Starting phenix.real_space_refine on Wed Jun 25 18:23:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e20_27826/06_2025/8e20_27826.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e20_27826/06_2025/8e20_27826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e20_27826/06_2025/8e20_27826.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e20_27826/06_2025/8e20_27826.map" model { file = "/net/cci-nas-00/data/ceres_data/8e20_27826/06_2025/8e20_27826.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e20_27826/06_2025/8e20_27826.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 106 5.16 5 C 18699 2.51 5 N 5322 2.21 5 O 5214 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 2.60s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29341 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 14633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2260, 14633 Classifications: {'peptide': 2260} Incomplete info: {'backbone_only': 6, 'truncation_to_alanine': 1122} Link IDs: {'PTRANS': 84, 'TRANS': 2175} Chain breaks: 23 Unresolved chain link angles: 44 Unresolved non-hydrogen bonds: 3446 Unresolved non-hydrogen angles: 4386 Unresolved non-hydrogen dihedrals: 2670 Unresolved non-hydrogen chiralities: 431 Planarities with less than four sites: {'GLN:plan1': 60, 'ASP:plan': 79, 'TYR:plan': 11, 'ASN:plan1': 75, 'TRP:plan': 3, 'HIS:plan': 17, 'PHE:plan': 16, 'GLU:plan': 98, 'ARG:plan': 39} Unresolved non-hydrogen planarities: 1575 Chain: "B" Number of atoms: 14708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2255, 14708 Classifications: {'peptide': 2255} Incomplete info: {'backbone_only': 6, 'truncation_to_alanine': 1080} Link IDs: {'PTRANS': 84, 'TRANS': 2170} Chain breaks: 24 Unresolved chain link angles: 44 Unresolved non-hydrogen bonds: 3331 Unresolved non-hydrogen angles: 4239 Unresolved non-hydrogen dihedrals: 2587 Unresolved non-hydrogen chiralities: 416 Planarities with less than four sites: {'GLN:plan1': 56, 'ASP:plan': 74, 'TYR:plan': 11, 'ASN:plan1': 71, 'TRP:plan': 3, 'HIS:plan': 17, 'PHE:plan': 16, 'GLU:plan': 94, 'ARG:plan': 39} Unresolved non-hydrogen planarities: 1516 Time building chain proxies: 19.81, per 1000 atoms: 0.68 Number of scatterers: 29341 At special positions: 0 Unit cell: (277.68, 215.28, 122.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 106 16.00 O 5214 8.00 N 5322 7.00 C 18699 6.00 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: 7.99 Conformation dependent library (CDL) restraints added in 4.4 seconds 8834 Ramachandran restraints generated. 4417 Oldfield, 0 Emsley, 4417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8692 Finding SS restraints... Secondary structure from input PDB file: 265 helices and 8 sheets defined 74.6% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.54 Creating SS restraints... Processing helix chain 'A' and resid 4 through 20 removed outlier: 3.751A pdb=" N GLN A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 26 Processing helix chain 'A' and resid 31 through 47 removed outlier: 4.384A pdb=" N SER A 35 " --> pdb=" O HIS A 31 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N THR A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 43 " --> pdb=" O ASN A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 73 through 97 removed outlier: 3.627A pdb=" N LYS A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 81 " --> pdb=" O LYS A 77 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 84 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 102 Processing helix chain 'A' and resid 106 through 117 Proline residue: A 115 - end of helix Processing helix chain 'A' and resid 130 through 149 removed outlier: 3.566A pdb=" N CYS A 147 " --> pdb=" O PHE A 143 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN A 148 " --> pdb=" O SER A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 167 removed outlier: 3.688A pdb=" N VAL A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 166 " --> pdb=" O GLN A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 186 through 202 removed outlier: 4.735A pdb=" N LYS A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 227 removed outlier: 3.689A pdb=" N LYS A 218 " --> pdb=" O ASN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.542A pdb=" N TYR A 235 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 256 removed outlier: 3.534A pdb=" N PHE A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 276 Proline residue: A 268 - end of helix removed outlier: 3.544A pdb=" N ILE A 272 " --> pdb=" O PRO A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 286 removed outlier: 3.817A pdb=" N SER A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS A 286 " --> pdb=" O GLN A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 292 No H-bonds generated for 'chain 'A' and resid 290 through 292' Processing helix chain 'A' and resid 293 through 308 Processing helix chain 'A' and resid 314 through 334 Processing helix chain 'A' and resid 341 through 358 removed outlier: 3.899A pdb=" N MET A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL A 351 " --> pdb=" O GLN A 347 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ASP A 352 " --> pdb=" O SER A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 387 Processing helix chain 'A' and resid 391 through 398 Processing helix chain 'A' and resid 403 through 419 Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.504A pdb=" N PHE A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 503 Processing helix chain 'A' and resid 504 through 509 removed outlier: 4.010A pdb=" N CYS A 509 " --> pdb=" O LYS A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 520 Processing helix chain 'A' and resid 521 through 531 Processing helix chain 'A' and resid 538 through 553 Processing helix chain 'A' and resid 554 through 559 Processing helix chain 'A' and resid 565 through 588 Processing helix chain 'A' and resid 592 through 618 Processing helix chain 'A' and resid 678 through 695 removed outlier: 3.636A pdb=" N LEU A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 721 removed outlier: 3.711A pdb=" N VAL A 705 " --> pdb=" O GLU A 701 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE A 710 " --> pdb=" O ALA A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 731 Processing helix chain 'A' and resid 734 through 747 removed outlier: 3.633A pdb=" N ALA A 742 " --> pdb=" O PHE A 738 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A 743 " --> pdb=" O MET A 739 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 745 " --> pdb=" O PHE A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 765 removed outlier: 3.662A pdb=" N LEU A 755 " --> pdb=" O GLY A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 794 removed outlier: 3.703A pdb=" N LEU A 790 " --> pdb=" O GLN A 786 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE A 791 " --> pdb=" O ALA A 787 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A 792 " --> pdb=" O THR A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 848 removed outlier: 3.507A pdb=" N GLY A 842 " --> pdb=" O ILE A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 855 removed outlier: 3.512A pdb=" N LEU A 852 " --> pdb=" O GLY A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 902 removed outlier: 4.033A pdb=" N MET A 895 " --> pdb=" O VAL A 891 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP A 896 " --> pdb=" O SER A 892 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A 902 " --> pdb=" O LEU A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 925 removed outlier: 3.658A pdb=" N LEU A 925 " --> pdb=" O VAL A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 928 No H-bonds generated for 'chain 'A' and resid 926 through 928' Processing helix chain 'A' and resid 929 through 942 removed outlier: 3.609A pdb=" N ASN A 939 " --> pdb=" O ASN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 974 Processing helix chain 'A' and resid 978 through 984 removed outlier: 3.684A pdb=" N HIS A 982 " --> pdb=" O GLY A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1001 removed outlier: 3.938A pdb=" N VAL A1001 " --> pdb=" O ARG A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1025 removed outlier: 3.695A pdb=" N ARG A1025 " --> pdb=" O VAL A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1046 removed outlier: 3.608A pdb=" N PHE A1037 " --> pdb=" O GLN A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1081 removed outlier: 3.726A pdb=" N ALA A1081 " --> pdb=" O VAL A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1116 removed outlier: 3.867A pdb=" N ASP A1116 " --> pdb=" O ASN A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1156 removed outlier: 4.126A pdb=" N ARG A1142 " --> pdb=" O LEU A1138 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A1155 " --> pdb=" O ASN A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1159 No H-bonds generated for 'chain 'A' and resid 1157 through 1159' Processing helix chain 'A' and resid 1160 through 1165 Processing helix chain 'A' and resid 1166 through 1169 Processing helix chain 'A' and resid 1175 through 1184 removed outlier: 4.437A pdb=" N GLU A1181 " --> pdb=" O ALA A1177 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL A1182 " --> pdb=" O THR A1178 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1186 No H-bonds generated for 'chain 'A' and resid 1185 through 1186' Processing helix chain 'A' and resid 1187 through 1191 removed outlier: 3.592A pdb=" N THR A1191 " --> pdb=" O GLN A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1217 removed outlier: 3.561A pdb=" N MET A1215 " --> pdb=" O LEU A1211 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A1216 " --> pdb=" O VAL A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1231 removed outlier: 3.553A pdb=" N MET A1225 " --> pdb=" O LEU A1221 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN A1229 " --> pdb=" O MET A1225 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A1230 " --> pdb=" O ALA A1226 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1234 No H-bonds generated for 'chain 'A' and resid 1232 through 1234' Processing helix chain 'A' and resid 1235 through 1248 removed outlier: 4.259A pdb=" N LEU A1239 " --> pdb=" O GLN A1235 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL A1244 " --> pdb=" O ALA A1240 