8833 (m-40) cc_final: 0.8021 (m110) REVERT: B 954 TYR cc_start: 0.8374 (t80) cc_final: 0.8140 (t80) REVERT: B 1016 SER cc_start: 0.8437 (p) cc_final: 0.8213 (p) REVERT: B 1056 ASN cc_start: 0.8565 (t0) cc_final: 0.8083 (t0) REVERT: B 1058 ASP cc_start: 0.9161 (p0) cc_final: 0.8880 (p0) REVERT: B 1227 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7855 (mt-10) REVERT: B 1286 GLU cc_start: 0.8379 (mp0) cc_final: 0.7763 (mp0) REVERT: B 1300 ASN cc_start: 0.7501 (t0) cc_final: 0.7263 (t0) outliers start: 0 outliers final: 0 residues processed: 660 average time/residue: 0.2620 time to fit residues: 276.5929 Evaluate side-chains 589 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 589 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 206 optimal weight: 0.5980 chunk 138 optimal weight: 0.9980 chunk 223 optimal weight: 0.6980 chunk 11 optimal weight: 0.0970 chunk 225 optimal weight: 0.1980 chunk 214 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 224 optimal weight: 0.7980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1038 ASN A1369 HIS B 212 ASN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 862 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.158431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.132410 restraints weight = 123843.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.138052 restraints weight = 61809.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.141678 restraints weight = 37094.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.144032 restraints weight = 25240.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.145569 restraints weight = 18969.126| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19136 Z= 0.117 Angle : 0.515 7.492 25829 Z= 0.276 Chirality : 0.034 0.163 3082 Planarity : 0.004 0.058 3232 Dihedral : 4.666 25.576 2457 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.65 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % 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: -0.02 (0.18), residues: 2299 helix: 0.73 (0.13), residues: 1475 sheet: None (None), residues: 0 loop : -1.32 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 80 TYR 0.018 0.001 TYR A1062 PHE 0.014 0.001 PHE A 699 TRP 0.014 0.001 TRP B 773 HIS 0.004 0.001 HIS A1369 Details of bonding type rmsd covalent geometry : bond 0.00264 (19136) covalent geometry : angle 0.51540 (25829) hydrogen bonds : bond 0.03635 ( 943) hydrogen bonds : angle 4.25893 ( 2754) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 648 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7777 (mm-30) REVERT: A 228 LYS cc_start: 0.9279 (mmmt) cc_final: 0.8907 (mttp) REVERT: A 372 ASP cc_start: 0.7853 (p0) cc_final: 0.7501 (p0) REVERT: A 393 LEU cc_start: 0.9327 (tp) cc_final: 0.8969 (tp) REVERT: A 435 PHE cc_start: 0.8229 (m-10) cc_final: 0.7892 (m-80) REVERT: A 552 GLU cc_start: 0.8137 (pm20) cc_final: 0.7817 (pm20) REVERT: A 597 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8437 (tm-30) REVERT: A 611 ILE cc_start: 0.8710 (mm) cc_final: 0.8409 (mm) REVERT: A 718 LYS cc_start: 0.7882 (pptt) cc_final: 0.7412 (tptm) REVERT: A 837 MET cc_start: 0.9398 (mmm) cc_final: 0.9012 (mmm) REVERT: A 936 LYS cc_start: 0.9096 (mtpp) cc_final: 0.8754 (mtmm) REVERT: A 1012 GLU cc_start: 0.8597 (mp0) cc_final: 0.8244 (mp0) REVERT: A 1036 GLU cc_start: 0.7840 (mp0) cc_final: 0.7158 (mp0) REVERT: A 1167 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8424 (mp0) REVERT: B 342 LEU cc_start: 0.9079 (tp) cc_final: 0.8852 (tp) REVERT: B 361 GLU cc_start: 0.7623 (mp0) cc_final: 0.7336 (mp0) REVERT: B 729 ASN cc_start: 0.7700 (t0) cc_final: 0.7473 (t0) REVERT: B 812 GLN cc_start: 0.7472 (tp-100) cc_final: 0.7248 (tp-100) REVERT: B 921 ASN cc_start: 0.8834 (m-40) cc_final: 0.8040 (m110) REVERT: B 954 TYR cc_start: 0.8387 (t80) cc_final: 0.8123 (t80) REVERT: B 1016 SER cc_start: 0.8445 (p) cc_final: 0.8230 (p) REVERT: B 1056 ASN cc_start: 0.8584 (t0) cc_final: 0.8108 (t0) REVERT: B 1058 ASP cc_start: 0.9188 (p0) cc_final: 0.8870 (p0) REVERT: B 1193 GLU cc_start: 0.7712 (mp0) cc_final: 0.7504 (mp0) REVERT: B 1286 GLU cc_start: 0.8388 (mp0) cc_final: 0.8105 (mp0) REVERT: B 1300 ASN cc_start: 0.7492 (t0) cc_final: 0.7290 (t0) outliers start: 0 outliers final: 0 residues processed: 648 average time/residue: 0.2723 time to fit residues: 285.6067 Evaluate side-chains 591 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 591 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 188 optimal weight: 0.0870 chunk 126 optimal weight: 0.0570 chunk 197 optimal weight: 0.3980 chunk 141 optimal weight: 0.5980 chunk 154 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 194 optimal weight: 0.5980 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1038 ASN A1369 HIS B 212 ASN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN ** B 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1180 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.157746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.132901 restraints weight = 117755.