Starting phenix.real_space_refine on Tue Aug 26 14:29:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6bq1_7129/08_2025/6bq1_7129_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bq1_7129/08_2025/6bq1_7129.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/6bq1_7129/08_2025/6bq1_7129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bq1_7129/08_2025/6bq1_7129.map" model { file = "/net/cci-nas-00/data/ceres_data/6bq1_7129/08_2025/6bq1_7129_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bq1_7129/08_2025/6bq1_7129_trim.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 216 5.16 5 C 23649 2.51 5 N 6447 2.21 5 O 6849 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37163 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1509, 10673 Classifications: {'peptide': 1509} Incomplete info: {'truncation_to_alanine': 476} Link IDs: {'PTRANS': 54, 'TRANS': 1454} Chain breaks: 33 Unresolved non-hydrogen bonds: 952 Unresolved non-hydrogen angles: 1428 Unresolved non-hydrogen dihedrals: 476 Planarities with less than four sites: {'UNK:plan-1': 476} Unresolved non-hydrogen planarities: 476 Chain: "B" Number of atoms: 5774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5774 Classifications: {'peptide': 728} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 698} Chain breaks: 6 Chain: "C" Number of atoms: 2091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2091 Classifications: {'peptide': 264} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 248} Chain breaks: 4 Chain: "E" Number of atoms: 10678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1510, 10678 Classifications: {'peptide': 1510} Incomplete info: {'truncation_to_alanine': 477} Link IDs: {'PTRANS': 54, 'TRANS': 1455} Chain breaks: 33 Unresolved non-hydrogen bonds: 954 Unresolved non-hydrogen angles: 1431 Unresolved non-hydrogen dihedrals: 477 Planarities with less than four sites: {'UNK:plan-1': 477} Unresolved non-hydrogen planarities: 477 Chain: "F" Number of atoms: 5774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5774 Classifications: {'peptide': 728} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 698} Chain breaks: 6 Chain: "G" Number of atoms: 2091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2091 Classifications: {'peptide': 264} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 248} Chain breaks: 4 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'E4S': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'E4S': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.88, per 1000 atoms: 0.21 Number of scatterers: 37163 At special positions: 0 Unit cell: (258.7, 200.2, 113.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 216 16.00 F 2 9.00 O 6849 8.00 N 6447 7.00 C 23649 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: 2.72 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9626 Finding SS restraints... Secondary structure from input PDB file: 258 helices and 4 sheets defined 91.7% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 1 through 15 Processing helix chain 'A' and resid 19 through 31 Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 54 through 67 Processing helix chain 'A' and resid 71 through 87 Processing helix chain 'A' and resid 91 through 101 Processing helix chain 'A' and resid 105 through 118 Processing helix chain 'A' and resid 122 through 137 Processing helix chain 'A' and resid 141 through 153 Processing helix chain 'A' and resid 157 through 173 removed outlier: 4.126A pdb=" N UNK A 161 " --> pdb=" O UNK A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 192 Processing helix chain 'A' and resid 196 through 209 removed outlier: 3.636A pdb=" N UNK A 208 " --> pdb=" O UNK A 204 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N UNK A 209 " --> pdb=" O UNK A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 222 Processing helix chain 'A' and resid 226 through 236 Processing helix chain 'A' and resid 239 through 251 Processing helix chain 'A' and resid 255 through 267 Processing helix chain 'A' and resid 271 through 286 Processing helix chain 'A' and resid 290 through 305 Processing helix chain 'A' and resid 309 through 322 Processing helix chain 'A' and resid 326 through 340 removed outlier: 3.514A pdb=" N UNK A 330 " --> pdb=" O UNK A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 359 Processing helix chain 'A' and resid 363 through 377 Processing helix chain 'A' and resid 381 through 393 Processing helix chain 'A' and resid 397 through 406 Processing helix chain 'A' and resid 409 through 419 removed outlier: 3.934A pdb=" N UNK A 415 " --> pdb=" O UNK A 411 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N UNK A 416 " --> pdb=" O UNK A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 435 removed outlier: 3.530A pdb=" N UNK A 427 " --> pdb=" O UNK A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 456 removed outlier: 3.873A pdb=" N UNK A 444 " --> pdb=" O UNK A 440 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N UNK A 447 " --> pdb=" O UNK A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 474 removed outlier: 3.534A pdb=" N UNK A 472 " --> pdb=" O UNK A 468 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N UNK A 473 " --> pdb=" O UNK A 469 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N UNK A 474 " --> pdb=" O UNK A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 953 removed outlier: 3.914A pdb=" N ASP A 941 " --> pdb=" O ILE A 937 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS A 942 " --> pdb=" O ALA A 938 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 943 " --> pdb=" O VAL A 939 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 953 " --> pdb=" O ASN A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 976 removed outlier: 3.570A pdb=" N ASN A 976 " --> pdb=" O LEU A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 997 removed outlier: 4.135A pdb=" N VAL A 985 " --> pdb=" O ARG A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1001 Processing helix chain 'A' and resid 1003 through 1023 removed outlier: 3.860A pdb=" N LYS A1008 " --> pdb=" O GLY A1004 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A1021 " --> pdb=" O LEU A1017 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER A1022 " --> pdb=" O SER A1018 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA A1023 " --> pdb=" O LEU A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1071 removed outlier: 3.820A pdb=" N ALA A1059 " --> pdb=" O LYS A1055 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A1060 " --> pdb=" O ASP A1056 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP A1071 " --> pdb=" O GLU A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1084 Processing helix chain 'A' and resid 1086 through 1092 removed outlier: 3.883A pdb=" N TRP A1090 " --> pdb=" O LYS A1086 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL A1091 " --> pdb=" O HIS A1087 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER A1092 " --> pdb=" O GLN A1088 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1086 through 1092' Processing helix chain 'A' and resid 1097 through 1110 removed outlier: 3.509A pdb=" N ALA A1101 " --> pdb=" O HIS A1097 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE A1110 " --> pdb=" O SER A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1158 removed outlier: 3.592A pdb=" N PHE A1139 " --> pdb=" O ASP A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1184 Processing helix chain 'A' and resid 1185 through 1202 Processing helix chain 'A' and resid 1207 through 1216 Processing helix chain 'A' and resid 1223 through 1241 removed outlier: 3.550A pdb=" N LYS A1241 " --> pdb=" O LEU A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1262 Processing helix chain 'A' and resid 1264 through 1268 Processing helix chain 'A' and resid 1292 through 1313 removed outlier: 5.104A pdb=" N TYR A1311 " --> pdb=" O GLU A1307 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1328 removed outlier: 3.644A pdb=" N GLU A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1344 No H-bonds generated for 'chain 'A' and resid 1342 through 1344' Processing helix chain 'A' and resid 1345 through 1362 removed outlier: 3.918A pdb=" N LYS A1351 " --> pdb=" O GLY A1347 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1386 removed outlier: 3.673A pdb=" N ARG A1371 " --> pdb=" O ASN A1367 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A1382 " --> pdb=" O ILE A1378 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE A1383 " --> pdb=" O TYR A1379 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1417 removed outlier: 4.421A pdb=" N GLU A1402 " --> pdb=" O LYS A1398 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP A1403 " --> pdb=" O ARG A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1478 through 1508 removed outlier: 3.718A pdb=" N ARG A1488 " --> pdb=" O TYR A1484 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN A1508 " --> pdb=" O ILE A1504 " (cutoff:3.500A) Processing helix chain 'A' and resid 1521 through 1534 Processing helix chain 'A' and resid 1540 through 1551 removed outlier: 3.506A pdb=" N VAL A1544 " --> pdb=" O TRP A1540 " (cutoff:3.500A) Processing helix chain 'A' and resid 1551 through 1558 Processing helix chain 'A' and resid 1566 through 1579 Processing helix chain 'A' and resid 1580 through 1583 Processing helix chain 'A' and resid 1588 through 1594 removed outlier: 3.943A pdb=" N PHE A1592 " --> pdb=" O GLU A1588 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A1593 " --> pdb=" O ALA A1589 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1612 removed outlier: 4.217A pdb=" N CYS A1611 " --> pdb=" O HIS A1608 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TRP A1612 " --> pdb=" O VAL A1609 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1608 through 1612' Processing helix chain 'A' and resid 1616 through 1621 Processing helix chain 'A' and resid 1622 through 1625 Processing helix chain 'A' and resid 1631 through 1645 removed outlier: 3.791A pdb=" N PHE A1645 " --> pdb=" O VAL A1641 " (cutoff:3.500A) Processing helix chain 'A' and resid 1646 through 1653 removed outlier: 3.866A pdb=" N TYR A1653 " --> pdb=" O ALA A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1654 through 1656 No H-bonds generated for 'chain 'A' and resid 1654 through 1656' Processing helix chain 'A' and resid 1657 through 1663 Processing helix chain 'A' and resid 1667 through 1680 Processing helix chain 'A' and resid 1680 through 1696 removed outlier: 4.513A pdb=" N TYR A1696 " --> pdb=" O LYS A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1708 through 1723 Processing helix chain 'A' and resid 1725 through 1747 Processing helix chain 'A' and resid 1751 through 1754 removed outlier: 3.563A pdb=" N GLY A1754 " --> pdb=" O TYR A1751 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1751 through 1754' Processing helix chain 'A' and resid 1755 through 1769 Processing helix chain 'A' and resid 1855 through 1876 removed outlier: 3.839A pdb=" N ALA A1861 " --> pdb=" O GLN A1857 " (cutoff:3.500A) Processing helix chain 'A' and resid 1916 through 1925 Processing helix chain 'A' and resid 1929 through 1954 removed outlier: 3.928A pdb=" N GLN A1933 " --> pdb=" O THR A1929 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN A1934 " --> pdb=" O LEU A1930 " (cutoff:3.500A) Processing helix chain 'A' and resid 1966 through 1970 removed outlier: 3.960A pdb=" N HIS A1970 " --> pdb=" O LYS A1967 " (cutoff:3.500A) Processing helix chain 'A' and resid 1975 through 1979 removed outlier: 3.858A pdb=" N PHE A1978 " --> pdb=" O ASP A1975 " (cutoff:3.500A) Processing helix chain 'A' and resid 1997 through 2003 removed outlier: 3.508A pdb=" N VAL A2001 " --> pdb=" O THR A1997 " (cutoff:3.500A) Processing helix chain 'A' and resid 2010 through 2028 Processing helix chain 'A' and resid 2030 through 2041 removed