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE A1247 " --> pdb=" O LEU A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1261 removed outlier: 3.754A pdb=" N LEU A1257 " --> pdb=" O LEU A1253 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TRP A1258 " --> pdb=" O TYR A1254 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASN A1259 " --> pdb=" O GLN A1255 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N MET A1260 " --> pdb=" O LEU A1256 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A1261 " --> pdb=" O LEU A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1268 removed outlier: 3.962A pdb=" N VAL A1265 " --> pdb=" O PHE A1261 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU A1266 " --> pdb=" O SER A1262 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU A1267 " --> pdb=" O LYS A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1273 removed outlier: 4.281A pdb=" N GLN A1272 " --> pdb=" O ASP A1269 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR A1273 " --> pdb=" O SER A1270 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1269 through 1273' Processing helix chain 'A' and resid 1284 through 1293 removed outlier: 3.699A pdb=" N PHE A1289 " --> pdb=" O MET A1285 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS A1290 " --> pdb=" O THR A1286 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1301 removed outlier: 3.704A pdb=" N LEU A1300 " --> pdb=" O TYR A1296 " (cutoff:3.500A) Processing helix chain 'A' and resid 1333 through 1338 removed outlier: 3.644A pdb=" N GLN A1336 " --> pdb=" O GLU A1333 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARG A1337 " --> pdb=" O GLU A1334 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ASN A1338 " --> pdb=" O ASN A1335 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1333 through 1338' Processing helix chain 'A' and resid 1339 through 1353 removed outlier: 3.960A pdb=" N THR A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS A1348 " --> pdb=" O GLU A1344 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA A1349 " --> pdb=" O LYS A1345 " (cutoff:3.500A) Processing helix chain 'A' and resid 1358 through 1376 removed outlier: 4.266A pdb=" N VAL A1364 " --> pdb=" O GLN A1360 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS A1365 " --> pdb=" O LEU A1361 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG A1375 " --> pdb=" O VAL A1371 " (cutoff:3.500A) Processing helix chain 'A' and resid 1381 through 1393 Processing helix chain 'A' and resid 1413 through 1431 removed outlier: 3.589A pdb=" N ILE A1424 " --> pdb=" O LEU A1420 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A1429 " --> pdb=" O LEU A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1451 removed outlier: 3.611A pdb=" N ASP A1445 " --> pdb=" O PRO A1442 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE A1446 " --> pdb=" O PHE A1443 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS A1448 " --> pdb=" O ASP A1445 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN A1450 " --> pdb=" O VAL A1447 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE A1451 " --> pdb=" O LYS A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1452 through 1463 removed outlier: 4.052A pdb=" N ARG A1456 " --> pdb=" O ASP A1452 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE A1457 " --> pdb=" O ALA A1453 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP A1460 " --> pdb=" O ARG A1456 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE A1461 " --> pdb=" O PHE A1457 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA A1462 " --> pdb=" O PHE A1458 " (cutoff:3.500A) Processing helix chain 'A' and resid 1488 through 1493 Processing helix chain 'A' and resid 1493 through 1502 removed outlier: 3.920A pdb=" N GLY A1498 " --> pdb=" O GLN A1494 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLN A1499 " --> pdb=" O GLU A1495 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A1500 " --> pdb=" O LYS A1496 " (cutoff:3.500A) Processing helix chain 'A' and resid 1516 through 1521 removed outlier: 3.904A pdb=" N THR A1520 " --> pdb=" O ASP A1516 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A1521 " --> pdb=" O LYS A1517 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1516 through 1521' Processing helix chain 'A' and resid 1590 through 1592 No H-bonds generated for 'chain 'A' and resid 1590 through 1592' Processing helix chain 'A' and resid 1598 through 1609 removed outlier: 3.707A pdb=" N LEU A1602 " --> pdb=" O ASN A1598 " (cutoff:3.500A) Processing helix chain 'A' and resid 1628 through 1632 Processing helix chain 'A' and resid 1634 through 1645 removed outlier: 3.975A pdb=" N PHE A1645 " --> pdb=" O TRP A1641 " (cutoff:3.500A) Processing helix chain 'A' and resid 1646 through 1652 removed outlier: 3.772A pdb=" N TYR A1650 " --> pdb=" O PRO A1646 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP A1651 " --> pdb=" O GLY A1647 " (cutoff:3.500A) Processing helix chain 'A' and resid 1662 through 1672 Processing helix chain 'A' and resid 1690 through 1697 removed outlier: 3.812A pdb=" N LEU A1694 " --> pdb=" O CYS A1690 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N HIS A1697 " --> pdb=" O LYS A1693 " (cutoff:3.500A) Processing helix chain 'A' and resid 1698 through 1702 Processing helix chain 'A' and resid 1706 through 1711 removed outlier: 3.756A pdb=" N LEU A1710 " --> pdb=" O PRO A1706 " (cutoff:3.500A) Processing helix chain 'A' and resid 1765 through 1767 No H-bonds generated for 'chain 'A' and resid 1765 through 1767' Processing helix chain 'A' and resid 1795 through 1813 Processing helix chain 'A' and resid 1828 through 1842 removed outlier: 3.789A pdb=" N ILE A1836 " --> pdb=" O THR A1832 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY A1842 " --> pdb=" O LEU A1838 " (cutoff:3.500A) Processing helix chain 'A' and resid 1845 through 1864 Processing helix chain 'A' and resid 1883 through 1898 Processing helix chain 'A' and resid 1903 through 1916 removed outlier: 3.985A pdb=" N SER A1914 " --> pdb=" O ILE A1910 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS A1915 " --> pdb=" O SER A1911 " (cutoff:3.500A) Processing helix chain 'A' and resid 1917 through 1933 Proline residue: A1930 - end of helix removed outlier: 4.497A pdb=" N SER A1933 " --> pdb=" O THR A1929 " (cutoff:3.500A) Processing helix chain 'A' and resid 1936 through 1941 removed outlier: 4.110A pdb=" N LYS A1940 " --> pdb=" O VAL A1936 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N HIS A1941 " --> pdb=" O ARG A1937 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1936 through 1941' Processing helix chain 'A' and resid 1943 through 1964 Processing helix chain 'A' and resid 1967 through 1980 removed outlier: 3.574A pdb=" N ALA A1973 " --> pdb=" O PRO A1969 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY A1977 " --> pdb=" O ALA A1973 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A1978 " --> pdb=" O LYS A1974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1981 through 1984 removed outlier: 6.041A pdb=" N ASP A1984 " --> pdb=" O GLN A1981 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1981 through 1984' Processing helix chain 'A' and resid 1985 through 2001 Processing helix chain 'A' and resid 2004 through 2021 removed outlier: 3.964A pdb=" N VAL A2015 " --> pdb=" O ALA A2011 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA A2016 " --> pdb=" O ASP A2012 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY A2020 " --> pdb=" O ALA A2016 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN A2021 " --> pdb=" O LEU A2017 " (cutoff:3.500A) Processing helix chain 'A' and resid 2021 through 2040 removed outlier: 3.521A pdb=" N MET A2033 " --> pdb=" O VAL A2029 " (cutoff:3.500A) Processing helix chain 'A' and resid 2041 through 2043 No H-bonds generated for 'chain 'A' and resid 2041 through 2043' Processing helix chain 'A' and resid 2053 through 2069 removed outlier: 3.577A pdb=" N ILE A2057 " --> pdb=" O MET A2053 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG A2062 " --> pdb=" O ALA A2058 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR A2063 " --> pdb=" O ILE A2059 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET A2064 " --> pdb=" O LEU A2060 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE A2069 " --> pdb=" O LEU A2065 " (cutoff:3.500A) Processing helix chain 'A' and resid 2070 through 2072 No H-bonds generated for 'chain 'A' and resid 2070 through 2072' Processing helix chain 'A' and resid 2074 through 2090 removed outlier: 3.649A pdb=" N HIS A2078 " --> pdb=" O ASP A2074 " (cutoff:3.500A) Proline residue: A2080 - end of helix Processing helix chain 'A' and resid 2094 through 2113 Processing helix chain 'A' and resid 2121 through 2135 Processing helix chain 'A' and resid 2137 through 2144 removed outlier: 3.765A pdb=" N TYR A2141 " --> pdb=" O LEU A2137 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU A2142 " --> pdb=" O PRO A2138 " (cutoff:3.500A) Processing helix chain 'A' and resid 2151 through 2157 removed outlier: 3.704A pdb=" N ILE A2155 " --> pdb=" O SER A2151 " (cutoff:3.500A) Processing helix chain 'A' and resid 2177 through 2197 removed outlier: 3.730A pdb=" N LEU A2181 " --> pdb=" O ALA A2177 " (cutoff:3.500A) Processing helix chain 'A' and resid 2203 through 2217 removed outlier: 3.972A pdb=" N PHE A2215 " --> pdb=" O LEU A2211 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE A2217 " --> pdb=" O GLN A2213 " (cutoff:3.500A) Processing helix chain 'A' and resid 2222 through 2235 removed outlier: 4.381A pdb=" N ARG A2226 " --> pdb=" O SER A2222 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A2229 " --> pdb=" O PRO A2225 " (cutoff:3.500A) Processing helix chain 'A' and resid 2239 through 2260 Processing helix chain 'A' and resid 2262 through 2281 removed outlier: 3.613A pdb=" N SER A2266 " --> pdb=" O ASP A2262 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL A2268 " --> pdb=" O TYR A2264 " (cutoff:3.500A) Processing helix chain 'A' and resid 2282 through 2284 No H-bonds generated for 'chain 'A' and resid 2282 through 2284' Processing helix chain 'A' and resid 2289 through 2304 removed outlier: 3.837A pdb=" N ALA A2293 " --> pdb=" O PRO A2289 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE A2295 " --> pdb=" O HIS