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.138410 restraints weight = 56633.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.141949 restraints weight = 33263.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.144226 restraints weight = 22299.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.145709 restraints weight = 16562.655| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 19136 Z= 0.108 Angle : 0.511 8.116 25829 Z= 0.273 Chirality : 0.034 0.135 3082 Planarity : 0.003 0.056 3232 Dihedral : 4.580 25.588 2457 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.39 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: 0.05 (0.18), residues: 2299 helix: 0.81 (0.14), residues: 1471 sheet: None (None), residues: 0 loop : -1.32 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 80 TYR 0.019 0.001 TYR A1062 PHE 0.032 0.001 PHE A 805 TRP 0.013 0.001 TRP B 773 HIS 0.004 0.001 HIS A1369 Details of bonding type rmsd covalent geometry : bond 0.00245 (19136) covalent geometry : angle 0.51065 (25829) hydrogen bonds : bond 0.03561 ( 943) hydrogen bonds : angle 4.18930 ( 2754) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 655 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 THR cc_start: 0.8675 (m) cc_final: 0.8310 (m) REVERT: A 208 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7513 (mm-30) REVERT: A 372 ASP cc_start: 0.7840 (p0) cc_final: 0.7451 (p0) REVERT: A 393 LEU cc_start: 0.9316 (tp) cc_final: 0.8964 (tp) REVERT: A 435 PHE cc_start: 0.8253 (m-10) cc_final: 0.7891 (m-80) REVERT: A 531 ASP cc_start: 0.8069 (m-30) cc_final: 0.7741 (m-30) REVERT: A 597 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8421 (tm-30) REVERT: A 611 ILE cc_start: 0.8727 (mm) cc_final: 0.8452 (mm) REVERT: A 718 LYS cc_start: 0.7919 (pptt) cc_final: 0.7420 (tptm) REVERT: A 837 MET cc_start: 0.9448 (mmm) cc_final: 0.9056 (mmm) REVERT: A 936 LYS cc_start: 0.9103 (mtpp) cc_final: 0.8755 (mtmm) REVERT: A 1012 GLU cc_start: 0.8563 (mp0) cc_final: 0.8260 (mp0) REVERT: A 1036 GLU cc_start: 0.7839 (mp0) cc_final: 0.7200 (mp0) REVERT: B 342 LEU cc_start: 0.8979 (tp) cc_final: 0.8743 (tp) REVERT: B 844 CYS cc_start: 0.9086 (m) cc_final: 0.8883 (m) REVERT: B 921 ASN cc_start: 0.8803 (m-40) cc_final: 0.7963 (m110) REVERT: B 954 TYR cc_start: 0.8351 (t80) cc_final: 0.8070 (t80) REVERT: B 1016 SER cc_start: 0.8439 (p) cc_final: 0.8221 (p) REVERT: B 1056 ASN cc_start: 0.8589 (t0) cc_final: 0.8113 (t0) REVERT: B 1058 ASP cc_start: 0.9169 (p0) cc_final: 0.8844 (p0) REVERT: B 1193 GLU cc_start: 0.7781 (mp0) cc_final: 0.7503 (mp0) REVERT: B 1300 ASN cc_start: 0.7484 (t0) cc_final: 0.7239 (t0) outliers start: 0 outliers final: 0 residues processed: 655 average time/residue: 0.2616 time to fit residues: 275.6241 Evaluate side-chains 586 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 586 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 130 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 110 optimal weight: 0.0870 chunk 169 optimal weight: 1.9990 chunk 193 optimal weight: 0.3980 chunk 165 optimal weight: 1.9990 chunk 195 optimal weight: 0.0870 chunk 68 optimal weight: 0.0870 chunk 171 optimal weight: 0.0020 chunk 188 optimal weight: 0.0980 chunk 61 optimal weight: 0.3980 overall best weight: 0.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1369 HIS B 212 ASN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1180 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.159871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.135226 restraints weight = 117079.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.140713 restraints weight = 56892.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.144220 restraints weight = 33504.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.146479 restraints weight = 22488.