outlier: 3.798A pdb=" N VAL A2034 " --> pdb=" O TYR A2030 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET A2041 " --> pdb=" O LEU A2037 " (cutoff:3.500A) Processing helix chain 'A' and resid 2052 through 2062 Processing helix chain 'A' and resid 2066 through 2084 removed outlier: 3.825A pdb=" N ALA A2071 " --> pdb=" O GLU A2067 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASN A2072 " --> pdb=" O ARG A2068 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A2084 " --> pdb=" O SER A2080 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 20 removed outlier: 3.554A pdb=" N GLU B 20 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 33 Processing helix chain 'B' and resid 42 through 60 removed outlier: 3.663A pdb=" N LEU B 46 " --> pdb=" O ASP B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 89 Processing helix chain 'B' and resid 92 through 111 Processing helix chain 'B' and resid 113 through 123 Processing helix chain 'B' and resid 134 through 154 Processing helix chain 'B' and resid 168 through 195 Processing helix chain 'B' and resid 215 through 233 removed outlier: 3.946A pdb=" N ALA B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N HIS B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 248 Processing helix chain 'B' and resid 254 through 272 Processing helix chain 'B' and resid 323 through 342 Processing helix chain 'B' and resid 355 through 376 removed outlier: 3.623A pdb=" N ALA B 362 " --> pdb=" O SER B 358 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 390 Processing helix chain 'B' and resid 396 through 410 removed outlier: 3.785A pdb=" N TRP B 400 " --> pdb=" O GLU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 427 Processing helix chain 'B' and resid 431 through 442 Processing helix chain 'B' and resid 447 through 460 Processing helix chain 'B' and resid 466 through 486 removed outlier: 3.955A pdb=" N LYS B 471 " --> pdb=" O GLU B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 511 Processing helix chain 'B' and resid 514 through 528 Processing helix chain 'B' and resid 530 through 545 Processing helix chain 'B' and resid 548 through 562 removed outlier: 3.561A pdb=" N LEU B 552 " --> pdb=" O ASP B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 579 Processing helix chain 'B' and resid 582 through 597 Processing helix chain 'B' and resid 598 through 617 removed outlier: 3.557A pdb=" N ALA B 602 " --> pdb=" O GLY B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 710 removed outlier: 4.257A pdb=" N TRP B 692 " --> pdb=" O PRO B 688 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET B 693 " --> pdb=" O LEU B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 726 removed outlier: 3.544A pdb=" N ALA B 715 " --> pdb=" O LYS B 711 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 725 " --> pdb=" O GLU B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 743 Processing helix chain 'B' and resid 745 through 760 removed outlier: 3.527A pdb=" N ALA B 758 " --> pdb=" O GLU B 754 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 759 " --> pdb=" O GLU B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 777 Processing helix chain 'B' and resid 779 through 794 Processing helix chain 'B' and resid 797 through 810 removed outlier: 3.929A pdb=" N TRP B 801 " --> pdb=" O ALA B 797 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 830 Processing helix chain 'B' and resid 835 through 839 removed outlier: 3.586A pdb=" N ILE B 839 " --> pdb=" O PHE B 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 17 removed outlier: 3.633A pdb=" N LYS C 17 " --> pdb=" O LEU C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 28 removed outlier: 3.583A pdb=" N TYR C 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 43 Processing helix chain 'C' and resid 52 through 66 removed outlier: 4.136A pdb=" N VAL C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER C 66 " --> pdb=" O GLU C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 76 removed outlier: 3.723A pdb=" N LEU C 72 " --> pdb=" O GLU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 91 removed outlier: 3.902A pdb=" N LEU C 82 " --> pdb=" O PHE C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 114 Processing helix chain 'C' and resid 176 through 187 Processing helix chain 'C' and resid 196 through 210 removed outlier: 3.687A pdb=" N LEU C 200 " --> pdb=" O PRO C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 222 removed outlier: 3.993A pdb=" N HIS C 219 " --> pdb=" O TYR C 215 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL C 220 " --> pdb=" O PRO C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 248 removed outlier: 4.255A pdb=" N GLY C 243 " --> pdb=" O GLN C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 253 through 271 Processing helix chain 'C' and resid 272 through 284 removed outlier: 3.765A pdb=" N LEU C 276 " --> pdb=" O TYR C 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 15 Processing helix chain 'E' and resid 19 through 31 Processing helix chain 'E' and resid 35 through 50 Processing helix chain 'E' and resid 54 through 67 Processing helix chain 'E' and resid 71 through 87 Processing helix chain 'E' and resid 91 through 101 Processing helix chain 'E' and resid 105 through 118 Processing helix chain 'E' and resid 122 through 137 Processing helix chain 'E' and resid 141 through 153 Processing helix chain 'E' and resid 157 through 173 removed outlier: 4.132A pdb=" N UNK E 161 " --> pdb=" O UNK E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 192 Processing helix chain 'E' and resid 196 through 210 removed outlier: 3.680A pdb=" N UNK E 205 " --> pdb=" O UNK E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 223 Processing helix chain 'E' and resid 227 through 237 Processing helix chain 'E' and resid 240 through 253 Processing helix chain 'E' and resid 257 through 269 Processing helix chain 'E' and resid 273 through 288 Processing helix chain 'E' and resid 292 through 307 Processing helix chain 'E' and resid 311 through 324 Processing helix chain 'E' and resid 328 through 341 Processing helix chain 'E' and resid 345 through 360 Processing helix chain 'E' and resid 364 through 378 Processing helix chain 'E' and resid 382 through 394 Processing helix chain 'E' and resid 398 through 407 Processing helix chain 'E' and resid 410 through 420 removed outlier: 3.929A pdb=" N UNK E 416 " --> pdb=" O UNK E 412 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N UNK E 417 " --> pdb=" O UNK E 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 436 removed outlier: 3.530A pdb=" N UNK E 428 " --> pdb=" O UNK E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 457 Processing helix chain 'E' and resid 465 through 475 removed outlier: 3.534A pdb=" N UNK E 473 " --> pdb=" O UNK E 469 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N UNK E 474 " --> pdb=" O UNK E 470 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N UNK E 475 " --> pdb=" O UNK E 471 " (cutoff:3.500A) Processing helix chain 'E' and resid 933 through 953 removed outlier: 3.913A pdb=" N ASP E 941 " --> pdb=" O ILE E 937 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS E 942 " --> pdb=" O ALA E 938 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL E 943 " --> pdb=" O VAL E 939 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP E 953 " --> pdb=" O ASN E 949 " (cutoff:3.500A) Processing helix chain 'E' and resid 957 through 976 removed outlier: 3.532A pdb=" N ASN E 976 " --> pdb=" O LEU E 972 " (cutoff:3.500A) Processing helix chain 'E' and resid 979 through 997 removed outlier: 3.534A pdb=" N ARG E 983 " --> pdb=" O HIS E 979 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL E 985 " --> pdb=" O ARG E 981 " (cutoff:3.500A) Processing helix chain 'E' and resid 998 through 1001 Processing helix chain 'E' and resid 1003 through 1023 removed outlier: 3.860A pdb=" N LYS E1008 " --> pdb=" O GLY E1004 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU E1021 " --> pdb=" O LEU E1017 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER E1022 " --> pdb=" O SER E1018 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA E1023 " --> pdb=" O LEU E1019 " (cutoff:3.500A) Processing helix chain 'E' and resid 1046 through 1071 removed outlier: 3.819A pdb=" N ALA E1059 " --> pdb=" O LYS E1055 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG E1060 " --> pdb=" O ASP E1056 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TRP E1071 " --> pdb=" O GLU E1067 " (cutoff:3.500A) Processing helix chain 'E' and resid 1072 through 1084 Processing helix chain 'E' and resid 1086 through 1092 removed outlier: 3.882A pdb=" N TRP E1090 " --> pdb=" O LYS E1086 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL E1091 " --> pdb=" O HIS E1087 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER E1092 " --> pdb=" O GLN E1088 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1086 through 1092' Processing helix chain 'E' and resid 1097 through 1110 removed outlier: 3.509A pdb=" N ALA E1101 " --> pdb=" O HIS E1097 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N PHE E1110 " --> pdb=" O SER E1106 " (cutoff:3.500A) Processing helix chain 'E' and resid 1135 through 1158 Processing helix chain 'E' and resid 1169 through 1184 Processing helix chain 'E' and resid 1185 through 1202 Processing helix chain 'E' and resid 1207 through 1216 Processing helix chain 'E' and resid 1223 through 1241 removed outlier: 3.550A pdb=" N LYS E1241 " --> pdb=" O LEU E1237 " (cutoff:3.500A) Processing helix chain 'E' and resid 1244 through 1262 Processing helix chain 'E' and resid 1264 through 1268 Processing helix chain 'E' and resid 1292 through 1313 removed outlier: 5.104A pdb=" N TYR E1311 " --> pdb=" O GLU E1307 " (cutoff:3.500A) Processing helix chain 'E' and resid 1314 through 1328 removed outlier: 3.644A pdb=" N GLU E1318 " --> pdb=" O SER E1314 " (cutoff:3.500A) Processing helix chain 'E' and resid 1342 through 1344 No H-bonds generated for 'chain 'E' and resid 1342 through 1344' Processing helix chain 'E' and resid 1345 through 1362 removed outlier: 3.918A pdb=" N LYS E1351 " --> pdb=" O GLY E1347 " (cutoff:3.500A) Processing helix chain 'E' and resid 1367 through 1386 removed outlier: 3.674A pdb=" N ARG E1371 " --> pdb=" O ASN E1367 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA E1382 " --> pdb=" O ILE E1378 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE E1383 " --> pdb=" O TYR E1379 " (cutoff:3.500A) Processing helix chain 'E' and resid 1396 through 1417 removed outlier: 4.421A pdb=" N GLU E1402 " --> pdb=" O LYS E1398 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP E1403 " --> pdb=" O ARG E1399 " (cutoff:3.500A) Processing helix chain 'E' and resid 1478 through 1508 removed outlier: 3.717A pdb=" N ARG E1488 " --> pdb=" O TYR E1484 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN E1508 " --> pdb=" O ILE E1504 " (cutoff:3.500A) Processing helix chain 'E' and resid 1521 through 1534 Processing helix chain 'E' and resid 1540 through 1551 removed outlier: 3.506A pdb=" N VAL E1544 " --> pdb=" O TRP E1540 " (cutoff:3.500A) Processing helix chain 'E' and resid 1551 through 1558 Processing helix chain 'E' and resid 1566 through 1579 Processing helix chain 'E' and resid 1580 through 1583 Processing helix chain 'E' and resid 1588 through 1594 removed outlier: 3.933A pdb=" N PHE E1592 " --> pdb=" O GLU E1588 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU E1593 " --> pdb=" O ALA E1589 " (cutoff:3.500A) Processing helix chain 'E' and resid 1608 through 1612 removed outlier: 4.218A pdb=" N CYS E1611 " --> pdb=" O HIS E1608 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TRP E1612 " --> pdb=" O VAL E1609 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1608 through 1612' Processing helix chain 'E' and resid 1616 through 1621 Processing helix chain 'E' and resid 1622 through 