A2291 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP A2296 " --> pdb=" O LYS A2292 " (cutoff:3.500A) Processing helix chain 'A' and resid 2306 through 2327 Processing helix chain 'A' and resid 2334 through 2344 removed outlier: 3.850A pdb=" N ALA A2341 " --> pdb=" O GLU A2337 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE A2342 " --> pdb=" O VAL A2338 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG A2343 " --> pdb=" O PHE A2339 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN A2344 " --> pdb=" O MET A2340 " (cutoff:3.500A) Processing helix chain 'A' and resid 2346 through 2358 removed outlier: 3.525A pdb=" N CYS A2350 " --> pdb=" O LEU A2346 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN A2352 " --> pdb=" O TRP A2348 " (cutoff:3.500A) Processing helix chain 'A' and resid 2364 through 2374 Processing helix chain 'A' and resid 2374 through 2379 removed outlier: 4.062A pdb=" N ARG A2378 " --> pdb=" O LEU A2374 " (cutoff:3.500A) Processing helix chain 'A' and resid 2381 through 2403 removed outlier: 3.923A pdb=" N VAL A2385 " --> pdb=" O SER A2381 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA A2386 " --> pdb=" O PRO A2382 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG A2403 " --> pdb=" O VAL A2399 " (cutoff:3.500A) Processing helix chain 'A' and resid 2413 through 2423 removed outlier: 4.499A pdb=" N TYR A2417 " --> pdb=" O GLN A2413 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N THR A2423 " --> pdb=" O ALA A2419 " (cutoff:3.500A) Processing helix chain 'A' and resid 2425 through 2431 removed outlier: 3.621A pdb=" N ARG A2431 " --> pdb=" O GLU A2427 " (cutoff:3.500A) Processing helix chain 'A' and resid 2591 through 2608 removed outlier: 3.724A pdb=" N TYR A2608 " --> pdb=" O THR A2604 " (cutoff:3.500A) Processing helix chain 'A' and resid 2611 through 2629 Processing helix chain 'A' and resid 2636 through 2651 removed outlier: 3.783A pdb=" N LEU A2640 " --> pdb=" O VAL A2636 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N SER A2642 " --> pdb=" O ASN A2638 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LYS A2643 " --> pdb=" O LEU A2639 " (cutoff:3.500A) Processing helix chain 'A' and resid 2653 through 2670 Proline residue: A2659 - end of helix removed outlier: 3.591A pdb=" N HIS A2670 " --> pdb=" O SER A2666 " (cutoff:3.500A) Processing helix chain 'A' and resid 2674 through 2677 Processing helix chain 'A' and resid 2678 through 2684 removed outlier: 4.301A pdb=" N LEU A2682 " --> pdb=" O GLN A2678 " (cutoff:3.500A) Processing helix chain 'A' and resid 2685 through 2686 No H-bonds generated for 'chain 'A' and resid 2685 through 2686' Processing helix chain 'A' and resid 2687 through 2692 removed outlier: 3.621A pdb=" N LEU A2690 " --> pdb=" O PHE A2687 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TRP A2691 " --> pdb=" O ASN A2688 " (cutoff:3.500A) Processing helix chain 'A' and resid 2706 through 2721 Processing helix chain 'B' and resid 4 through 21 removed outlier: 3.816A pdb=" N GLU B 8 " --> pdb=" O HIS B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 26 Processing helix chain 'B' and resid 31 through 47 removed outlier: 4.279A pdb=" N SER B 35 " --> pdb=" O HIS B 31 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU B 37 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N HIS B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU B 43 " --> pdb=" O ASN B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 73 through 97 removed outlier: 3.595A pdb=" N LYS B 77 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 84 " --> pdb=" O TYR B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 102 Processing helix chain 'B' and resid 106 through 117 Proline residue: B 115 - end of helix Processing helix chain 'B' and resid 130 through 149 removed outlier: 3.904A pdb=" N ASN B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 167 removed outlier: 3.747A pdb=" N VAL B 153 " --> pdb=" O ASN B 149 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 166 " --> pdb=" O GLN B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 182 Processing helix chain 'B' and resid 186 through 202 removed outlier: 4.815A pdb=" N LYS B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 227 removed outlier: 3.779A pdb=" N LYS B 218 " --> pdb=" O ASN B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 237 Processing helix chain 'B' and resid 239 through 256 Processing helix chain 'B' and resid 259 through 276 Proline residue: B 268 - end of helix removed outlier: 3.660A pdb=" N ILE B 272 " --> pdb=" O PRO B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 286 removed outlier: 3.817A pdb=" N SER B 285 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS B 286 " --> pdb=" O GLN B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 292 No H-bonds generated for 'chain 'B' and resid 290 through 292' Processing helix chain 'B' and resid 293 through 308 Processing helix chain 'B' and resid 314 through 334 Processing helix chain 'B' and resid 341 through 358 removed outlier: 3.948A pdb=" N MET B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL B 351 " --> pdb=" O GLN B 347 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ASP B 352 " --> pdb=" O SER B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 387 Processing helix chain 'B' and resid 391 through 398 Processing helix chain 'B' and resid 403 through 419 Processing helix chain 'B' and resid 432 through 434 No H-bonds generated for 'chain 'B' and resid 432 through 434' Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.622A pdb=" N PHE B 443 " --> pdb=" O LEU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 503 Processing helix chain 'B' and resid 515 through 520 Processing helix chain 'B' and resid 521 through 533 removed outlier: 3.612A pdb=" N LEU B 532 " --> pdb=" O GLY B 528 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 553 Processing helix chain 'B' and resid 554 through 560 removed outlier: 3.639A pdb=" N LEU B 560 " --> pdb=" O ASP B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 588 Processing helix chain 'B' and resid 592 through 618 Processing helix chain 'B' and resid 678 through 697 removed outlier: 3.524A pdb=" N LEU B 695 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TRP B 696 " --> pdb=" O TYR B 692 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN B 697 " --> pdb=" O MET B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 721 removed outlier: 4.263A pdb=" N PHE B 710 " --> pdb=" O ALA B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 731 Processing helix chain 'B' and resid 734 through 747 removed outlier: 3.543A pdb=" N ALA B 742 " --> pdb=" O PHE B 738 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER B 743 " --> pdb=" O MET B 739 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N SER B 745 " --> pdb=" O PHE B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 765 removed outlier: 3.632A pdb=" N LEU B 755 " --> pdb=" O GLY B 751 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG B 765 " --> pdb=" O ALA B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 793 removed outlier: 3.654A pdb=" N THR B 774 " --> pdb=" O THR B 770 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 789 " --> pdb=" O GLU B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 848 Processing helix chain 'B' and resid 848 through 856 removed outlier: 3.749A pdb=" N LEU B 852 " --> pdb=" O GLY B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 901 Processing helix chain 'B' and resid 902 through 904 No H-bonds generated for 'chain 'B' and resid 902 through 904' Processing helix chain 'B' and resid 910 through 925 removed outlier: 3.784A pdb=" N LEU B 925 " --> pdb=" O VAL B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 928 No H-bonds generated for 'chain 'B' and resid 926 through 928' Processing helix chain 'B' and resid 929 through 942 removed outlier: 3.724A pdb=" N ASN B 939 " --> pdb=" O ASN B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 974 removed outlier: 3.506A pdb=" N ASN B 974 " --> pdb=" O ASN B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 984 removed outlier: 3.640A pdb=" N HIS B 982 " --> pdb=" O GLY B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1001 removed outlier: 3.820A pdb=" N MET B 992 " --> pdb=" O ILE B 988 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL B1001 " --> pdb=" O ARG B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1024 Processing helix chain 'B' and resid 1033 through 1046 removed outlier: 3.596A pdb=" N PHE B1037 " --> pdb=" O GLN B1033 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1081 removed outlier: 3.694A pdb=" N ALA B1081 " --> pdb=" O VAL B1077 " (cutoff:3.500A) Processing helix chain 'B' and resid 1094 through 1116 removed outlier: 3.601A pdb=" N ASP B1116 " --> pdb=" O ASN B1112 " (cutoff:3.500A) Processing helix chain 'B' and resid 1136 through 1156 removed outlier: 4.141A pdb=" N ARG B1142 " --> pdb=" O LEU B1138 " (cutoff:3.500A) Processing helix chain 'B' and resid 1157 through 1159 No H-bonds generated for 'chain 'B' and resid 1157 through 1159' Processing helix chain 'B' and resid 1160 through 1165 Processing helix chain 'B' and resid 1166 through 1169 Processing helix chain 'B' and resid 1175 through 1184 removed outlier: 4.311A pdb=" N GLU B1181 " --> pdb=" O ALA B1177 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL B1182 " --> pdb=" O THR B1178 " (cutoff:3.500A) Processing helix chain 'B' and resid 1187 through 1191 removed outlier: 3.505A pdb=" N THR B1191 " --> pdb=" O GLN B1188 " (cutoff:3.500A) Processing helix chain 'B' and resid 1211 through 1216 removed outlier: 3.886A pdb=" N GLY B1216 " --> pdb=" O VAL B1212 " (cutoff:3.500A) Processing helix chain 'B' and resid 1221 through 1231 removed outlier: 3.927A pdb=" N ASN B1229 " --> pdb=" O MET B1225 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B1230 " --> pdb=" O ALA B1226 " (cutoff:3.500A) Processing helix chain 'B' and resid 1232 through 1234 No H-bonds generated for 'chain 'B' and resid 1232 through 1234' Processing helix chain 'B' and resid 1235 through 1246 removed outlier: 4.158A pdb=" N LEU B1239 " --> pdb=" O GLN B1235 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL B1244 " --> pdb=" O ALA B1240 " (cutoff:3.500A) Processing helix