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.147974 restraints weight = 16719.109| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 19136 Z= 0.099 Angle : 0.509 8.426 25829 Z= 0.268 Chirality : 0.034 0.147 3082 Planarity : 0.004 0.057 3232 Dihedral : 4.421 24.366 2457 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.74 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: 0.12 (0.18), residues: 2299 helix: 0.87 (0.14), residues: 1468 sheet: None (None), residues: 0 loop : -1.32 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 490 TYR 0.022 0.001 TYR A 703 PHE 0.032 0.001 PHE A 125 TRP 0.014 0.001 TRP B 768 HIS 0.004 0.001 HIS A1369 Details of bonding type rmsd covalent geometry : bond 0.00224 (19136) covalent geometry : angle 0.50864 (25829) hydrogen bonds : bond 0.03362 ( 943) hydrogen bonds : angle 4.00428 ( 2754) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 647 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 THR cc_start: 0.8562 (m) cc_final: 0.8212 (m) REVERT: A 208 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7569 (mm-30) REVERT: A 372 ASP cc_start: 0.7866 (p0) cc_final: 0.7572 (p0) REVERT: A 393 LEU cc_start: 0.9272 (tp) cc_final: 0.8897 (tp) REVERT: A 435 PHE cc_start: 0.8235 (m-10) cc_final: 0.7920 (m-80) REVERT: A 531 ASP cc_start: 0.8105 (m-30) cc_final: 0.7851 (m-30) REVERT: A 562 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6906 (mm-30) REVERT: A 597 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8475 (tm-30) REVERT: A 611 ILE cc_start: 0.8710 (mm) cc_final: 0.8429 (mm) REVERT: A 718 LYS cc_start: 0.7856 (pptt) cc_final: 0.7396 (tptm) REVERT: A 837 MET cc_start: 0.9478 (mmm) cc_final: 0.9064 (mmm) REVERT: A 936 LYS cc_start: 0.9117 (mtpp) cc_final: 0.8764 (mtmm) REVERT: A 1012 GLU cc_start: 0.8515 (mp0) cc_final: 0.8251 (mp0) REVERT: A 1036 GLU cc_start: 0.7905 (mp0) cc_final: 0.7348 (mp0) REVERT: A 1311 VAL cc_start: 0.9443 (t) cc_final: 0.9234 (p) REVERT: B 218 MET cc_start: 0.8161 (tpp) cc_final: 0.7934 (tpp) REVERT: B 342 LEU cc_start: 0.8940 (tp) cc_final: 0.8690 (tp) REVERT: B 411 LEU cc_start: 0.8582 (tp) cc_final: 0.8228 (tp) REVERT: B 414 THR cc_start: 0.7959 (m) cc_final: 0.7741 (p) REVERT: B 817 ILE cc_start: 0.8959 (mm) cc_final: 0.8694 (mm) REVERT: B 921 ASN cc_start: 0.8777 (m-40) cc_final: 0.7944 (m110) REVERT: B 954 TYR cc_start: 0.8305 (t80) cc_final: 0.8064 (t80) REVERT: B 966 ASP cc_start: 0.7495 (t70) cc_final: 0.7293 (t70) REVERT: B 975 ASN cc_start: 0.8160 (m-40) cc_final: 0.7690 (m-40) REVERT: B 1056 ASN cc_start: 0.8493 (t0) cc_final: 0.8050 (t0) REVERT: B 1058 ASP cc_start: 0.9137 (p0) cc_final: 0.8879 (p0) REVERT: B 1123 CYS cc_start: 0.8773 (t) cc_final: 0.8479 (t) REVERT: B 1193 GLU cc_start: 0.7737 (mp0) cc_final: 0.7484 (mp0) REVERT: B 1286 GLU cc_start: 0.8382 (mp0) cc_final: 0.8044 (mp0) REVERT: B 1300 ASN cc_start: 0.7462 (t0) cc_final: 0.7240 (t0) outliers start: 0 outliers final: 0 residues processed: 647 average time/residue: 0.2599 time to fit residues: 271.6315 Evaluate side-chains 588 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 588 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 86 optimal weight: 0.2980 chunk 73 optimal weight: 0.4980 chunk 196 optimal weight: 0.4980 chunk 63 optimal weight: 0.9980 chunk 188 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 134 optimal weight: 0.3980 chunk 155 optimal weight: 0.0030 chunk 179 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 overall best weight: 0.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1038 ASN A1369 HIS B 212 ASN B 422 ASN B 424 GLN ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1126 GLN B1180 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.158412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.133610 restraints weight = 117665.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.139156 restraints weight = 56876.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.142716 restraints weight = 33360.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.145000 restraints weight = 22344.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.146528 restraints weight = 16615.400| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 19136 Z= 0.103 Angle : 0.503 8.177 25829 Z= 0.267 Chirality : 0.034 0.140 3082 Planarity : 0.003 0.057 3232 Dihedral : 4.391 24.983 2457 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.57 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 0.18 (0.18), residues: 2299 helix: 0.92 (0.14), residues: 1470 sheet: None (None), residues: 0 loop : -1.29 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 80 TYR 0.022 0.001 TYR A 703 PHE 0.026 0.001 PHE A 805 TRP 0.015 0.001 TRP B 768 HIS 0.004 0.001 HIS A1369 Details of bonding type rmsd covalent geometry : bond 0.00237 (19136) covalent geometry : angle 0.50272 (25829) hydrogen bonds : bond 0.03331 ( 943) hydrogen bonds : angle 4.05980 ( 2754) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6950.47 seconds wall clock time: 118 minutes 54.61 seconds (7134.61 seconds total)