1625 Processing helix chain 'E' and resid 1631 through 1645 removed outlier: 3.792A pdb=" N PHE E1645 " --> pdb=" O VAL E1641 " (cutoff:3.500A) Processing helix chain 'E' and resid 1646 through 1653 removed outlier: 3.866A pdb=" N TYR E1653 " --> pdb=" O ALA E1649 " (cutoff:3.500A) Processing helix chain 'E' and resid 1654 through 1656 No H-bonds generated for 'chain 'E' and resid 1654 through 1656' Processing helix chain 'E' and resid 1657 through 1663 Processing helix chain 'E' and resid 1667 through 1680 Processing helix chain 'E' and resid 1680 through 1696 removed outlier: 4.544A pdb=" N TYR E1696 " --> pdb=" O LYS E1692 " (cutoff:3.500A) Processing helix chain 'E' and resid 1708 through 1723 Processing helix chain 'E' and resid 1725 through 1747 Processing helix chain 'E' and resid 1751 through 1754 removed outlier: 3.563A pdb=" N GLY E1754 " --> pdb=" O TYR E1751 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1751 through 1754' Processing helix chain 'E' and resid 1755 through 1769 Processing helix chain 'E' and resid 1855 through 1876 removed outlier: 3.839A pdb=" N ALA E1861 " --> pdb=" O GLN E1857 " (cutoff:3.500A) Processing helix chain 'E' and resid 1916 through 1925 Processing helix chain 'E' and resid 1929 through 1954 Processing helix chain 'E' and resid 1966 through 1970 removed outlier: 3.960A pdb=" N HIS E1970 " --> pdb=" O LYS E1967 " (cutoff:3.500A) Processing helix chain 'E' and resid 1975 through 1979 removed outlier: 3.880A pdb=" N PHE E1978 " --> pdb=" O ASP E1975 " (cutoff:3.500A) Processing helix chain 'E' and resid 1997 through 2003 removed outlier: 3.507A pdb=" N VAL E2001 " --> pdb=" O THR E1997 " (cutoff:3.500A) Processing helix chain 'E' and resid 2010 through 2028 Processing helix chain 'E' and resid 2030 through 2041 removed outlier: 3.798A pdb=" N VAL E2034 " --> pdb=" O TYR E2030 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET E2041 " --> pdb=" O LEU E2037 " (cutoff:3.500A) Processing helix chain 'E' and resid 2052 through 2062 Processing helix chain 'E' and resid 2066 through 2084 removed outlier: 3.826A pdb=" N ALA E2071 " --> pdb=" O GLU E2067 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASN E2072 " --> pdb=" O ARG E2068 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER E2084 " --> pdb=" O SER E2080 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 20 removed outlier: 3.554A pdb=" N GLU F 20 " --> pdb=" O ARG F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 33 Processing helix chain 'F' and resid 42 through 60 removed outlier: 3.662A pdb=" N LEU F 46 " --> pdb=" O ASP F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 89 Processing helix chain 'F' and resid 92 through 111 Processing helix chain 'F' and resid 113 through 123 Processing helix chain 'F' and resid 134 through 154 Processing helix chain 'F' and resid 168 through 195 Processing helix chain 'F' and resid 215 through 233 removed outlier: 3.946A pdb=" N ALA F 225 " --> pdb=" O GLY F 221 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N HIS F 226 " --> pdb=" O LEU F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 248 Processing helix chain 'F' and resid 254 through 272 Processing helix chain 'F' and resid 323 through 342 Processing helix chain 'F' and resid 355 through 376 removed outlier: 3.624A pdb=" N ALA F 362 " --> pdb=" O SER F 358 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG F 376 " --> pdb=" O ALA F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 390 Processing helix chain 'F' and resid 396 through 410 removed outlier: 3.785A pdb=" N TRP F 400 " --> pdb=" O GLU F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 427 Processing helix chain 'F' and resid 431 through 442 Processing helix chain 'F' and resid 447 through 460 Processing helix chain 'F' and resid 466 through 486 removed outlier: 3.954A pdb=" N LYS F 471 " --> pdb=" O GLU F 467 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 511 Processing helix chain 'F' and resid 514 through 528 Processing helix chain 'F' and resid 530 through 545 Processing helix chain 'F' and resid 548 through 562 removed outlier: 3.562A pdb=" N LEU F 552 " --> pdb=" O ASP F 548 " (cutoff:3.500A) Processing helix chain 'F' and resid 564 through 579 Processing helix chain 'F' and resid 582 through 597 Processing helix chain 'F' and resid 598 through 617 removed outlier: 3.557A pdb=" N ALA F 602 " --> pdb=" O GLY F 598 " (cutoff:3.500A) Processing helix chain 'F' and resid 688 through 710 removed outlier: 4.258A pdb=" N TRP F 692 " --> pdb=" O PRO F 688 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET F 693 " --> pdb=" O LEU F 689 " (cutoff:3.500A) Processing helix chain 'F' and resid 711 through 726 removed outlier: 3.543A pdb=" N ALA F 715 " --> pdb=" O LYS F 711 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU F 725 " --> pdb=" O GLU F 721 " (cutoff:3.500A) Processing helix chain 'F' and resid 729 through 743 Processing helix chain 'F' and resid 745 through 760 removed outlier: 3.528A pdb=" N ALA F 758 " --> pdb=" O GLU F 754 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE F 759 " --> pdb=" O GLU F 755 " (cutoff:3.500A) Processing helix chain 'F' and resid 764 through 777 Processing helix chain 'F' and resid 779 through 794 Processing helix chain 'F' and resid 797 through 810 removed outlier: 3.929A pdb=" N TRP F 801 " --> pdb=" O ALA F 797 " (cutoff:3.500A) Processing helix chain 'F' and resid 813 through 830 Processing helix chain 'F' and resid 835 through 839 removed outlier: 3.585A pdb=" N ILE F 839 " --> pdb=" O PHE F 836 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 17 removed outlier: 3.634A pdb=" N LYS G 17 " --> pdb=" O LEU G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 28 removed outlier: 3.584A pdb=" N TYR G 27 " --> pdb=" O LEU G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 43 Processing helix chain 'G' and resid 52 through 66 removed outlier: 4.135A pdb=" N VAL G 56 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER G 66 " --> pdb=" O GLU G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 76 removed outlier: 3.721A pdb=" N LEU G 72 " --> pdb=" O GLU G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 91 removed outlier: 3.902A pdb=" N LEU G 82 " --> pdb=" O PHE G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 114 Processing helix chain 'G' and resid 176 through 187 Processing helix chain 'G' and resid 196 through 210 removed outlier: 3.688A pdb=" N LEU G 200 " --> pdb=" O PRO G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 222 removed outlier: 3.993A pdb=" N HIS G 219 " --> pdb=" O TYR G 215 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL G 220 " --> pdb=" O PRO G 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 248 removed outlier: 4.256A pdb=" N GLY G 243 " --> pdb=" O GLN G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 251 No H-bonds generated for 'chain 'G' and resid 249 through 251' Processing helix chain 'G' and resid 253 through 271 Processing helix chain 'G' and resid 272 through 284 removed outlier: 3.764A pdb=" N LEU G 276 " --> pdb=" O TYR G 272 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1031 through 1033 Processing sheet with id=AA2, first strand: chain 'A' and resid 1804 through 1806 removed outlier: 3.845A pdb=" N ALA A1847 " --> pdb=" O ALA A1805 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 1031 through 1033 Processing sheet with id=AA4, first strand: chain 'E' and resid 1804 through 1806 removed outlier: 3.845A pdb=" N ALA E1847 " --> pdb=" O ALA E1805 " (cutoff:3.500A) 2548 hydrogen bonds defined for protein. 7590 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: 7.50 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 10104 1.33 - 1.46: 10091 1.46 - 1.58: 17294 1.58 - 1.71: 1 1.71 - 1.84: 347 Bond restraints: 37837 Sorted by residual: bond pdb=" C06 E4S E2201 " pdb=" N01 E4S E2201 " ideal model delta sigma weight residual 1.328 1.510 -0.182 2.00e-02 2.50e+03 8.25e+01 bond pdb=" C06 E4S A2201 " pdb=" N01 E4S A2201 " ideal model delta sigma weight residual 1.328 1.474 -0.146 2.00e-02 2.50e+03 5.33e+01 bond pdb=" C14 E4S E2201 " pdb=" C19 E4S E2201 " ideal model delta sigma weight residual 1.385 1.529 -0.144 2.00e-02 2.50e+03 5.21e+01 bond pdb=" C27 E4S A2201 " pdb=" C28 E4S A2201 " ideal model delta sigma weight residual 1.388 1.528 -0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C27 E4S E2201 " pdb=" C28 E4S E2201 " ideal model delta sigma weight residual 1.388 1.527 -0.139 2.00e-02 2.50e+03 4.84e+01 ... (remaining 37832 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.57: 50802 3.57 - 7.14: 484 7.14 - 10.71: 64 10.71 - 14.28: 8 14.28 - 17.85: 3 Bond angle restraints: 51361 Sorted by residual: angle pdb=" N ILE E1994 " pdb=" CA ILE E1994 " pdb=" C ILE E1994 " ideal model delta sigma weight residual 110.21 123.31 -13.10 1.13e+00 7.83e-01 1.34e+02 angle pdb=" N MET E1979 " pdb=" CA MET E1979 " pdb=" C MET E1979 " ideal model delta sigma weight residual 111.07 121.19 -10.12 1.07e+00 8.73e-01 8.95e+01 angle pdb=" N HIS E1702 " pdb=" CA HIS E1702 " pdb=" C HIS E1702 " ideal model delta sigma weight residual 111.28 101.34 9.94 1.09e+00 8.42e-01 8.32e+01 angle pdb=" C VAL E1586 " pdb=" CA VAL E1586 " pdb=" CB VAL E1586 " ideal model delta sigma weight residual 114.35 105.69 8.66 1.06e+00 8.90e-01 6.67e+01 angle pdb=" C VAL A1586 " pdb=" CA VAL A1586 " pdb=" CB VAL A1586 " ideal model delta sigma weight residual 114.35 105.86 8.49 1.06e+00 8.90e-01 6.41e+01 ... (remaining 51356 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.99: 22407 22.99 - 45.97: 390 45.97 - 68.96: 26 68.96 - 91.94: 14 91.94 - 114.93: 4 Dihedral angle restraints: 22841 sinusoidal: 8140 harmonic: 14701 Sorted by residual: dihedral pdb=" N LYS E1956 " pdb=" C LYS E1956 " pdb=" CA LYS E1956 " pdb=" CB LYS E1956 " ideal model delta harmonic sigma weight residual 122.80 140.39 -17.59 0 2.50e+00 1.60e-01 4.95e+01 dihedral pdb=" C LYS E1956 " pdb=" N LYS E1956 " pdb=" CA LYS E1956 " pdb=" CB LYS E1956 " ideal model delta harmonic sigma weight residual -122.60 -139.70 17.10 0 2.50e+00 1.60e-01 4.68e+01 dihedral pdb=" N TYR A1507 " pdb=" C TYR A1507 " pdb=" CA TYR A1507 " pdb=" CB TYR A1507 " ideal model delta harmonic sigma weight residual 122.80 138.09 -15.29 0 2.50e+00 1.60e-01 3.74e+01 ... (remaining 22838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 5858 0.148 - 0.296: 70 0.296 - 0.444: 11 0.444 - 0.592: 4 0.592 - 0.739: 2 Chirality restraints: 5945 Sorted by residual: chirality pdb=" CA LYS E1956 " pdb=" N LYS E1956 " pdb=" C LYS E1956 " pdb=" CB LYS E1956 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.37e+01 chirality pdb=" CA TYR A1507 " pdb=" N TYR A1507 " pdb=" C TYR A1507 " pdb=" CB TYR A1507 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.62e+00 chirality pdb=" CA TYR E1507 " pdb=" N TYR E1507 " pdb=" C TYR E1507 " pdb=" CB TYR E1507 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.54e+00 ... (remaining 5942 not shown) Planarity restraints: 6593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A1132 " -0.023 2.00e-02 2.50e+03 4.78e-02 2.28e+01 pdb=" C VAL A1132 " 0.083 2.00e-02 2.50e+03 pdb=" O VAL A1132 " -0.032 2.00e-02 2.50e+03 pdb=" N LYS A1133 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A1929 " 0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C THR A1929 " -0.063 2.00e-02 2.50e+03 pdb=" O THR A1929 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU A1930 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 E4S E2201 " 0.007 2.00e-02 2.50e+03 2.33e-02 1.22e+01 pdb=" C03 E4S E2201 " 0.005 2.00e-02 2.50e+03 pdb=" C04 E4S E2201 " -0.007 2.00e-02 2.50e+03 pdb=" C05 E4S E2201 " 0.048 2.00e-02 2.50e+03 pdb=" C06 E4S E2201 " -0.046 2.00e-02 2.50e+03 pdb=" C07 E4S E2201 " -0.005 2.00e-02 2.50e+03 pdb=" N01 E4S E2201 " 0.007 2.00e-02 2.50e+03 pdb=" O01 E4S E2201 " 0.005 2.00e-02 2.50e+03 pdb=" S01 E4S E2201 " -0.014 2.00e-02 2.50e+03 ... (remaining 6590 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 243 2.50 - 3.10: 29417 3.10 - 3.70: 59204 3.70 - 4.30: 82745 4.30 - 4.90: 131215 Nonbonded interactions: 302824 Sorted by model distance: nonbonded pdb=" O GLY E1112 " pdb=" OD2 ASP E1135 " model vdw 1.899 3.040 nonbonded pdb=" O CYS E1902 " pdb=" OG1 THR E1903 " model vdw 2.146 3.040 nonbonded pdb=" O CYS A1902 " pdb=" OG1 THR A1903 " model vdw 2.146 3.040 nonbonded pdb=" CZ PHE A1932 " pdb=" CD ARG A1936 " model vdw 2.195 3.740 nonbonded pdb=" O GLU C 112 " pdb=" NZ LYS C 116 " model vdw 2.195 3.120 ... (remaining 302819 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' selection = (chain 'E' and resid 2 through 2201) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 31.700 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4935 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 : 0.007 0.182 37837 Z= 0.379 Angle : 0.945 17.848 51361 Z= 0.535 Chirality : 0.053 0.739 5945 Planarity : 0.006 0.068 6593 Dihedral : 9.328 114.927 13215 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 27.