chain 'B' and resid 1252 through 1257 removed outlier: 3.789A pdb=" N LEU B1257 " --> pdb=" O LEU B1253 " (cutoff:3.500A) Processing helix chain 'B' and resid 1260 through 1268 removed outlier: 4.431A pdb=" N GLU B1264 " --> pdb=" O MET B1260 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL B1265 " --> pdb=" O PHE B1261 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU B1266 " --> pdb=" O SER B1262 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B1267 " --> pdb=" O LYS B1263 " (cutoff:3.500A) Processing helix chain 'B' and resid 1282 through 1293 removed outlier: 3.554A pdb=" N PHE B1289 " --> pdb=" O MET B1285 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS B1290 " --> pdb=" O THR B1286 " (cutoff:3.500A) Processing helix chain 'B' and resid 1296 through 1301 removed outlier: 3.679A pdb=" N LEU B1300 " --> pdb=" O TYR B1296 " (cutoff:3.500A) Processing helix chain 'B' and resid 1333 through 1338 removed outlier: 3.567A pdb=" N GLN B1336 " --> pdb=" O GLU B1333 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG B1337 " --> pdb=" O GLU B1334 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ASN B1338 " --> pdb=" O ASN B1335 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1333 through 1338' Processing helix chain 'B' and resid 1339 through 1353 removed outlier: 4.108A pdb=" N THR B1343 " --> pdb=" O LEU B1339 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS B1348 " --> pdb=" O GLU B1344 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA B1349 " --> pdb=" O LYS B1345 " (cutoff:3.500A) Processing helix chain 'B' and resid 1358 through 1376 removed outlier: 3.972A pdb=" N VAL B1364 " --> pdb=" O GLN B1360 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS B1365 " --> pdb=" O LEU B1361 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG B1375 " --> pdb=" O VAL B1371 " (cutoff:3.500A) Processing helix chain 'B' and resid 1381 through 1393 Processing helix chain 'B' and resid 1393 through 1399 removed outlier: 3.962A pdb=" N VAL B1398 " --> pdb=" O ASN B1394 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER B1399 " --> pdb=" O PRO B1395 " (cutoff:3.500A) Processing helix chain 'B' and resid 1413 through 1431 removed outlier: 3.586A pdb=" N ILE B1424 " --> pdb=" O LEU B1420 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA B1429 " --> pdb=" O LEU B1425 " (cutoff:3.500A) Processing helix chain 'B' and resid 1442 through 1446 removed outlier: 4.170A pdb=" N ASP B1445 " --> pdb=" O PRO B1442 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE B1446 " --> pdb=" O PHE B1443 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1442 through 1446' Processing helix chain 'B' and resid 1447 through 1451 removed outlier: 3.532A pdb=" N ASN B1450 " --> pdb=" O VAL B1447 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE B1451 " --> pdb=" O LYS B1448 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1447 through 1451' Processing helix chain 'B' and resid 1452 through 1463 removed outlier: 3.866A pdb=" N ARG B1456 " --> pdb=" O ASP B1452 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B1457 " --> pdb=" O ALA B1453 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP B1460 " --> pdb=" O ARG B1456 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE B1461 " --> pdb=" O PHE B1457 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA B1462 " --> pdb=" O PHE B1458 " (cutoff:3.500A) Processing helix chain 'B' and resid 1488 through 1493 Processing helix chain 'B' and resid 1493 through 1502 removed outlier: 3.878A pdb=" N GLY B1498 " --> pdb=" O GLN B1494 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N GLN B1499 " --> pdb=" O GLU B1495 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR B1500 " --> pdb=" O LYS B1496 " (cutoff:3.500A) Processing helix chain 'B' and resid 1516 through 1521 removed outlier: 3.879A pdb=" N THR B1520 " --> pdb=" O ASP B1516 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B1521 " --> pdb=" O LYS B1517 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1516 through 1521' Processing helix chain 'B' and resid 1589 through 1592 Processing helix chain 'B' and resid 1598 through 1610 removed outlier: 3.608A pdb=" N LEU B1602 " --> pdb=" O ASN B1598 " (cutoff:3.500A) Processing helix chain 'B' and resid 1628 through 1632 Processing helix chain 'B' and resid 1634 through 1645 removed outlier: 3.914A pdb=" N PHE B1645 " --> pdb=" O TRP B1641 " (cutoff:3.500A) Processing helix chain 'B' and resid 1646 through 1652 removed outlier: 3.775A pdb=" N TYR B1650 " --> pdb=" O PRO B1646 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP B1651 " --> pdb=" O GLY B1647 " (cutoff:3.500A) Processing helix chain 'B' and resid 1662 through 1672 removed outlier: 3.602A pdb=" N ARG B1666 " --> pdb=" O ASN B1662 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU B1667 " --> pdb=" O SER B1663 " (cutoff:3.500A) Processing helix chain 'B' and resid 1690 through 1697 removed outlier: 3.858A pdb=" N LEU B1694 " --> pdb=" O CYS B1690 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N HIS B1697 " --> pdb=" O LYS B1693 " (cutoff:3.500A) Processing helix chain 'B' and resid 1698 through 1702 Processing helix chain 'B' and resid 1706 through 1711 Processing helix chain 'B' and resid 1765 through 1767 No H-bonds generated for 'chain 'B' and resid 1765 through 1767' Processing helix chain 'B' and resid 1795 through 1813 Processing helix chain 'B' and resid 1828 through 1842 removed outlier: 3.793A pdb=" N ILE B1836 " --> pdb=" O THR B1832 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY B1842 " --> pdb=" O LEU B1838 " (cutoff:3.500A) Processing helix chain 'B' and resid 1845 through 1864 Processing helix chain 'B' and resid 1883 through 1898 Processing helix chain 'B' and resid 1903 through 1916 removed outlier: 3.995A pdb=" N SER B1914 " --> pdb=" O ILE B1910 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LYS B1915 " --> pdb=" O SER B1911 " (cutoff:3.500A) Processing helix chain 'B' and resid 1917 through 1933 Proline residue: B1930 - end of helix removed outlier: 4.493A pdb=" N SER B1933 " --> pdb=" O THR B1929 " (cutoff:3.500A) Processing helix chain 'B' and resid 1934 through 1940 removed outlier: 3.762A pdb=" N LYS B1940 " --> pdb=" O ARG B1937 " (cutoff:3.500A) Processing helix chain 'B' and resid 1943 through 1964 Processing helix chain 'B' and resid 1967 through 1980 removed outlier: 3.595A pdb=" N ALA B1973 " --> pdb=" O PRO B1969 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY B1977 " --> pdb=" O ALA B1973 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER B1978 " --> pdb=" O LYS B1974 " (cutoff:3.500A) Processing helix chain 'B' and resid 1981 through 1984 removed outlier: 6.048A pdb=" N ASP B1984 " --> pdb=" O GLN B1981 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1981 through 1984' Processing helix chain 'B' and resid 1985 through 2001 Processing helix chain 'B' and resid 2004 through 2021 removed outlier: 3.967A pdb=" N VAL B2015 " --> pdb=" O ALA B2011 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA B2016 " --> pdb=" O ASP B2012 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY B2020 " --> pdb=" O ALA B2016 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN B2021 " --> pdb=" O LEU B2017 " (cutoff:3.500A) Processing helix chain 'B' and resid 2021 through 2040 removed outlier: 3.534A pdb=" N MET B2033 " --> pdb=" O VAL B2029 " (cutoff:3.500A) Processing helix chain 'B' and resid 2041 through 2043 No H-bonds generated for 'chain 'B' and resid 2041 through 2043' Processing helix chain 'B' and resid 2053 through 2069 removed outlier: 3.570A pdb=" N ILE B2057 " --> pdb=" O MET B2053 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG B2062 " --> pdb=" O ALA B2058 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR B2063 " --> pdb=" O ILE B2059 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET B2064 " --> pdb=" O LEU B2060 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE B2069 " --> pdb=" O LEU B2065 " (cutoff:3.500A) Processing helix chain 'B' and resid 2070 through 2072 No H-bonds generated for 'chain 'B' and resid 2070 through 2072' Processing helix chain 'B' and resid 2074 through 2090 removed outlier: 3.657A pdb=" N HIS B2078 " --> pdb=" O ASP B2074 " (cutoff:3.500A) Proline residue: B2080 - end of helix Processing helix chain 'B' and resid 2094 through 2113 Processing helix chain 'B' and resid 2121 through 2135 Processing helix chain 'B' and resid 2137 through 2144 removed outlier: 3.757A pdb=" N TYR B2141 " --> pdb=" O LEU B2137 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU B2142 " --> pdb=" O PRO B2138 " (cutoff:3.500A) Processing helix chain 'B' and resid 2151 through 2157 removed outlier: 3.706A pdb=" N ILE B2155 " --> pdb=" O SER B2151 " (cutoff:3.500A) Processing helix chain 'B' and resid 2177 through 2197 removed outlier: 3.731A pdb=" N LEU B2181 " --> pdb=" O ALA B2177 " (cutoff:3.500A) Processing helix chain 'B' and resid 2203 through 2217 removed outlier: 4.095A pdb=" N PHE B2215 " --> pdb=" O LEU B2211 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE B2217 " --> pdb=" O GLN B2213 " (cutoff:3.500A) Processing helix chain 'B' and resid 2222 through 2235 removed outlier: 4.398A pdb=" N ARG B2226 " --> pdb=" O SER B2222 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B2229 " --> pdb=" O PRO B2225 " (cutoff:3.500A) Processing helix chain 'B' and resid 2239 through 2260 Processing helix chain 'B' and resid 2262 through 2281 removed outlier: 3.631A pdb=" N SER B2266 " --> pdb=" O ASP B2262 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL B2268 " --> pdb=" O TYR B2264 " (cutoff:3.500A) Processing helix chain 'B' and resid 2282 through 2284 No H-bonds generated for 'chain 'B' and resid 2282 through 2284' Processing helix chain 'B' and resid 2289 through 2304 removed outlier: 3.819A pdb=" N ALA B2293 " --> pdb=" O PRO B2289 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE B2295 " --> pdb=" O HIS B2291 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TRP B2296 " --> pdb=" O LYS B2292 " (cutoff:3.500A) Processing helix chain 'B' and resid 2306 through 2327 Processing helix chain 'B' and resid 2334 through 2340 Processing helix chain 'B' and resid 2341 through 2342 No H-bonds generated for 'chain 'B' and resid 2341 through 