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.11 % Allowed : 2.03 % Favored : 97.86 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.86 (0.11), residues: 3974 helix: -2.31 (0.08), residues: 2622 sheet: -1.24 (0.84), residues: 32 loop : -2.78 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E1050 TYR 0.021 0.002 TYR E1884 PHE 0.031 0.003 PHE A1687 TRP 0.046 0.004 TRP A1298 HIS 0.024 0.003 HIS A1361 Details of bonding type rmsd covalent geometry : bond 0.00740 (37837) covalent geometry : angle 0.94540 (51361) hydrogen bonds : bond 0.12890 ( 2548) hydrogen bonds : angle 9.50808 ( 7590) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1043 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1039 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 944 PHE cc_start: 0.8144 (t80) cc_final: 0.7379 (t80) REVERT: A 974 ASN cc_start: 0.8130 (m-40) cc_final: 0.7678 (m110) REVERT: A 983 ARG cc_start: 0.6033 (ptt90) cc_final: 0.5803 (ptt-90) REVERT: A 989 TYR cc_start: 0.7078 (m-10) cc_final: 0.6869 (m-10) REVERT: A 1051 GLU cc_start: 0.6275 (tt0) cc_final: 0.6065 (tm-30) REVERT: A 1110 PHE cc_start: 0.6640 (p90) cc_final: 0.6296 (p90) REVERT: A 1113 TYR cc_start: 0.6015 (m-10) cc_final: 0.5762 (m-80) REVERT: A 1134 LYS cc_start: 0.4940 (mmtt) cc_final: 0.4610 (mmtt) REVERT: A 1307 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7896 (tm-30) REVERT: A 1501 GLU cc_start: 0.6971 (pt0) cc_final: 0.5908 (mm-30) REVERT: A 1665 LYS cc_start: 0.8676 (ttpt) cc_final: 0.7671 (mmtt) REVERT: A 1671 GLU cc_start: 0.8303 (tt0) cc_final: 0.8019 (pp20) REVERT: A 1723 LEU cc_start: 0.8452 (mt) cc_final: 0.8249 (mp) REVERT: A 1858 ASP cc_start: 0.8494 (t0) cc_final: 0.8264 (t0) REVERT: A 1937 TYR cc_start: 0.6972 (t80) cc_final: 0.6415 (t80) REVERT: A 1956 LYS cc_start: 0.6386 (mmtt) cc_final: 0.4558 (tttm) REVERT: A 1979 MET cc_start: 0.6713 (ptm) cc_final: 0.5381 (ptm) REVERT: A 2008 MET cc_start: 0.6962 (tpt) cc_final: 0.6745 (tpp) REVERT: A 2027 VAL cc_start: 0.7585 (t) cc_final: 0.7163 (t) REVERT: A 2031 MET cc_start: 0.7562 (ttp) cc_final: 0.7276 (ttp) REVERT: A 2058 LYS cc_start: 0.8351 (tttt) cc_final: 0.7773 (ttpt) REVERT: B 795 SER cc_start: 0.5788 (p) cc_final: 0.5553 (p) REVERT: B 821 PHE cc_start: 0.4645 (m-10) cc_final: 0.4273 (m-10) REVERT: B 826 GLU cc_start: 0.4394 (mt-10) cc_final: 0.4166 (pt0) REVERT: E 974 ASN cc_start: 0.7798 (m-40) cc_final: 0.7215 (m110) REVERT: E 1022 SER cc_start: 0.8027 (m) cc_final: 0.7619 (p) REVERT: E 1113 TYR cc_start: 0.6667 (m-10) cc_final: 0.6244 (m-80) REVERT: E 1132 VAL cc_start: 0.7284 (t) cc_final: 0.7058 (p) REVERT: E 1183 ARG cc_start: 0.8083 (ttm110) cc_final: 0.7777 (ttp80) REVERT: E 1209 GLN cc_start: 0.8384 (tt0) cc_final: 0.8013 (tp40) REVERT: E 1221 MET cc_start: 0.8599 (ttt) cc_final: 0.8124 (ttm) REVERT: E 1286 LYS cc_start: 0.8304 (pttt) cc_final: 0.7915 (ptpp) REVERT: E 1296 TYR cc_start: 0.8561 (t80) cc_final: 0.8145 (t80) REVERT: E 1411 TRP cc_start: 0.6159 (t60) cc_final: 0.5821 (t60) REVERT: E 1535 LEU cc_start: 0.8532 (mt) cc_final: 0.7674 (pp) REVERT: E 1566 GLU cc_start: 0.7913 (tp30) cc_final: 0.7458 (tp30) REVERT: E 1627 MET cc_start: 0.8018 (ptp) cc_final: 0.5802 (mmt) REVERT: E 1653 TYR cc_start: 0.8698 (m-80) cc_final: 0.8415 (m-80) REVERT: E 1747 ILE cc_start: 0.7803 (pp) cc_final: 0.7438 (pt) REVERT: E 1858 ASP cc_start: 0.8569 (t0) cc_final: 0.8216 (t0) REVERT: E 1979 MET cc_start: 0.6417 (ptm) cc_final: 0.5493 (ptm) REVERT: E 2008 MET cc_start: 0.6690 (tpt) cc_final: 0.6441 (tpp) REVERT: E 2024 TYR cc_start: 0.7795 (t80) cc_final: 0.7316 (t80) REVERT: E 2075 MET cc_start: 0.7186 (ptm) cc_final: 0.6882 (ptm) REVERT: F 147 THR cc_start: 0.2370 (m) cc_final: 0.1417 (t) REVERT: F 359 LEU cc_start: 0.8445 (tm) cc_final: 0.8206 (tm) REVERT: F 390 MET cc_start: 0.7724 (mmm) cc_final: 0.7399 (mmp) outliers start: 4 outliers final: 2 residues processed: 1043 average time/residue: 0.2334 time to fit residues: 386.2758 Evaluate side-chains 573 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 571 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1929 THR Chi-restraints excluded: chain E residue 1955 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.0770 chunk 91 optimal weight: 2.9990 overall best weight: 1.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1015 GLN A1081 GLN A1116 GLN A1117 ASN ** A1178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1257 HIS A1325 GLN A1527 ASN A1557 GLN A1631 HIS ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1702 HIS A1771 GLN A1779 ASN ** A1796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2072 ASN B 107 ASN ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 ASN B 730 HIS ** C 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 HIS C 205 GLN E 960 ASN E 967 HIS ** E 977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1015 GLN E1081 GLN E1096 GLN E1116 GLN ** E1178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1257 HIS E1557 GLN E1779 ASN ** E1959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1973 HIS E2072 ASN F 107 ASN ** F 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 ASN F 351 HIS F 724 ASN F 730 HIS G 137 HIS G 166 HIS G 175 GLN ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.172413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.148924 restraints weight = 81436.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.147828 restraints weight = 81523.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.148829 restraints weight = 70956.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.149059 restraints weight = 46435.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.150218 restraints weight = 42869.831| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 37837 Z= 0.218 Angle : 0.766 11.470 51361 Z= 0.385 Chirality : 0.042 0.260 5945 Planarity : 0.006 0.072 6593 Dihedral : 7.119 110.736 5318 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.81 % Favored : 95.17 % Rotamer: Outliers : 2.40 % Allowed : 9.56 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.00 (0.12), residues: 3974 helix: -0.60 (0.09), residues: 2672 sheet: -1.13 (0.77), residues: 32 loop : -2.78 (0.15), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 355 TYR 0.022 0.002 TYR C 272 PHE 0.031 0.003 PHE G 74 TRP 0.021 0.002 TRP E1411 HIS 0.016 0.002 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00496 (37837) covalent geometry : angle 0.76648 (51361) hydrogen bonds : bond 0.04649 ( 2548) hydrogen bonds : angle 5.46838 ( 7590) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 649 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 951 MET cc_start: 0.7397 (mmp) cc_final: 0.7083 (mmt) REVERT: A 1069 MET cc_start: 0.7665 (mmt) cc_final: 0.7453 (mmm) REVERT: A 1665 LYS cc_start: 0.7791 (ttpt) cc_final: 0.7533 (mmtt) REVERT: A 1691 MET cc_start: 0.7273 (mmm) cc_final: 0.6797 (mmm) REVERT: A 1956 LYS cc_start: 0.7388 (mmtt) cc_final: 0.5970 (tttp) REVERT: A 2008 MET cc_start: 0.6629 (tpt) cc_final: 0.6418 (tpp) REVERT: A 2017 MET cc_start: 0.6685 (tpt) cc_final: 0.6431 (tpp) REVERT: B 273 MET cc_start: 0.6445 (mtp) cc_final: 0.6165 (ptp) REVERT: B 356 LEU cc_start: 0.8140 (mt) cc_final: 0.7457 (pp) REVERT: B 380 GLU cc_start: 0.7020 (tm-30) cc_final: 0.6805 (tm-30) REVERT: B 408 MET cc_start: 0.7753 (ttm) cc_final: 0.7351 (ttm) REVERT: B 471 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7470 (mtmt) REVERT: B 514 ASP cc_start: 0.7487 (OUTLIER) cc_final: 0.7277 (t0) REVERT: B 784 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7330 (tm-30) REVERT: B 821 PHE cc_start: 0.6172 (m-10) cc_final: 0.5386 (m-10) REVERT: C 126 THR cc_start: 0.6968 (p) cc_final: 0.6718 (t) REVERT: C 169 ARG cc_start: 0.7245 (mmt-90) cc_final: 0.6925 (mmt-90) REVERT: C 280 ASN cc_start: 0.6771 (t0) cc_final: 0.6393 (t0) REVERT: E 983 ARG cc_start: 0.7108 (ppt170) cc_final: 0.6841 (ptt180) REVERT: E 1307 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7121 (tm-30) REVERT: E 1627 MET cc_start: 0.6618 (ptp) cc_final: 0.5762 (mmt) REVERT: E 1747 ILE cc_start: 0.7567 (pp) cc_final: 0.7166 (pt) REVERT: E 1765 LEU cc_start: 0.7513 (tt) cc_final: 0.6945 (mp) REVERT: F 219 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.7113 (pp20) REVERT: F 344 VAL cc_start: 0.8079 (OUTLIER) cc_final: 0.7841 (p) REVERT: F 356 LEU cc_start: 0.8493 (mt) cc_final: 0.7835 (pp) REVERT: G 240 MET cc_start: 0.6806 (tmm) cc_final: 0.6568 (tmm) REVERT: G 272 TYR cc_start: 0.7769 (m-10) cc_final: 0.7429 (m-10) outliers start: 84 outliers final: 51 residues processed: 693 average time/residue: 0.2233 time to fit residues: 253.5794 Evaluate side-chains 572 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 517 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1102 MET Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1275 ASP Chi-restraints excluded: chain A residue 1322 SER Chi-restraints excluded: chain A residue 1365 VAL Chi-restraints excluded: chain A residue 1384 ASP Chi-restraints excluded: chain A residue 1507 TYR Chi-restraints excluded: chain A residue 1510 LEU Chi-restraints excluded: chain A residue 1554 LEU Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain A residue 1586 VAL Chi-restraints excluded: chain A residue 1678 SER Chi-restraints excluded: chain A residue 1731 TYR Chi-restraints excluded: chain A residue 1962 ASN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 471 LYS Chi-restraints excluded: chain B residue 514 ASP Chi-restraints excluded: chain B residue 543 GLN Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain E residue 960 ASN Chi-restraints excluded: chain E residue 990 LEU Chi-restraints excluded: chain E residue 1120 LEU Chi-restraints excluded: chain E residue 1178 HIS Chi-restraints excluded: chain E residue 1237 LEU Chi-restraints excluded: chain E residue 1303 VAL Chi-restraints excluded: chain E residue 1322 SER Chi-restraints excluded: chain E residue 1507 TYR Chi-restraints excluded: chain E residue 1510 LEU Chi-restraints excluded: chain E residue 1554 LEU Chi-restraints excluded: chain E residue 1558 LEU Chi-restraints excluded: chain E residue 1586 VAL Chi-restraints excluded: chain E residue 1610 LEU Chi-restraints excluded: chain E residue 1654 ILE Chi-restraints excluded: chain E residue 1704 LYS Chi-restraints excluded: chain E residue 1731 TYR Chi-restraints excluded: chain E residue 1929 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 219 GLU Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 543 GLN Chi-restraints excluded: chain F residue 590 VAL Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 760 SER Chi-restraints excluded: chain F residue 834 VAL Chi-restraints excluded: chain G residue 187 CYS Chi-restraints excluded: chain G residue 193 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 25 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 170 optimal weight: 0.5980 chunk 168 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN B 351 HIS ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN C 175 GLN ** E1178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1631 HIS ** E1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1873 GLN ** E1959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 234 ASN F 608 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.173203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.150240 restraints weight = 81552.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.149323 restraints weight = 85475.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.150733 restraints weight = 75581.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.150626 restraints weight = 47894.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.151464 restraints weight = 45067.718| |-----------------------------------------------------------------------------| r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37837 Z= 0.155 Angle : 0.656 10.466 51361 Z= 0.330 Chirality : 0.039 0.214 5945 Planarity : 0.005 0.050 6593 Dihedral : 6.719 110.777 5316 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.11 % Allowed : 11.64 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.13), residues: 3974 helix: 0.26 (0.09), residues: 2722 sheet: -1.32 (0.75), residues: 32 loop : -2.58 (0.16), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 983 TYR 0.026 0.002 TYR B 706 PHE 0.029 0.002 PHE G 74 TRP 0.049 0.002 TRP A1411 HIS 0.008 0.001 HIS G 166 Details of bonding type rmsd covalent geometry : bond 0.00349 (37837) covalent geometry : angle 0.65595 (51361) hydrogen bonds : bond 0.03904 ( 2548) hydrogen bonds : angle 4.70507 ( 7590) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 614 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1047 TYR cc_start: 0.7153 (m-10) cc_final: 0.6887 (m-10) REVERT: A 1069 MET cc_start: 0.7750 (mmt) cc_final: 0.7473 (mmm) REVERT: A 1862 LEU cc_start: 0.8209 (tp) cc_final: 0.8001 (tp) REVERT: A 1956 LYS cc_start: 0.7449 (mmtt) cc_final: 0.5881 (tttp) REVERT: A 2058 LYS cc_start: 0.7544 (ttpt) cc_final: 0.6792 (ttmt) REVERT: A 2060 ARG cc_start: 0.6190 (OUTLIER) cc_final: 0.5771 (mtp85) REVERT: B 356 LEU cc_start: 0.8103 (mt) cc_final: 0.7483 (pp) REVERT: B 471 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.6885 (ttmt) REVERT: B 755 GLU cc_start: 0.6352 (OUTLIER) cc_final: 0.5792 (tt0) REVERT: B 821 PHE cc_start: 0.6362 (m-10) cc_final: 0.5665 (m-10) REVERT: C 62 GLU cc_start: 0.6733 (tm-30) cc_final: 0.6484 (tm-30) REVERT: C 217 ARG cc_start: 0.7715 (mmt90) cc_final: 0.7284 (mmt90) REVERT: C 280 ASN cc_start: 0.6765 (t0) cc_final: 0.6468 (t0) REVERT: E 983 ARG cc_start: 0.7233 (ppt170) cc_final: 0.6685 (ptt180) REVERT: E 1307 GLU cc_start: 0.7532 (tm-30) cc_final: 0.7124 (tm-30) REVERT: E 1627 MET cc_start: 0.6445 (ptp) cc_final: 0.5604 (mmt) REVERT: E 1747 ILE cc_start: 0.7404 (pp) cc_final: 0.6990 (pt) REVERT: E 1765 LEU cc_start: 0.7533 (tt) cc_final: 0.7182 (mp) REVERT: E 1943 MET cc_start: 0.8241 (ttp) cc_final: 0.7977 (ttp) REVERT: E 1979 MET cc_start: 0.4962 (ptm) cc_final: 0.4681 (ptm) REVERT: E 2008 MET cc_start: 0.6744 (tpp) cc_final: 0.6518 (tpp) REVERT: F 126 ASP cc_start: 0.6581 (m-30) cc_final: 0.5871 (p0) REVERT: F 356 LEU cc_start: 0.8471 (mt) cc_final: 0.7834 (pp) REVERT: F 728 MET cc_start: 0.6687 (mmp) cc_final: 0.6385 (mmp) REVERT: F 822 LEU cc_start: 0.6684 (OUTLIER) cc_final: 0.6330 (mm) REVERT: G 116 LYS cc_start: 0.4358 (mppt) cc_final: 0.3877 (pttm) REVERT: G 224 LYS cc_start: 0.6820 (mttt) cc_final: 0.6117 (mppt) outliers start: 109 outliers final: 58 residues processed: 668 average time/residue: 0.2420 time to fit residues: 262.2502 Evaluate side-chains 567 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 505 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1022 SER Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1206 CYS Chi-restraints excluded: chain A residue 1222 PHE Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1252 MET Chi-restraints excluded: chain A residue 1275 ASP Chi-restraints excluded: chain A residue 1322 SER Chi-restraints excluded: chain A residue 1365 VAL Chi-restraints excluded: chain A residue 1384 ASP Chi-restraints excluded: chain A residue 1507 TYR Chi-restraints excluded: chain A residue 1510 LEU Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain A residue 1666 MET Chi-restraints excluded: chain A residue 1689 TRP Chi-restraints excluded: chain A residue 1731 TYR Chi-restraints excluded: chain A residue 2032 ASP Chi-restraints excluded: chain A residue 2060 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 471 LYS Chi-restraints excluded: chain B residue 543 GLN Chi-restraints excluded: chain B residue 573 ASP Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain E residue 990 LEU Chi-restraints excluded: chain E residue 1017 LEU Chi-restraints excluded: chain E residue 1022 SER Chi-restraints excluded: chain E residue 1237 LEU Chi-restraints excluded: chain E residue 1303 VAL Chi-restraints excluded: chain E residue 1322 SER Chi-restraints excluded: chain E residue 1365 VAL Chi-restraints excluded: chain E residue 1510 LEU Chi-restraints excluded: chain E residue 1532 TYR Chi-restraints excluded: chain E residue 1610 LEU Chi-restraints excluded: chain E residue 1654 ILE Chi-restraints excluded: chain E residue 1704 LYS Chi-restraints excluded: chain E residue 1889 THR Chi-restraints excluded: chain E residue 1898 CYS Chi-restraints excluded: chain E residue 2032 ASP Chi-restraints excluded: chain E residue 2044 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 370 THR Chi-restraints excluded: chain F residue 543 GLN Chi-restraints excluded: chain F residue 608 HIS Chi-restraints excluded: chain F residue 609 MET Chi-restraints excluded: chain F residue 822 LEU Chi-restraints excluded: chain F residue 834 VAL Chi-restraints excluded: chain G residue 187 CYS Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 269 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 97 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 159 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 27 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 167 optimal weight: 7.9990 chunk 169 optimal weight: 8.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1225 HIS A1959 HIS B 322 GLN ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1863 GLN ** E1959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1973 HIS F 340 ASN ** F 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 608 HIS ** G 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.168986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.145002 restraints weight = 79797.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.143145 restraints weight = 97384.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.144157 restraints weight = 89891.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.145010 restraints weight = 56616.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.145081 restraints weight = 53761.582| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 37837 Z= 0.161 Angle : 0.659 11.938 51361 Z= 0.328 Chirality : 0.039 0.311 5945 Planarity : 0.005 0.050 6593 Dihedral : 6.579 109.277 5315 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.31 % Allowed : 13.09 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.13), residues: 3974 helix: 0.64 (0.10), residues: 2716 sheet: -1.14 (0.80), residues: 32 loop : -2.47 (0.16), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 983 TYR 0.023 0.002 TYR G 64 PHE 0.023 0.002 PHE C 74 TRP 0.043 0.002 TRP A1411 HIS 0.010 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00368 (37837) covalent geometry : angle 0.65867 (51361) hydrogen bonds : bond 0.03824 ( 2548) hydrogen bonds : angle 4.49982 ( 7590) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 557 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1069 MET cc_start: 0.7836 (mmt) cc_final: 0.7597 (mmm) REVERT: A 1956 LYS cc_start: 0.7413 (mmtt) cc_final: 0.5936 (tttp) REVERT: A 2058 LYS cc_start: 0.7618 (ttpt) cc_final: 0.6766 (ttmt) REVERT: A 2060 ARG cc_start: 0.6260 (OUTLIER) cc_final: 0.5662 (mtp85) REVERT: B 185 LEU cc_start: 0.6702 (mm) cc_final: 0.6226 (tp) REVERT: B 356 LEU cc_start: 0.8116 (mt) cc_final: 0.7604 (pp) REVERT: B 471 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7117 (ttpt) REVERT: B 755 GLU cc_start: 0.6476 (OUTLIER) cc_final: 0.5761 (tp30) REVERT: B 821 PHE cc_start: 0.6484 (m-10) cc_final: 0.5910 (m-10) REVERT: C 62 GLU cc_start: 0.6915 (tm-30) cc_final: 0.6668 (tm-30) REVERT: C 217 ARG cc_start: 0.7786 (mmt90) cc_final: 0.7362 (mmt90) REVERT: C 280 ASN cc_start: 0.6839 (t0) cc_final: 0.6518 (t0) REVERT: E 983 ARG cc_start: 0.7281 (ppt170) cc_final: 0.6821 (ptt180) REVERT: E 1307 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7222 (tm-30) REVERT: E 1411 TRP cc_start: 0.6302 (t60) cc_final: 0.5917 (t60) REVERT: E 1554 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7257 (tp) REVERT: E 1627 MET cc_start: 0.6484 (ptp) cc_final: 0.5582 (mmt) REVERT: E 1747 ILE cc_start: 0.7422 (pp) cc_final: 0.7037 (pt) REVERT: F 126 ASP cc_start: 0.6463 (m-30) cc_final: 0.5871 (p0) REVERT: F 344 VAL cc_start: 0.8030 (OUTLIER) cc_final: 0.7737 (p) REVERT: F 356 LEU cc_start: 0.8498 (mt) cc_final: 0.7857 (pp) REVERT: F 473 TYR cc_start: 0.7092 (OUTLIER) cc_final: 0.6208 (m-10) REVERT: F 804 LEU cc_start: 0.7761 (tp) cc_final: 0.7351 (tp) REVERT: F 822 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6481 (mm) REVERT: G 116 LYS cc_start: 0.4433 (mppt) cc_final: 0.4128 (pttm) REVERT: G 224 LYS cc_start: 0.7179 (mttt) cc_final: 0.6292 (mppt) outliers start: 116 outliers final: 78 residues processed: 622 average time/residue: 0.2307 time to fit residues: 236.4205 Evaluate side-chains 596 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 511 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1022 SER Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1206 CYS Chi-restraints excluded: chain A residue 1222 PHE Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1252 MET Chi-restraints excluded: chain A residue 1275 ASP Chi-restraints excluded: chain A residue 1280 SER Chi-restraints excluded: chain A residue 1318 GLU Chi-restraints excluded: chain A residue 1322 SER Chi-restraints excluded: chain A residue 1323 LEU Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1365 VAL Chi-restraints excluded: chain A residue 1507 TYR Chi-restraints excluded: chain A residue 1510 LEU Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain A residue 1610 LEU Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1666 MET Chi-restraints excluded: chain A residue 1689 TRP Chi-restraints excluded: chain A residue 1712 LEU Chi-restraints excluded: chain A residue 1731 TYR Chi-restraints excluded: chain A residue 1787 ILE Chi-restraints excluded: chain A residue 1943 MET Chi-restraints excluded: chain A residue 2011 THR Chi-restraints excluded: chain A residue 2032 ASP Chi-restraints excluded: chain A residue 2060 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 471 LYS Chi-restraints excluded: chain B residue 573 ASP Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain E residue 990 LEU Chi-restraints excluded: chain E residue 1022 SER Chi-restraints excluded: chain E residue 1120 LEU Chi-restraints excluded: chain E residue 1237 LEU Chi-restraints excluded: chain E residue 1303 VAL Chi-restraints excluded: chain E residue 1322 SER Chi-restraints excluded: chain E residue 1339 MET Chi-restraints excluded: chain E residue 1365 VAL Chi-restraints excluded: chain E residue 1496 LEU Chi-restraints excluded: chain E residue 1507 