2342' Processing helix chain 'B' and resid 2343 through 2345 No H-bonds generated for 'chain 'B' and resid 2343 through 2345' Processing helix chain 'B' and resid 2346 through 2358 removed outlier: 3.783A pdb=" N GLN B2352 " --> pdb=" O TRP B2348 " (cutoff:3.500A) Processing helix chain 'B' and resid 2364 through 2374 Processing helix chain 'B' and resid 2374 through 2379 removed outlier: 4.084A pdb=" N ARG B2378 " --> pdb=" O LEU B2374 " (cutoff:3.500A) Processing helix chain 'B' and resid 2381 through 2403 removed outlier: 3.906A pdb=" N VAL B2385 " --> pdb=" O SER B2381 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B2386 " --> pdb=" O PRO B2382 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG B2403 " --> pdb=" O VAL B2399 " (cutoff:3.500A) Processing helix chain 'B' and resid 2413 through 2423 removed outlier: 4.534A pdb=" N TYR B2417 " --> pdb=" O GLN B2413 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR B2423 " --> pdb=" O ALA B2419 " (cutoff:3.500A) Processing helix chain 'B' and resid 2591 through 2608 removed outlier: 3.722A pdb=" N TYR B2608 " --> pdb=" O THR B2604 " (cutoff:3.500A) Processing helix chain 'B' and resid 2611 through 2629 Processing helix chain 'B' and resid 2636 through 2651 removed outlier: 4.750A pdb=" N SER B2642 " --> pdb=" O ASN B2638 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS B2643 " --> pdb=" O LEU B2639 " (cutoff:3.500A) Processing helix chain 'B' and resid 2653 through 2670 Proline residue: B2659 - end of helix Processing helix chain 'B' and resid 2674 through 2677 Processing helix chain 'B' and resid 2678 through 2684 removed outlier: 4.258A pdb=" N LEU B2682 " --> pdb=" O GLN B2678 " (cutoff:3.500A) Processing helix chain 'B' and resid 2706 through 2721 Processing sheet with id=AA1, first strand: chain 'A' and resid 1572 through 1577 removed outlier: 4.399A pdb=" N ILE A1584 " --> pdb=" O ALA A1575 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL A1621 " --> pdb=" O PRO A1583 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N PHE A1585 " --> pdb=" O VAL A1621 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASP A1623 " --> pdb=" O PHE A1585 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N TYR A1587 " --> pdb=" O ASP A1623 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N TYR A1618 " --> pdb=" O VAL A1653 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ALA A1655 " --> pdb=" O TYR A1618 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N VAL A1686 " --> pdb=" O SER A1654 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL A1656 " --> pdb=" O VAL A1686 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE A1688 " --> pdb=" O VAL A1656 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE A1658 " --> pdb=" O ILE A1688 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1717 through 1718 removed outlier: 3.596A pdb=" N LYS A1717 " --> pdb=" O VAL A1736 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A1736 " --> pdb=" O LYS A1717 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1717 through 1718 removed outlier: 3.596A pdb=" N LYS A1717 " --> pdb=" O VAL A1736 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A1736 " --> pdb=" O LYS A1717 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A1730 " --> pdb=" O LYS A1724 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A1725 " --> pdb=" O THR A1790 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N THR A1790 " --> pdb=" O LEU A1725 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE A1791 " --> pdb=" O PHE A1778 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE A1778 " --> pdb=" O PHE A1791 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N THR A1779 " --> pdb=" O CYS A1771 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N CYS A1771 " --> pdb=" O THR A1779 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A1781 " --> pdb=" O GLU A1769 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU A1769 " --> pdb=" O THR A1781 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1749 through 1751 Processing sheet with id=AA5, first strand: chain 'B' and resid 1572 through 1577 removed outlier: 4.569A pdb=" N ILE B1584 " --> pdb=" O ALA B1575 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL B1621 " --> pdb=" O PRO B1583 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N PHE B1585 " --> pdb=" O VAL B1621 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASP B1623 " --> pdb=" O PHE B1585 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TYR B1587 " --> pdb=" O ASP B1623 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR B1618 " --> pdb=" O VAL B1653 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ALA B1655 " --> pdb=" O TYR B1618 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N VAL B1686 " --> pdb=" O SER B1654 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL B1656 " --> pdb=" O VAL B1686 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ILE B1688 " --> pdb=" O VAL B1656 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE B1658 " --> pdb=" O ILE B1688 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1717 through 1718 removed outlier: 3.580A pdb=" N LYS B1717 " --> pdb=" O VAL B1736 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B1736 " --> pdb=" O LYS B1717 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1717 through 1718 removed outlier: 3.580A pdb=" N LYS B1717 " --> pdb=" O VAL B1736 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B1736 " --> pdb=" O LYS B1717 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR B1730 " --> pdb=" O LYS B1724 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B1722 " --> pdb=" O VAL B1732 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B1723 " --> pdb=" O MET B1792 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N THR B1790 " --> pdb=" O LEU B1725 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE B1791 " --> pdb=" O PHE B1778 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE B1778 " --> pdb=" O PHE B1791 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1749 through 1751 2083 hydrogen bonds defined for protein. 6108 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: 15.83 Time building geometry restraints manager: 9.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5247 1.32 - 1.45: 7606 1.45 - 1.57: 16826 1.57 - 1.69: 0 1.69 - 1.81: 172 Bond restraints: 29851 Sorted by residual: bond pdb=" CA SER A1916 " pdb=" CB SER A1916 " ideal model delta sigma weight residual 1.526 1.458 0.068 1.44e-02 4.82e+03 2.22e+01 bond pdb=" CA SER A1917 " pdb=" CB SER A1917 " ideal model delta sigma weight residual 1.532 1.456 0.076 1.74e-02 3.30e+03 1.90e+01 bond pdb=" N ILE B2234 " pdb=" CA ILE B2234 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.22e-02 6.72e+03 1.08e+01 bond pdb=" N GLN B1086 " pdb=" CA GLN B1086 " ideal model delta sigma weight residual 1.463 1.437 0.026 8.80e-03 1.29e+04 8.54e+00 bond pdb=" N ILE A1734 " pdb=" CA ILE A1734 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.20e-02 6.94e+03 8.47e+00 ... (remaining 29846 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 40297 2.52 - 5.04: 534 5.04 - 7.56: 46 7.56 - 10.08: 9 10.08 - 12.60: 3 Bond angle restraints: 40889 Sorted by residual: angle pdb=" N LYS A1921 " pdb=" CA LYS A1921 " pdb=" C LYS A1921 " ideal model delta sigma weight residual 111.14 102.17 8.97 1.08e+00 8.57e-01 6.89e+01 angle pdb=" N PHE A 17 " pdb=" CA PHE A 17 " pdb=" C PHE A 17 " ideal model delta sigma weight residual 111.28 103.47 7.81 1.09e+00 8.42e-01 5.14e+01 angle pdb=" N VAL A 10 " pdb=" CA VAL A 10 " pdb=" C VAL A 10 " ideal model delta sigma weight residual 110.42 103.65 6.77 9.60e-01 1.09e+00 4.97e+01 angle pdb=" N LEU A2392 " pdb=" CA LEU A2392 " pdb=" C LEU A2392 " ideal model delta sigma weight residual 111.14 104.54 6.60 1.08e+00 8.57e-01 3.73e+01 angle pdb=" N PRO A 6 " pdb=" CA PRO A 6 " pdb=" C PRO A 6 " ideal model delta sigma weight residual 112.47 100.21 12.26 2.06e+00 2.36e-01 3.54e+01 ... (remaining 40884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.68: 16198 16.68 - 33.35: 928 33.35 - 50.03: 220 50.03 - 66.71: 35 66.71 - 83.39: 13 Dihedral angle restraints: 17394 sinusoidal: 4138 harmonic: 13256 Sorted by residual: dihedral pdb=" CA TYR B 794 " pdb=" C TYR B 794 " pdb=" N PRO B 795 " pdb=" CA PRO B 795 " ideal model delta harmonic sigma weight residual 180.00 137.82 42.18 0 5.00e+00 4.00e-02 7.12e+01 dihedral pdb=" CA HIS A1170 " pdb=" C HIS A1170 " pdb=" N LYS A1171 " pdb=" CA LYS A1171 " ideal model delta harmonic sigma weight residual -180.00 -137.82 -42.18 0 5.00e+00 4.00e-02 7.12e+01 dihedral pdb=" CA HIS B1170 " pdb=" C HIS B1170 " pdb=" N LYS B1171 " pdb=" CA LYS B1171 " ideal model delta harmonic sigma weight residual -180.00 -137.85 -42.15 0 5.00e+00 4.00e-02 7.11e+01 ... (remaining 17391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3959 0.052 - 0.103: 905 0.103 - 0.155: 85 0.155 - 0.207: 14 0.207 - 0.258: 9 Chirality restraints: 4972 Sorted by residual: chirality pdb=" CA VAL A 10 " pdb=" N VAL A 10 " pdb=" C VAL A 10 " pdb=" CB VAL A 10 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA ILE A1918 " pdb=" N ILE A1918 " pdb=" C ILE A1918 " pdb=" CB ILE A1918 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA MET B 442 " pdb=" N MET B 442 " pdb=" C MET B 442 " pdb=" CB MET B 442 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 4969 not shown) Planarity restraints: 5354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 440 " -0.964 9.50e-02 1.11e+02 4.32e-01 1.13e+02 pdb=" NE ARG B 440 " 0.057 2.00e-02 2.50e+03 pdb=" CZ ARG B 440 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG B 440 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 440 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 304 " -0.934 9.50e-02 1.11e+02 4.18e-01 1.06e+02 pdb=" NE ARG B 304 " 0.056 2.00e-02 2.50e+03 pdb=" CZ ARG B 304 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 304 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 304 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 304 " 0.514 9.50e-02 1.11e+02 2.30e-01 3.24e+01 pdb=" NE ARG A 304 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A 304 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 304 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 304 " 0.018 2.00e-02 2.50e+03 ... (remaining 5351 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 5856 2.77 - 3.30: 30089 3.30 - 3.83: 48355 3.83 - 4.37: 51246 4.37 - 4.90: 86082 Nonbonded interactions: 221628 Sorted by model distance: nonbonded pdb=" O PHE A1275 " pdb=" OG SER A1282 " model vdw 2.233 3.040 nonbonded pdb=" O ALA B 771 " pdb=" OG1 THR B 774 " model vdw 2.249 3.040 nonbonded pdb=" O LEU A2657 " pdb=" ND1 HIS A2661 " model vdw 2.250 3.120 nonbonded pdb=" O HIS A 4 " pdb=" N VAL A 7 " model vdw 2.255 3.120 nonbonded pdb=" O LEU B 972 " pdb=" NH2 ARG B1025 " model vdw 2.257 3.120 ... (remaining 221623 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 3 through 5 or (resid 6 through 8 and (name N or name CA o \ r name C or name O or name CB )) or resid 9 or (resid 10 through 16 and (name N \ or name CA or name C or name O or name CB )) or resid 17 through 1431 or resid 1 \ 442 through 1781 or resid 1787 through 1902 or (resid 1903 through 1904 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1905 through 1917 or ( \ resid 1918 through 1920 and (name N or name CA or name C or name O or name CB )) \ or resid 1921 through 2389 or (resid 2390 through 2392 and (name N or name CA o \ r name C or name O or name CB )) or resid 2393 through 2722)) selection = (chain 'B' and (resid 3 through 772 or (resid 773 through 776 and (name N or nam \ e CA or name C or name O or name CB )) or resid 777 or (resid 778 through 780 an \ d (name N or name CA or name C or name O or name CB )) or resid 781 through 784 \ or (resid 785 and (name N or name CA or name C or name O or name CB )) or resid \ 786 through 795 or (resid 828 through 836 and (name N or name CA or name C or na \ me O or name CB )) or resid 837 or (resid 838 through 841 and (name N or name CA \ or name C or name O or name CB )) or resid 842 through 844 or (resid 845 throug \ h 847 and (name N or name CA or name C or name O or name CB )) or resid 848 thro \ ugh 849 or (resid 850 through 858 and (name N or name CA or name C or name O or \ name CB )) or resid 889 through 890 or (resid 891 through 892 and (name N or nam \ e CA or name C or name O or name CB )) or resid 893 through 895 or (resid 896 an \ d (name N or name CA or name C or name O or name CB )) or resid 897 through 900 \ or (resid 901 and (name N or name CA or name C or name O or name CB )) or resid \ 902 through 907 or (resid 908 through 909 and (name N or name CA or name C or na \ me O or name CB )) or resid 910 or (resid 911 through 913 and (name N or name CA \ or name C or name O or name CB )) or resid 914 or (resid 915 through 921 and (n \ ame N or name CA or name C or name O or name CB )) or resid 922 or (resid 923 th \ rough 929 and (name N or name CA or name C or name O or name CB )) or resid 930 \ through 2722)) } 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=0.00 max=1.00 mean=0.99 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: 8.050 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: 0.020 Extract box with map and model: 1.110 Check model and map are aligned: 0.210 Set scattering table: 0.240 Process input model: 73.920 Find NCS groups from input model: 2.010 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 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 : 0.004 0.076 29851 Z= 0.256 Angle : 0.758 12.597 40889 Z= 0.504 Chirality : 0.043 0.258 4972 Planarity : 0.010 0.432 5354 Dihedral : 12.317 83.386 8702 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.39 % Favored : 94.41 % Rotamer: Outliers : 0.82 % Allowed : 0.82 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.13), residues: 4417 helix: 1.13 (0.10), residues: 2805 sheet: 1.41 (0.53), residues: 111 loop : -1.21 (0.17), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A2208 HIS 0.010 0.001 HIS A2084 PHE 0.033 0.002 PHE A1037 TYR 0.031 0.002 TYR B1169 ARG 0.006 0.001 ARG B1038 Details of bonding type rmsd hydrogen bonds : bond 0.17089 ( 2083) hydrogen bonds : angle 6.06110 ( 6108) covalent geometry : bond 0.00433 (29851) covalent geometry : angle 0.75776 (40889) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8834 Ramachandran restraints generated. 4417 Oldfield, 0 Emsley, 4417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8834 Ramachandran restraints generated. 4417 Oldfield, 0 Emsley, 4417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 3.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 991 MET cc_start: 0.7235 (ppp) cc_final: 0.6944 (tmm) REVERT: A 1421 MET cc_start: 0.6664 (ppp) cc_final: 0.6459 (ppp) REVERT: A 1440 MET cc_start: 0.4827 (ppp) cc_final: 0.4622 (mmm) REVERT: A 1733 SER cc_start: 0.5569 (OUTLIER) cc_final: 0.5110 (t) REVERT: B 1733 SER cc_start: 0.5610 (OUTLIER) cc_final: 0.4936 (t) outliers start: 15 outliers final: 7 residues processed: 156 average time/residue: 0.3535 time to fit residues: 96.8650 Evaluate side-chains 142 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 3.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 1733 SER Chi-restraints excluded: chain A residue 2387 ARG Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 1733 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 380 optimal weight: 0.9980 chunk 341 optimal weight: 20.0000 chunk 189 optimal weight: 3.9990 chunk 116 optimal weight: 20.0000 chunk 230 optimal weight: 1.9990 chunk 182 optimal weight: 0.7980 chunk 353 optimal weight: 0.1980 chunk 136 optimal weight: 9.9990 chunk 214 optimal weight: 3.9990 chunk 263 optimal weight: 0.9990 chunk 409 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN A 781 HIS ** B 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.105755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.067134 restraints weight = 205534.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.064805 restraints weight = 175249.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.064583 restraints weight = 155737.760| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 29851 Z= 0.113 Angle : 0.508 8.546 40889 Z= 0.280 Chirality : 0.039 0.181 4972 Planarity : 0.003 0.075 5354 Dihedral : 4.724 58.586 4684 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.75 % Favored : 95.11 % Rotamer: Outliers : 0.55 % Allowed : 5.90 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.13), residues: 4417 helix: 1.72 (0.10), residues: 2848 sheet: 1.01 (0.50), residues: 119 loop : -0.85 (0.18), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B1258 HIS 0.007 0.001 HIS B 501 PHE 0.033 0.001 PHE B 443 TYR 0.023 0.001 TYR A1927 ARG 0.017 0.001 ARG B 440 Details of bonding type rmsd hydrogen bonds : bond 0.04019 ( 2083) hydrogen bonds : angle 4.47541 ( 6108) covalent geometry : bond 0.00209 (29851) covalent geometry : angle 0.50765 (40889) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8834 Ramachandran restraints generated. 4417 Oldfield, 0 Emsley, 4417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8834 Ramachandran restraints generated. 4417 Oldfield, 0 Emsley, 4417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 3.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.6065 (OUTLIER) cc_final: 0.5707 (mtm-85) REVERT: A 1111 MET cc_start: 0.8941 (mpp) cc_final: 0.8627 (mpp) REVERT: A 1421 MET cc_start: 0.7155 (ppp) cc_final: 0.6844 (ppp) REVERT: B 840 MET cc_start: 0.8159 (ttt) cc_final: 0.7844 (ttp) REVERT: B 1180 MET cc_start: 0.7395 (mtp) cc_final: 0.7155 (mtp) REVERT: B 1733 SER cc_start: 0.4656 (OUTLIER) cc_final: 0.4323 (t) outliers start: 10 outliers final: 4 residues processed: 143 average time/residue: 0.3246 time to fit residues: 84.0113 Evaluate side-chains 140 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 134 time to evaluate : 3.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 1518 MET Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 1733 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 122 optimal weight: 5.9990 chunk 314 optimal weight: 0.9980 chunk 187 optimal weight: 0.9980 chunk 449 optimal weight: 0.0980 chunk 315 optimal weight: 1.9990 chunk 392 optimal weight: 0.0980 chunk 264 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 181 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 364 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2110 HIS ** B 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2110 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.105868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.067393 restraints weight = 205882.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.064555 restraints weight = 179731.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.064873 restraints weight = 154436.988| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 29851 Z= 0.095 Angle : 0.452 8.832 40889 Z= 0.248 Chirality : 0.037 0.211 4972 Planarity : 0.003 0.071 5354 Dihedral : 4.081 56.931 4667 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.14 % Favored : 95.72 % Rotamer: Outliers : 0.98 % Allowed : 8.52 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.13), residues: 4417 helix: 2.07 (0.10), residues: 2870 sheet: 0.99 (0.48), residues: 118 loop : -0.70 (0.18), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1258 HIS 0.006 0.001 HIS B 501 PHE 0.025 0.001 PHE A1037 TYR 0.020 0.001 TYR A1927 ARG 0.002 0.000 ARG A1391 Details of bonding type rmsd hydrogen bonds : bond 0.03216 ( 2083) hydrogen bonds : angle 3.94232 ( 6108) covalent geometry : bond 0.00178 (29851) covalent geometry : angle 0.45193 (40889) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8834 Ramachandran restraints generated. 4417 Oldfield, 0 Emsley, 4417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8834 Ramachandran restraints generated. 4417 Oldfield, 0 Emsley, 4417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 3.457 Fit side-chains revert: symmetry clash REVERT: A 1111 MET cc_start: 0.8896 (mpp) cc_final: 0.8607 (mpp) REVERT: A 1421 MET cc_start: 0.7120 (ppp) cc_final: 0.6758 (ppp) REVERT: A 1440 MET cc_start: 0.5571 (ppp) cc_final: 0.5129 (mmm) outliers start: 18 outliers final: 4 residues processed: 150 average time/residue: 0.3222 time to fit residues: 89.0809 Evaluate side-chains 139 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 135 time to evaluate : 3.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 1743 VAL Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 1760 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 277 optimal weight: 6.9990 chunk 326 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 364 optimal weight: 0.4980 chunk 269 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 chunk 385 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.105807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.067263 restraints weight = 207020.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.064857 restraints weight = 176607.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.064776 restraints weight = 179985.780| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 29851 Z= 0.100 Angle : 0.453 9.175 40889 Z= 0.245 Chirality : 0.038 0.188 4972 Planarity : 0.003 0.067 5354 Dihedral : 3.898 39.574 4661 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.48 % Favored : 95.38 % Rotamer: Outliers : 1.04 % Allowed : 9.93 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.13), residues: 4417 helix: 2.18 (0.10), residues: 2880 sheet: 0.94 (0.48), residues: 118 loop : -0.71 (0.18), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 696 HIS 0.006 0.001 HIS A2084 PHE 0.020 0.001 PHE B 443 TYR 0.015 0.001 TYR B1927 ARG 0.003 0.000 ARG A 5 Details of bonding type rmsd hydrogen bonds : bond 0.03073 ( 2083) hydrogen bonds : angle 3.83148 ( 6108) covalent geometry : bond 0.00197 (29851) covalent geometry : angle 0.45254 (40889) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8834 Ramachandran restraints generated. 4417 Oldfield, 0 Emsley, 4417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8834 Ramachandran restraints generated. 4417 Oldfield, 0 Emsley, 4417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 3.476 Fit side-chains revert: symmetry clash REVERT: A 1111 MET cc_start: 0.8965 (mpp) cc_final: 0.8686 (mpp) REVERT: A 1421 MET cc_start: 0.7133 (ppp) cc_final: 0.6784 (ppp) REVERT: B 1421 MET cc_start: 0.7136 (ppp) cc_final: 0.6850 (ppp) outliers start: 19 outliers final: 5 residues processed: 151 average time/residue: 0.3114 time to fit residues: 86.8798 Evaluate side-chains 139 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 3.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 1229 ASN Chi-restraints excluded: chain A residue 1518 MET Chi-restraints excluded: chain A residue 1743 VAL Chi-restraints excluded: chain B residue 903 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 106 optimal weight: 5.9990 chunk 450 optimal weight: 0.9990 chunk 213 optimal weight: 5.9990 chunk 126 optimal weight: 0.0770 chunk 22 optimal weight: 7.9990 chunk 109 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 323 optimal weight: 5.9990 chunk 426 optimal weight: 0.9990 chunk 425 optimal weight: 0.6980 chunk 421 optimal weight: 2.9990 overall best weight: 1.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 HIS ** A1660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 793 ASN ** B1660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.105803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.067341 restraints weight = 205413.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.065265 restraints weight = 185132.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.065106 restraints weight = 178504.608| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 29851 Z= 0.095 Angle : 0.451 13.853 40889 Z= 0.243 Chirality : 0.038 0.200 4972 Planarity : 0.003 0.067 5354 Dihedral : 3.815 38.599 4661 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.39 % Favored : 95.47 % Rotamer: Outliers : 1.20 % Allowed : 11.03 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.13), residues: 4417 helix: 2.28 (0.10), residues: 2888 sheet: 0.90 (0.47), residues: 123 loop : -0.68 (0.18), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1258 HIS 0.006 0.001 HIS B1143 PHE 0.020 0.001 PHE B 443 TYR 0.016 0.001 TYR A1927 ARG 0.003 0.000 ARG A1807 Details of bonding type rmsd hydrogen bonds : bond 0.02975 ( 2083) hydrogen bonds : angle 3.73563 ( 6108) covalent geometry : bond 0.00185 (29851) covalent geometry : angle 0.45097 (40889) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8834 Ramachandran restraints generated. 4417 Oldfield, 0 Emsley, 4417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8834 Ramachandran restraints generated. 4417 Oldfield, 0 Emsley, 4417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 3.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1421 MET cc_start: 0.7169 (ppp) cc_final: 0.6889 (ppp) REVERT: B 1421 MET cc_start: 0.7186 (ppp) cc_final: 0.6862 (ppp) outliers start: 22 outliers final: 6 residues processed: 152 average time/residue: 0.3278 time to fit residues: 91.4414 Evaluate side-chains 140 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 134 time to evaluate : 3.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 1518 MET Chi-restraints excluded: chain A residue 1743 VAL Chi-restraints excluded: chain B residue 693 MET Chi-restraints excluded: chain B residue 903 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 428 optimal weight: 6.9990 chunk 179 optimal weight: 8.9990 chunk 266 optimal weight: 7.9990 chunk 307 optimal weight: 9.9990 chunk 327 optimal weight: 0.9990 chunk 447 optimal weight: 5.9990 chunk 426 optimal weight: 4.9990 chunk 1 optimal weight: 0.0670 chunk 402 optimal weight: 0.6980 chunk 356 optimal weight: 10.0000 chunk 233 optimal weight: 6.9990 overall best weight: 2.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 975 HIS A1156 ASN ** A1660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1156 ASN ** B1660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.105663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.067444 restraints weight = 204559.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.064485 restraints weight = 181547.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.064495 restraints weight = 189489.834| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29851 Z= 0.148 Angle : 0.486 8.127 40889 Z= 0.264 Chirality : 0.039 0.192 4972 Planarity : 0.003 0.064 5354 Dihedral : 3.976 37.670 4661 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.82 % Favored : 95.04 % Rotamer: Outliers : 1.26 % Allowed : 11.63 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.13), residues: 4417 helix: 2.26 (0.10), residues: 2868 sheet: 0.97 (0.46), residues: 123 loop : -0.72 (0.18), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 696 HIS 0.007 0.001 HIS A2084 PHE 0.018 0.002 PHE B 443 TYR 0.020 0.001 TYR A1169 ARG 0.003 0.000 ARG B 440 Details of bonding type rmsd hydrogen bonds : bond 0.03323 ( 2083) hydrogen bonds : angle 3.83645 ( 6108) covalent geometry : bond 0.00297 (29851) covalent geometry : angle 0.48555 (40889) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8834 Ramachandran restraints generated. 4417 Oldfield, 0 Emsley, 4417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8834 Ramachandran restraints generated. 4417 Oldfield, 0 Emsley, 4417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 3.301 Fit side-chains revert: symmetry clash REVERT: A 1421 MET cc_start: 0.7120 (ppp) cc_final: 0.6881 (ppp) REVERT: B 1421 MET cc_start: 0.7209 (ppp) cc_final: 0.6836 (ppp) outliers start: 23 outliers final: 10 residues processed: 154 average time/residue: 0.3116 time to fit residues: 88.4925 Evaluate side-chains 144 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 3.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 1229 ASN Chi-restraints excluded: chain A residue 1518 MET Chi-restraints excluded: chain A residue 1743 VAL Chi-restraints excluded: chain A residue 1841 LEU Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 1229 ASN Chi-restraints excluded: chain B residue 1760 ASP Chi-restraints excluded: chain B residue 1841 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 437 optimal weight: 30.0000 chunk 306 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 313 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 377 optimal weight: 10.0000 chunk 252 optimal weight: 0.9990 chunk 312 optimal weight: 5.9990 chunk 233 optimal weight: 5.9990 chunk 441 optimal weight: 20.0000 chunk 349 optimal weight: 0.0000 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 ASN ** B1660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.105622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.067598 restraints weight = 206096.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.064415 restraints weight = 196034.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.064144 restraints weight = 170569.968| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 29851 Z= 0.095 Angle : 0.450 10.707 40889 Z= 0.242 Chirality : 0.037 0.180 4972 Planarity : 0.003 0.063 5354 Dihedral : 3.815 38.873 4661 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.37 % Favored : 95.52 % Rotamer: Outliers : 1.04 % Allowed : 12.12 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.13), residues: 4417 helix: 2.39 (0.10), residues: 2896 sheet: 1.23 (0.47), residues: 117 loop : -0.64 (0.18), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2208 HIS 0.007 0.001 HIS B2661 PHE 0.020 0.001 PHE B1037 TYR 0.017 0.001 TYR B1927 ARG 0.003 0.000 ARG A1807 Details of bonding type rmsd hydrogen bonds : bond 0.02925 ( 2083) hydrogen bonds : angle 3.67910 ( 6108) covalent geometry : bond 0.00187 (29851) covalent geometry : angle 0.44985 (40889) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8834 Ramachandran restraints generated. 4417 Oldfield, 0 Emsley, 4417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8834 Ramachandran restraints generated. 4417 Oldfield, 0 Emsley, 4417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 3.153 Fit side-chains revert: symmetry clash REVERT: A 1421 MET cc_start: 0.7100 (ppp) cc_final: 0.6860 (ppp) REVERT: B 1421 MET cc_start: 0.7227 (ppp) cc_final: 0.6948 (ppp) REVERT: B 1733 SER cc_start: 0.4465 (OUTLIER) cc_final: 0.4125 (t) outliers start: 19 outliers final: 9 residues processed: 149 average time/residue: 0.3231 time to fit residues: 88.8782 Evaluate side-chains 144 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 3.