TYR Chi-restraints excluded: chain E residue 1510 LEU Chi-restraints excluded: chain E residue 1532 TYR Chi-restraints excluded: chain E residue 1535 LEU Chi-restraints excluded: chain E residue 1554 LEU Chi-restraints excluded: chain E residue 1610 LEU Chi-restraints excluded: chain E residue 1654 ILE Chi-restraints excluded: chain E residue 1666 MET Chi-restraints excluded: chain E residue 1689 TRP Chi-restraints excluded: chain E residue 1704 LYS Chi-restraints excluded: chain E residue 1889 THR Chi-restraints excluded: chain E residue 2011 THR Chi-restraints excluded: chain E residue 2044 THR Chi-restraints excluded: chain E residue 2059 HIS Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 370 THR Chi-restraints excluded: chain F residue 473 TYR Chi-restraints excluded: chain F residue 543 GLN Chi-restraints excluded: chain F residue 608 HIS Chi-restraints excluded: chain F residue 609 MET Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 822 LEU Chi-restraints excluded: chain F residue 834 VAL Chi-restraints excluded: chain G residue 187 CYS Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 269 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 61 optimal weight: 0.0570 chunk 54 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 97 optimal weight: 0.4980 chunk 156 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1175 GLN ** A1178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1325 GLN ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1659 GLN E1694 ASN ** E1796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1863 GLN ** E1959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 608 HIS G 137 HIS ** G 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.169980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.146220 restraints weight = 79376.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.144481 restraints weight = 105935.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.145831 restraints weight = 92652.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.145998 restraints weight = 59100.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.146547 restraints weight = 55646.641| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 37837 Z= 0.134 Angle : 0.626 11.531 51361 Z= 0.313 Chirality : 0.038 0.276 5945 Planarity : 0.004 0.047 6593 Dihedral : 6.421 107.354 5315 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.11 % Allowed : 14.12 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.13), residues: 3974 helix: 0.94 (0.10), residues: 2722 sheet: -1.56 (0.82), residues: 30 loop : -2.28 (0.17), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1643 TYR 0.022 0.002 TYR B 229 PHE 0.026 0.002 PHE C 74 TRP 0.048 0.001 TRP A1411 HIS 0.009 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00305 (37837) covalent geometry : angle 0.62623 (51361) hydrogen bonds : bond 0.03546 ( 2548) hydrogen bonds : angle 4.25427 ( 7590) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 566 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1069 MET cc_start: 0.7825 (mmt) cc_final: 0.7571 (mmm) REVERT: A 1862 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7830 (mp) REVERT: A 1903 THR cc_start: 0.7324 (m) cc_final: 0.7123 (m) REVERT: A 1956 LYS cc_start: 0.7439 (mmtt) cc_final: 0.5906 (tttp) REVERT: A 2008 MET cc_start: 0.6635 (tpp) cc_final: 0.6429 (tpp) REVERT: A 2032 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7334 (t0) REVERT: A 2058 LYS cc_start: 0.7596 (ttpt) cc_final: 0.6802 (ttmt) REVERT: A 2060 ARG cc_start: 0.6085 (OUTLIER) cc_final: 0.5591 (mtp85) REVERT: B 332 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8045 (mm) REVERT: B 356 LEU cc_start: 0.8117 (mt) cc_final: 0.7600 (pp) REVERT: B 471 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7227 (ttpt) REVERT: B 755 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.5690 (tp30) REVERT: B 821 PHE cc_start: 0.6533 (m-10) cc_final: 0.6009 (m-10) REVERT: C 62 GLU cc_start: 0.7082 (tm-30) cc_final: 0.6785 (tm-30) REVERT: C 217 ARG cc_start: 0.7748 (mmt90) cc_final: 0.7444 (mmt90) REVERT: C 280 ASN cc_start: 0.6210 (t0) cc_final: 0.5773 (t0) REVERT: E 983 ARG cc_start: 0.7288 (ppt170) cc_final: 0.6732 (ptt180) REVERT: E 1307 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7207 (tm-30) REVERT: E 1411 TRP cc_start: 0.6088 (t60) cc_final: 0.5784 (t60) REVERT: E 1627 MET cc_start: 0.6524 (ptp) cc_final: 0.5477 (mmt) REVERT: E 1704 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7875 (mmmt) REVERT: E 1747 ILE cc_start: 0.7295 (pp) cc_final: 0.6976 (pt) REVERT: F 126 ASP cc_start: 0.6242 (m-30) cc_final: 0.5682 (p0) REVERT: F 216 PHE cc_start: 0.4592 (t80) cc_final: 0.4156 (t80) REVERT: F 356 LEU cc_start: 0.8512 (mt) cc_final: 0.7866 (pp) REVERT: F 473 TYR cc_start: 0.7073 (OUTLIER) cc_final: 0.6247 (m-10) REVERT: F 524 GLN cc_start: 0.7628 (tp40) cc_final: 0.7090 (tp40) REVERT: F 804 LEU cc_start: 0.7733 (tp) cc_final: 0.7329 (tp) REVERT: F 822 LEU cc_start: 0.6712 (OUTLIER) cc_final: 0.6458 (mm) REVERT: G 63 PHE cc_start: 0.6064 (OUTLIER) cc_final: 0.5742 (m-10) REVERT: G 224 LYS cc_start: 0.6991 (mttt) cc_final: 0.6150 (mppt) outliers start: 109 outliers final: 66 residues processed: 622 average time/residue: 0.2398 time to fit residues: 245.3522 Evaluate side-chains 583 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 507 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1022 SER Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1190 THR Chi-restraints excluded: chain A residue 1206 CYS Chi-restraints excluded: chain A residue 1222 PHE Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1252 MET Chi-restraints excluded: chain A residue 1322 SER Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1365 VAL Chi-restraints excluded: chain A residue 1507 TYR Chi-restraints excluded: chain A residue 1510 LEU Chi-restraints excluded: chain A residue 1554 LEU Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain A residue 1610 LEU Chi-restraints excluded: chain A residue 1623 TYR Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1666 MET Chi-restraints excluded: chain A residue 1689 TRP Chi-restraints excluded: chain A residue 1862 LEU Chi-restraints excluded: chain A residue 2011 THR Chi-restraints excluded: chain A residue 2032 ASP Chi-restraints excluded: chain A residue 2060 ARG Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 471 LYS Chi-restraints excluded: chain B residue 573 ASP Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain E residue 937 ILE Chi-restraints excluded: chain E residue 990 LEU Chi-restraints excluded: chain E residue 1017 LEU Chi-restraints excluded: chain E residue 1120 LEU Chi-restraints excluded: chain E residue 1178 HIS Chi-restraints excluded: chain E residue 1237 LEU Chi-restraints excluded: chain E residue 1322 SER Chi-restraints excluded: chain E residue 1339 MET Chi-restraints excluded: chain E residue 1365 VAL Chi-restraints excluded: chain E residue 1507 TYR Chi-restraints excluded: chain E residue 1510 LEU Chi-restraints excluded: chain E residue 1532 TYR Chi-restraints excluded: chain E residue 1535 LEU Chi-restraints excluded: chain E residue 1558 LEU Chi-restraints excluded: chain E residue 1654 ILE Chi-restraints excluded: chain E residue 1694 ASN Chi-restraints excluded: chain E residue 1704 LYS Chi-restraints excluded: chain E residue 1889 THR Chi-restraints excluded: chain E residue 1952 LEU Chi-restraints excluded: chain E residue 2011 THR Chi-restraints excluded: chain E residue 2032 ASP Chi-restraints excluded: chain E residue 2044 THR Chi-restraints excluded: chain E residue 2059 HIS Chi-restraints excluded: chain E residue 2075 MET Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 473 TYR Chi-restraints excluded: chain F residue 494 GLU Chi-restraints excluded: chain F residue 609 MET Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 822 LEU Chi-restraints excluded: chain F residue 834 VAL Chi-restraints excluded: chain G residue 63 PHE Chi-restraints excluded: chain G residue 187 CYS Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 264 ILE Chi-restraints excluded: chain G residue 269 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 129 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 137 optimal weight: 0.6980 chunk 154 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 974 ASN ** A 977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1863 GLN ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 593 GLN ** B 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1694 ASN E1796 GLN E1857 GLN E1863 GLN ** E1959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 608 HIS G 175 GLN ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.169707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.145663 restraints weight = 78291.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.144032 restraints weight = 95109.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.145250 restraints weight = 83642.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.145668 restraints weight = 55067.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.146077 restraints weight = 52434.320| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 37837 Z= 0.139 Angle : 0.623 10.970 51361 Z= 0.312 Chirality : 0.038 0.241 5945 Planarity : 0.004 0.050 6593 Dihedral : 6.322 106.305 5315 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.48 % Allowed : 14.43 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.13), residues: 3974 helix: 1.08 (0.10), residues: 2732 sheet: -1.45 (0.86), residues: 30 loop : -2.21 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E1856 TYR 0.025 0.002 TYR C 272 PHE 0.024 0.002 PHE C 74 TRP 0.048 0.001 TRP A1411 HIS 0.007 0.001 HIS G 58 Details of bonding type rmsd covalent geometry : bond 0.00315 (37837) covalent geometry : angle 0.62348 (51361) hydrogen bonds : bond 0.03458 ( 2548) hydrogen bonds : angle 4.15241 ( 7590) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 545 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1069 MET cc_start: 0.7756 (mmt) cc_final: 0.7457 (mmm) REVERT: A 1562 PHE cc_start: 0.6199 (t80) cc_final: 0.5961 (t80) REVERT: A 1862 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7889 (mp) REVERT: A 1943 MET cc_start: 0.8434 (ttp) cc_final: 0.8133 (ttp) REVERT: A 1956 LYS cc_start: 0.7364 (mmtt) cc_final: 0.5812 (tttp) REVERT: A 2032 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7477 (t0) REVERT: A 2058 LYS cc_start: 0.7594 (ttpt) cc_final: 0.6820 (ttmt) REVERT: A 2060 ARG cc_start: 0.6056 (OUTLIER) cc_final: 0.5371 (mtp85) REVERT: B 259 MET cc_start: 0.8082 (mmm) cc_final: 0.7804 (mmm) REVERT: B 344 VAL cc_start: 0.6959 (OUTLIER) cc_final: 0.6416 (p) REVERT: B 356 LEU cc_start: 0.8139 (mt) cc_final: 0.7596 (pp) REVERT: B 471 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7162 (ttpt) REVERT: B 755 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.5576 (tp30) REVERT: B 823 THR cc_start: 0.4258 (m) cc_final: 0.4019 (m) REVERT: C 62 GLU cc_start: 0.7261 (tm-30) cc_final: 0.6926 (tm-30) REVERT: C 217 ARG cc_start: 0.7752 (mmt90) cc_final: 0.7409 (mmt90) REVERT: C 224 LYS cc_start: 0.5467 (mmtm) cc_final: 0.3589 (mttm) REVERT: C 239 GLN cc_start: 0.6316 (OUTLIER) cc_final: 0.5657 (mm-40) REVERT: C 240 MET cc_start: 0.7088 (tmm) cc_final: 0.6718 (tmm) REVERT: C 280 ASN cc_start: 0.6371 (t0) cc_final: 0.5863 (t0) REVERT: E 983 ARG cc_start: 0.7274 (ppt170) cc_final: 0.6744 (ptt180) REVERT: E 1307 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7266 (tm-30) REVERT: E 1411 TRP cc_start: 0.6072 (t60) cc_final: 0.5792 (t60) REVERT: E 1554 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7193 (tp) REVERT: E 1627 MET cc_start: 0.6543 (ptp) cc_final: 0.5449 (mmt) REVERT: E 1699 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6533 (mm-30) REVERT: E 1704 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7919 (mmmt) REVERT: E 1747 ILE cc_start: 0.7321 (pp) cc_final: 0.7008 (pt) REVERT: E 2075 MET cc_start: 0.5594 (ptp) cc_final: 0.4951 (mtm) REVERT: F 122 ARG cc_start: 0.6090 (ptt90) cc_final: 0.5824 (ptt90) REVERT: F 126 ASP cc_start: 0.6243 (m-30) cc_final: 0.5705 (p0) REVERT: F 356 LEU cc_start: 0.8386 (mt) cc_final: 0.7865 (pp) REVERT: F 473 TYR cc_start: 0.7111 (OUTLIER) cc_final: 0.6272 (m-10) REVERT: F 524 GLN cc_start: 0.7620 (tp40) cc_final: 0.7067 (tp40) REVERT: F 804 LEU cc_start: 0.7780 (tp) cc_final: 0.7419 (tp) REVERT: F 822 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6630 (mm) REVERT: F 825 LEU cc_start: 0.6208 (OUTLIER) cc_final: 0.5842 (mt) REVERT: G 63 PHE cc_start: 0.6213 (OUTLIER) cc_final: 0.5777 (m-10) REVERT: G 224 LYS cc_start: 0.6985 (mttt) cc_final: 0.6199 (mppt) outliers start: 122 outliers final: 80 residues processed: 616 average time/residue: 0.2124 time to fit residues: 216.9690 Evaluate side-chains 597 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 503 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1022 SER Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1206 CYS Chi-restraints excluded: chain A residue 1222 PHE Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1252 MET Chi-restraints excluded: chain A residue 1275 ASP Chi-restraints excluded: chain A residue 1280 SER Chi-restraints excluded: chain A residue 1322 SER Chi-restraints excluded: chain A residue 1323 LEU Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1365 VAL Chi-restraints excluded: chain A residue 1384 ASP Chi-restraints excluded: chain A residue 1507 TYR Chi-restraints excluded: chain A residue 1510 LEU Chi-restraints excluded: chain A residue 1554 LEU Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain A residue 1610 LEU Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1666 MET Chi-restraints excluded: chain A residue 1689 TRP Chi-restraints excluded: chain A residue 1712 LEU Chi-restraints excluded: chain A residue 1723 LEU Chi-restraints excluded: chain A residue 1862 LEU Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 2011 THR Chi-restraints excluded: chain A residue 2032 ASP Chi-restraints excluded: chain A residue 2060 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 471 LYS Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 573 ASP Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain E residue 937 ILE Chi-restraints excluded: chain E residue 990 LEU Chi-restraints excluded: chain E residue 1017 LEU Chi-restraints excluded: chain E residue 1022 SER Chi-restraints excluded: chain E residue 1074 THR Chi-restraints excluded: chain E residue 1120 LEU Chi-restraints excluded: chain E residue 1178 HIS Chi-restraints excluded: chain E residue 1237 LEU Chi-restraints excluded: chain E residue 1303 VAL Chi-restraints excluded: chain E residue 1322 SER Chi-restraints excluded: chain E residue 1339 MET Chi-restraints excluded: chain E residue 1365 VAL Chi-restraints excluded: chain E residue 1507 TYR Chi-restraints excluded: chain E residue 1510 LEU Chi-restraints excluded: chain E residue 1532 TYR Chi-restraints excluded: chain E residue 1535 LEU Chi-restraints excluded: chain E residue 1554 LEU Chi-restraints excluded: chain E residue 1558 LEU Chi-restraints excluded: chain E residue 1610 LEU Chi-restraints excluded: chain E residue 1612 TRP Chi-restraints excluded: chain E residue 1654 ILE Chi-restraints excluded: chain E residue 1699 GLU Chi-restraints excluded: chain E residue 1704 LYS Chi-restraints excluded: chain E residue 1857 GLN Chi-restraints excluded: chain E residue 1889 THR Chi-restraints excluded: chain E residue 1952 LEU Chi-restraints excluded: chain E residue 2011 THR Chi-restraints excluded: chain E residue 2032 ASP Chi-restraints excluded: chain E residue 2044 THR Chi-restraints excluded: chain E residue 2059 HIS Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 473 TYR Chi-restraints excluded: chain F residue 494 GLU Chi-restraints excluded: chain F residue 608 HIS Chi-restraints excluded: chain F residue 609 MET Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 822 LEU Chi-restraints excluded: chain F residue 825 LEU Chi-restraints excluded: chain F residue 834 VAL Chi-restraints excluded: chain G residue 63 PHE Chi-restraints excluded: chain G residue 187 CYS Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 269 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 188 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 180 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 163 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 73 optimal weight: 0.0010 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 608 HIS ** G 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 280 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 = 0.4338 r_free = 0.4338 target = 0.169733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.145643 restraints weight = 79422.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.143800 restraints weight = 96984.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.144942 restraints weight = 86174.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.145828 restraints weight = 54081.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.145867 restraints weight = 54539.943| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 37837 Z= 0.134 Angle : 0.632 15.151 51361 Z= 0.314 Chirality : 0.039 0.250 5945 Planarity : 0.004 0.049 6593 Dihedral : 6.280 105.382 5315 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.22 % Allowed : 15.12 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.13), residues: 3974 helix: 1.21 (0.10), residues: 2720 sheet: -1.40 (0.88), residues: 30 loop : -2.13 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E1643 TYR 0.038 0.002 TYR B 145 PHE 0.024 0.002 PHE C 74 TRP 0.072 0.001 TRP A1411 HIS 0.020 0.001 HIS F 608 Details of bonding type rmsd covalent geometry : bond 0.00307 (37837) covalent geometry : angle 0.63234 (51361) hydrogen bonds : bond 0.03383 ( 2548) hydrogen bonds : angle 4.08678 ( 7590) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 526 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1069 MET cc_start: 0.7711 (mmt) cc_final: 0.7443 (mmm) REVERT: A 1330 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8144 (tt) REVERT: A 1404 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7708 (tp) REVERT: A 1562 PHE cc_start: 0.6132 (t80) cc_final: 0.5869 (t80) REVERT: A 1862 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7912 (mp) REVERT: A 1943 MET cc_start: 0.8425 (ttp) cc_final: 0.8148 (ttp) REVERT: A 1956 LYS cc_start: 0.7350 (mmtt) cc_final: 0.5841 (tttp) REVERT: A 2004 MET cc_start: 0.5704 (OUTLIER) cc_final: 0.5262 (mtt) REVERT: A 2008 MET cc_start: 0.6540 (tpp) cc_final: 0.6268 (tpp) REVERT: A 2032 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7356 (t0) REVERT: A 2058 LYS cc_start: 0.7536 (ttpt) cc_final: 0.6814 (ttmt) REVERT: A 2060 ARG cc_start: 0.5970 (OUTLIER) cc_final: 0.5265 (mtp85) REVERT: B 259 MET cc_start: 0.8094 (mmm) cc_final: 0.7834 (mmm) REVERT: B 344 VAL cc_start: 0.6992 (OUTLIER) cc_final: 0.6440 (p) REVERT: B 356 LEU cc_start: 0.8138 (mt) cc_final: 0.7618 (pp) REVERT: B 471 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7156 (ttpt) REVERT: B 755 GLU cc_start: 0.6451 (OUTLIER) cc_final: 0.5492 (tp30) REVERT: B 775 HIS cc_start: 0.8071 (OUTLIER) cc_final: 0.7717 (t70) REVERT: C 62 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6907 (tm-30) REVERT: C 224 LYS cc_start: 0.5423 (mmtm) cc_final: 0.3633 (mttm) REVERT: C 239 GLN cc_start: 0.5804 (OUTLIER) cc_final: 0.5552 (mm-40) REVERT: C 240 MET cc_start: 0.7013 (tmm) cc_final: 0.6634 (tmm) REVERT: C 280 ASN cc_start: 0.6104 (t0) cc_final: 0.5561 (t0) REVERT: E 951 MET cc_start: 0.7175 (mmp) cc_final: 0.6956 (mmp) REVERT: E 983 ARG cc_start: 0.7230 (ppt170) cc_final: 0.6706 (ptt180) REVERT: E 1051 GLU cc_start: 0.5998 (tm-30) cc_final: 0.5701 (tm-30) REVERT: E 1173 MET cc_start: 0.8366 (mmt) cc_final: 0.8101 (mmt) REVERT: E 1307 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7205 (tm-30) REVERT: E 1411 TRP cc_start: 0.6024 (t60) cc_final: 0.5781 (t60) REVERT: E 1554 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7057 (tp) REVERT: E 1627 MET cc_start: 0.6484 (ptp) cc_final: 0.5430 (mmt) REVERT: E 1704 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7910 (mmmt) REVERT: E 1747 ILE cc_start: 0.7442 (pp) cc_final: 0.7128 (pt) REVERT: E 1795 MET cc_start: 0.5343 (ttm) cc_final: 0.4916 (ttm) REVERT: E 1796 GLN cc_start: 0.5511 (mp10) cc_final: 0.5147 (mp10) REVERT: E 2009 GLU cc_start: 0.6914 (mt-10) cc_final: 0.5979 (mt-10) REVERT: F 126 ASP cc_start: 0.6332 (m-30) cc_final: 0.5714 (p0) REVERT: F 356 LEU cc_start: 0.8372 (mt) cc_final: 0.7757 (pp) REVERT: F 473 TYR cc_start: 0.7064 (OUTLIER) cc_final: 0.6216 (m-10) REVERT: F 524 GLN cc_start: 0.7603 (tp40) cc_final: 0.7113 (tp40) REVERT: F 739 ILE cc_start: 0.7148 (mt) cc_final: 0.6909 (pt) REVERT: F 804 LEU cc_start: 0.7768 (tp) cc_final: 0.7426 (tp) REVERT: F 822 LEU cc_start: 0.6757 (OUTLIER) cc_final: 0.6477 (mm) REVERT: F 825 LEU cc_start: 0.6247 (OUTLIER) cc_final: 0.5878 (mt) REVERT: G 63 PHE cc_start: 0.5871 (OUTLIER) cc_final: 0.5453 (m-10) REVERT: G 116 LYS cc_start: 0.4329 (mppt) cc_final: 0.4087 (pttm) REVERT: G 224 LYS cc_start: 0.6937 (mttt) cc_final: 0.6352 (mmtm) outliers start: 113 outliers final: 80 residues processed: 588 average time/residue: 0.2137 time to fit residues: 206.2312 Evaluate side-chains 598 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 501 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1022 SER Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1206 CYS Chi-restraints excluded: chain A residue 1222 PHE Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1252 MET Chi-restraints excluded: chain A residue 1322 SER Chi-restraints excluded: chain A residue 1323 LEU Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1365 VAL Chi-restraints excluded: chain A residue 1404 ILE Chi-restraints excluded: chain A residue 1507 TYR Chi-restraints excluded: chain A residue 1510 LEU Chi-restraints excluded: chain A residue 1554 LEU Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain A residue 1610 LEU Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1666 MET Chi-restraints excluded: chain A residue 1674 LEU Chi-restraints excluded: chain A residue 1689 TRP Chi-restraints excluded: chain A residue 1712 LEU Chi-restraints excluded: chain A residue 1862 LEU Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 2004 MET Chi-restraints excluded: chain A residue 2011 THR Chi-restraints excluded: chain A residue 2032 ASP Chi-restraints excluded: chain A residue 2041 MET Chi-restraints excluded: chain A residue 2060 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 471 LYS Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 573 ASP Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain B residue 775 HIS Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain E residue 937 ILE Chi-restraints excluded: chain E residue 990 LEU Chi-restraints excluded: chain E residue 1017 LEU Chi-restraints excluded: chain E residue 1022 SER Chi-restraints excluded: chain E residue 1074 THR Chi-restraints excluded: chain E residue 1120 LEU Chi-restraints excluded: chain E residue 1178 HIS Chi-restraints excluded: chain E residue 1222 PHE Chi-restraints excluded: chain E residue 1237 LEU Chi-restraints excluded: chain E residue 1246 VAL Chi-restraints excluded: chain E residue 1275 ASP Chi-restraints excluded: chain E residue 1322 SER Chi-restraints excluded: chain E residue 1339 MET Chi-restraints excluded: chain E residue 1365 VAL Chi-restraints excluded: chain E residue 1507 TYR Chi-restraints excluded: chain E residue 1510 LEU Chi-restraints excluded: chain E residue 1532 TYR