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 1180 MET Chi-restraints excluded: chain A residue 1518 MET Chi-restraints excluded: chain A residue 1743 VAL Chi-restraints excluded: chain B residue 693 MET Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 1733 SER Chi-restraints excluded: chain B residue 1760 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 5 optimal weight: 9.9990 chunk 252 optimal weight: 5.9990 chunk 43 optimal weight: 0.4980 chunk 312 optimal weight: 9.9990 chunk 116 optimal weight: 0.8980 chunk 261 optimal weight: 10.0000 chunk 435 optimal weight: 0.0170 chunk 417 optimal weight: 3.9990 chunk 272 optimal weight: 0.0670 chunk 80 optimal weight: 3.9990 chunk 216 optimal weight: 5.9990 overall best weight: 1.0958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.105666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.067265 restraints weight = 206360.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.064882 restraints weight = 180021.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.064802 restraints weight = 183570.265| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 29851 Z= 0.093 Angle : 0.451 10.473 40889 Z= 0.241 Chirality : 0.038 0.191 4972 Planarity : 0.003 0.063 5354 Dihedral : 3.754 37.111 4661 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.37 % Favored : 95.52 % Rotamer: Outliers : 0.93 % Allowed : 12.39 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.13), residues: 4417 helix: 2.44 (0.10), residues: 2902 sheet: 1.19 (0.46), residues: 123 loop : -0.62 (0.18), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2208 HIS 0.006 0.001 HIS B2661 PHE 0.039 0.001 PHE A1179 TYR 0.016 0.001 TYR A1927 ARG 0.009 0.000 ARG A1241 Details of bonding type rmsd hydrogen bonds : bond 0.02848 ( 2083) hydrogen bonds : angle 3.61104 ( 6108) covalent geometry : bond 0.00186 (29851) covalent geometry : angle 0.45120 (40889) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8834 Ramachandran restraints generated. 4417 Oldfield, 0 Emsley, 4417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8834 Ramachandran restraints generated. 4417 Oldfield, 0 Emsley, 4417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 3.507 Fit side-chains revert: symmetry clash REVERT: A 1107 PHE cc_start: 0.8624 (t80) cc_final: 0.8210 (t80) REVERT: A 1421 MET cc_start: 0.7082 (ppp) cc_final: 0.6802 (ppp) REVERT: B 840 MET cc_start: 0.8123 (ttt) cc_final: 0.7747 (ttt) REVERT: B 1107 PHE cc_start: 0.8450 (t80) cc_final: 0.8088 (t80) REVERT: B 1421 MET cc_start: 0.7230 (ppp) cc_final: 0.6947 (ppp) REVERT: B 1733 SER cc_start: 0.4437 (OUTLIER) cc_final: 0.4105 (t) outliers start: 17 outliers final: 10 residues processed: 148 average time/residue: 0.3142 time to fit residues: 86.8797 Evaluate side-chains 146 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 3.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 1180 MET Chi-restraints excluded: chain A residue 1518 MET Chi-restraints excluded: chain A residue 1743 VAL Chi-restraints excluded: chain B residue 693 MET Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 1733 SER Chi-restraints excluded: chain B residue 1760 ASP Chi-restraints excluded: chain B residue 1841 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 229 optimal weight: 8.9990 chunk 315 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 393 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 196 optimal weight: 0.8980 chunk 341 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 175 optimal weight: 9.9990 chunk 390 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.105493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.067669 restraints weight = 205053.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.064454 restraints weight = 184094.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.064336 restraints weight = 190745.880| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 29851 Z= 0.114 Angle : 0.470 11.120 40889 Z= 0.251 Chirality : 0.038 0.195 4972 Planarity : 0.003 0.062 5354 Dihedral : 3.806 36.583 4661 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.60 % Favored : 95.29 % Rotamer: Outliers : 0.87 % Allowed : 12.88 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.13), residues: 4417 helix: 2.43 (0.10), residues: 2897 sheet: 1.42 (0.46), residues: 118 loop : -0.70 (0.18), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1258 HIS 0.006 0.001 HIS A2084 PHE 0.027 0.001 PHE A1179 TYR 0.016 0.001 TYR B1169 ARG 0.003 0.000 ARG A1807 Details of bonding type rmsd hydrogen bonds : bond 0.02994 ( 2083) hydrogen bonds : angle 3.66094 ( 6108) covalent geometry : bond 0.00231 (29851) covalent geometry : angle 0.46975 (40889) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8834 Ramachandran restraints generated. 4417 Oldfield, 0 Emsley, 4417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8834 Ramachandran restraints generated. 4417 Oldfield, 0 Emsley, 4417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 3.324 Fit side-chains revert: symmetry clash REVERT: A 1421 MET cc_start: 0.7067 (ppp) cc_final: 0.6848 (ppp) REVERT: B 1107 PHE cc_start: 0.8503 (t80) cc_final: 0.8173 (t80) REVERT: B 1421 MET cc_start: 0.7205 (ppp) cc_final: 0.6931 (ppp) outliers start: 16 outliers final: 12 residues processed: 148 average time/residue: 0.3151 time to fit residues: 85.9383 Evaluate side-chains 147 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 3.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 1180 MET Chi-restraints excluded: chain A residue 1229 ASN Chi-restraints excluded: chain A residue 1518 MET Chi-restraints excluded: chain A residue 1841 LEU Chi-restraints excluded: chain B residue 693 MET Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 1229 ASN Chi-restraints excluded: chain B residue 1760 ASP Chi-restraints excluded: chain B residue 1841 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 314 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 266 optimal weight: 0.0000 chunk 182 optimal weight: 1.9990 chunk 285 optimal weight: 2.9990 chunk 234 optimal weight: 5.9990 chunk 363 optimal weight: 9.9990 chunk 402 optimal weight: 0.3980 chunk 82 optimal weight: 2.9990 chunk 265 optimal weight: 1.9990 overall best weight: 1.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.105546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.067650 restraints weight = 206238.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.064521 restraints weight = 196576.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.064330 restraints weight = 155363.088| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 29851 Z= 0.101 Angle : 0.463 11.207 40889 Z= 0.245 Chirality : 0.038 0.216 4972 Planarity : 0.003 0.062 5354 Dihedral : 3.756 36.995 4661 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.53 % Favored : 95.36 % Rotamer: Outliers : 0.82 % Allowed : 13.05 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.13), residues: 4417 helix: 2.49 (0.10), residues: 2892 sheet: 1.58 (0.47), residues: 111 loop : -0.67 (0.18), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1258 HIS 0.006 0.001 HIS B2661 PHE 0.026 0.001 PHE A1179 TYR 0.016 0.001 TYR A1927 ARG 0.003 0.000 ARG A1391 Details of bonding type rmsd hydrogen bonds : bond 0.02850 ( 2083) hydrogen bonds : angle 3.60190 ( 6108) covalent geometry : bond 0.00203 (29851) covalent geometry : angle 0.46250 (40889) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8834 Ramachandran restraints generated. 4417 Oldfield, 0 Emsley, 4417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8834 Ramachandran restraints generated. 4417 Oldfield, 0 Emsley, 4417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 3.781 Fit side-chains revert: symmetry clash REVERT: A 1107 PHE cc_start: 0.8555 (t80) cc_final: 0.7984 (t80) REVERT: A 1421 MET cc_start: 0.7085 (ppp) cc_final: 0.6822 (ppp) REVERT: B 840 MET cc_start: 0.7947 (ttt) cc_final: 0.7625 (ttp) REVERT: B 1107 PHE cc_start: 0.8524 (t80) cc_final: 0.8090 (t80) REVERT: B 1421 MET cc_start: 0.7223 (ppp) cc_final: 0.6943 (ppp) REVERT: B 1733 SER cc_start: 0.4525 (OUTLIER) cc_final: 0.4193 (t) REVERT: B 2353 MET cc_start: 0.8871 (ttm) cc_final: 0.8425 (ptt) outliers start: 15 outliers final: 13 residues processed: 148 average time/residue: 0.3277 time to fit residues: 89.5879 Evaluate side-chains 150 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 3.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 1180 MET Chi-restraints excluded: chain A residue 1229 ASN Chi-restraints excluded: chain A residue 1518 MET Chi-restraints excluded: chain A residue 1841 LEU Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 693 MET Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 1229 ASN Chi-restraints excluded: chain B residue 1733 SER Chi-restraints excluded: chain B residue 1760 ASP Chi-restraints excluded: chain B residue 1841 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 103 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 437 optimal weight: 30.0000 chunk 44 optimal weight: 0.9980 chunk 446 optimal weight: 4.9990 chunk 277 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 218 optimal weight: 6.9990 chunk 60 optimal weight: 0.0670 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.105597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.067745 restraints weight = 206134.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.064980 restraints weight = 174463.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.064623 restraints weight = 173939.026| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 29851 Z= 0.093 Angle : 0.457 12.277 40889 Z= 0.242 Chirality : 0.037 0.219 4972 Planarity : 0.003 0.061 5354 Dihedral : 3.683 36.193 4661 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.23 % Favored : 95.65 % Rotamer: Outliers : 0.71 % Allowed : 13.16 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.13), residues: 4417 helix: 2.55 (0.10), residues: 2890 sheet: 1.66 (0.47), residues: 111 loop : -0.64 (0.18), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2208 HIS 0.006 0.001 HIS B2661 PHE 0.023 0.001 PHE A1179 TYR 0.016 0.001 TYR A1927 ARG 0.002 0.000 ARG A1807 Details of bonding type rmsd hydrogen bonds : bond 0.02767 ( 2083) hydrogen bonds : angle 3.55361 ( 6108) covalent geometry : bond 0.00188 (29851) covalent geometry : angle 0.45740 (40889) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15216.44 seconds wall clock time: 261 minutes 36.37 seconds (15696.37 seconds total)