Chi-restraints excluded: chain E residue 1535 LEU Chi-restraints excluded: chain E residue 1554 LEU Chi-restraints excluded: chain E residue 1558 LEU Chi-restraints excluded: chain E residue 1610 LEU Chi-restraints excluded: chain E residue 1612 TRP Chi-restraints excluded: chain E residue 1654 ILE Chi-restraints excluded: chain E residue 1704 LYS Chi-restraints excluded: chain E residue 1889 THR Chi-restraints excluded: chain E residue 1952 LEU Chi-restraints excluded: chain E residue 2011 THR Chi-restraints excluded: chain E residue 2032 ASP Chi-restraints excluded: chain E residue 2044 THR Chi-restraints excluded: chain E residue 2059 HIS Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 473 TYR Chi-restraints excluded: chain F residue 609 MET Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 822 LEU Chi-restraints excluded: chain F residue 825 LEU Chi-restraints excluded: chain F residue 834 VAL Chi-restraints excluded: chain G residue 63 PHE Chi-restraints excluded: chain G residue 187 CYS Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 269 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 127 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 73 optimal weight: 0.0170 chunk 70 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 123 optimal weight: 0.3980 chunk 165 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 179 optimal weight: 0.9990 chunk 184 optimal weight: 10.0000 overall best weight: 0.5420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1796 GLN ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1863 GLN ** E1959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 280 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 = 0.4348 r_free = 0.4348 target = 0.170606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.147406 restraints weight = 78902.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.145837 restraints weight = 105085.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.147060 restraints weight = 93696.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.147218 restraints weight = 59531.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.147728 restraints weight = 56236.128| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37837 Z= 0.124 Angle : 0.620 13.134 51361 Z= 0.308 Chirality : 0.038 0.217 5945 Planarity : 0.004 0.049 6593 Dihedral : 6.176 104.139 5315 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.11 % Allowed : 15.26 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.13), residues: 3974 helix: 1.35 (0.10), residues: 2728 sheet: -1.34 (0.91), residues: 30 loop : -2.14 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E1643 TYR 0.039 0.002 TYR B 145 PHE 0.025 0.002 PHE C 74 TRP 0.083 0.001 TRP A1411 HIS 0.009 0.001 HIS G 58 Details of bonding type rmsd covalent geometry : bond 0.00283 (37837) covalent geometry : angle 0.61959 (51361) hydrogen bonds : bond 0.03245 ( 2548) hydrogen bonds : angle 3.96700 ( 7590) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 547 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1069 MET cc_start: 0.7686 (mmt) cc_final: 0.7420 (mmm) REVERT: A 1330 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8179 (tt) REVERT: A 1404 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7576 (tt) REVERT: A 1562 PHE cc_start: 0.5875 (t80) cc_final: 0.5614 (t80) REVERT: A 1862 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7906 (mp) REVERT: A 1956 LYS cc_start: 0.7321 (mmtt) cc_final: 0.5852 (tttp) REVERT: A 2032 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7376 (t0) REVERT: A 2058 LYS cc_start: 0.7586 (ttpt) cc_final: 0.6861 (ttmt) REVERT: A 2060 ARG cc_start: 0.5851 (OUTLIER) cc_final: 0.5581 (mpp80) REVERT: B 259 MET cc_start: 0.8084 (mmm) cc_final: 0.7850 (mmm) REVERT: B 344 VAL cc_start: 0.7005 (OUTLIER) cc_final: 0.6573 (p) REVERT: B 356 LEU cc_start: 0.8129 (mt) cc_final: 0.7647 (pp) REVERT: B 390 MET cc_start: 0.7371 (tpt) cc_final: 0.7063 (tpt) REVERT: B 471 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7160 (ttpt) REVERT: B 591 LYS cc_start: 0.6681 (mmtm) cc_final: 0.6368 (mmtm) REVERT: B 755 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.5599 (tp30) REVERT: B 775 HIS cc_start: 0.8008 (OUTLIER) cc_final: 0.7776 (t70) REVERT: B 788 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.6896 (ptm160) REVERT: C 62 GLU cc_start: 0.7175 (tm-30) cc_final: 0.6828 (tm-30) REVERT: C 239 GLN cc_start: 0.6180 (OUTLIER) cc_final: 0.5576 (mm-40) REVERT: C 240 MET cc_start: 0.7069 (tmm) cc_final: 0.6630 (tmm) REVERT: C 280 ASN cc_start: 0.6087 (t0) cc_final: 0.5514 (t0) REVERT: E 983 ARG cc_start: 0.7217 (ppt170) cc_final: 0.6795 (ptt180) REVERT: E 1307 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7189 (tm-30) REVERT: E 1554 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7345 (tp) REVERT: E 1627 MET cc_start: 0.6409 (ptp) cc_final: 0.5395 (mmt) REVERT: E 1699 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6472 (mm-30) REVERT: E 1704 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7871 (mmmt) REVERT: E 1747 ILE cc_start: 0.7429 (pp) cc_final: 0.7110 (pt) REVERT: E 2009 GLU cc_start: 0.6972 (mt-10) cc_final: 0.6158 (mt-10) REVERT: F 115 GLU cc_start: 0.6602 (tm-30) cc_final: 0.6257 (mm-30) REVERT: F 126 ASP cc_start: 0.6319 (m-30) cc_final: 0.5833 (p0) REVERT: F 356 LEU cc_start: 0.8322 (mt) cc_final: 0.7945 (pp) REVERT: F 473 TYR cc_start: 0.7009 (OUTLIER) cc_final: 0.6158 (m-10) REVERT: F 524 GLN cc_start: 0.7573 (tp40) cc_final: 0.7245 (tp40) REVERT: F 739 ILE cc_start: 0.7129 (mt) cc_final: 0.6924 (pt) REVERT: F 804 LEU cc_start: 0.7749 (tp) cc_final: 0.7423 (tp) REVERT: F 822 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.6554 (mm) REVERT: F 825 LEU cc_start: 0.6277 (OUTLIER) cc_final: 0.5899 (mt) REVERT: G 63 PHE cc_start: 0.5841 (OUTLIER) cc_final: 0.5543 (m-10) REVERT: G 112 GLU cc_start: 0.6297 (tp30) cc_final: 0.5887 (tp30) REVERT: G 224 LYS cc_start: 0.6738 (mttt) cc_final: 0.6214 (mmtm) outliers start: 109 outliers final: 75 residues processed: 606 average time/residue: 0.2192 time to fit residues: 219.0745 Evaluate side-chains 600 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 507 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1022 SER Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1055 LYS Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1140 MET Chi-restraints excluded: chain A residue 1206 CYS Chi-restraints excluded: chain A residue 1222 PHE Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1252 MET Chi-restraints excluded: chain A residue 1322 SER Chi-restraints excluded: chain A residue 1323 LEU Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1365 VAL Chi-restraints excluded: chain A residue 1404 ILE Chi-restraints excluded: chain A residue 1510 LEU Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain A residue 1610 LEU Chi-restraints excluded: chain A residue 1623 TYR Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1674 LEU Chi-restraints excluded: chain A residue 1689 TRP Chi-restraints excluded: chain A residue 1862 LEU Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 2011 THR Chi-restraints excluded: chain A residue 2032 ASP Chi-restraints excluded: chain A residue 2060 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 471 LYS Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 573 ASP Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain B residue 775 HIS Chi-restraints excluded: chain B residue 788 ARG Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain E residue 990 LEU Chi-restraints excluded: chain E residue 1017 LEU Chi-restraints excluded: chain E residue 1022 SER Chi-restraints excluded: chain E residue 1074 THR Chi-restraints excluded: chain E residue 1120 LEU Chi-restraints excluded: chain E residue 1178 HIS Chi-restraints excluded: chain E residue 1222 PHE Chi-restraints excluded: chain E residue 1237 LEU Chi-restraints excluded: chain E residue 1246 VAL Chi-restraints excluded: chain E residue 1322 SER Chi-restraints excluded: chain E residue 1339 MET Chi-restraints excluded: chain E residue 1365 VAL Chi-restraints excluded: chain E residue 1507 TYR Chi-restraints excluded: chain E residue 1510 LEU Chi-restraints excluded: chain E residue 1532 TYR Chi-restraints excluded: chain E residue 1535 LEU Chi-restraints excluded: chain E residue 1554 LEU Chi-restraints excluded: chain E residue 1558 LEU Chi-restraints excluded: chain E residue 1610 LEU Chi-restraints excluded: chain E residue 1612 TRP Chi-restraints excluded: chain E residue 1654 ILE Chi-restraints excluded: chain E residue 1699 GLU Chi-restraints excluded: chain E residue 1704 LYS Chi-restraints excluded: chain E residue 1948 LEU Chi-restraints excluded: chain E residue 1952 LEU Chi-restraints excluded: chain E residue 2011 THR Chi-restraints excluded: chain E residue 2032 ASP Chi-restraints excluded: chain E residue 2041 MET Chi-restraints excluded: chain E residue 2044 THR Chi-restraints excluded: chain E residue 2059 HIS Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 473 TYR Chi-restraints excluded: chain F residue 609 MET Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 822 LEU Chi-restraints excluded: chain F residue 825 LEU Chi-restraints excluded: chain F residue 834 VAL Chi-restraints excluded: chain G residue 63 PHE Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 187 CYS Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 269 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 57 optimal weight: 8.9990 chunk 167 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 188 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 193 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 151 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1175 GLN ** A1178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1527 ASN ** A1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1933 GLN B 170 GLN ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 GLN F 378 GLN ** F 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 497 GLN ** F 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.166658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.142517 restraints weight = 79658.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.140580 restraints weight = 100890.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.141635 restraints weight = 90108.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.142343 restraints weight = 57461.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.142392 restraints weight = 56790.900| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.5345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 37837 Z= 0.207 Angle : 0.704 14.425 51361 Z= 0.351 Chirality : 0.042 0.324 5945 Planarity : 0.005 0.050 6593 Dihedral : 6.351 106.459 5315 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.31 % Allowed : 15.40 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.13), residues: 3974 helix: 1.15 (0.10), residues: 2712 sheet: -1.34 (0.91), residues: 30 loop : -2.14 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E1643 TYR 0.050 0.002 TYR C 272 PHE 0.023 0.002 PHE C 74 TRP 0.066 0.002 TRP A1411 HIS 0.011 0.001 HIS F 608 Details of bonding type rmsd covalent geometry : bond 0.00483 (37837) covalent geometry : angle 0.70381 (51361) hydrogen bonds : bond 0.03707 ( 2548) hydrogen bonds : angle 4.24128 ( 7590) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 494 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1069 MET cc_start: 0.7751 (mmt) cc_final: 0.7475 (mmm) REVERT: A 1330 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8064 (tt) REVERT: A 1562 PHE cc_start: 0.6234 (t80) cc_final: 0.5934 (t80) REVERT: A 1862 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8034 (mp) REVERT: A 1956 LYS cc_start: 0.7528 (mmtt) cc_final: 0.5907 (tttp) REVERT: A 2004 MET cc_start: 0.5848 (OUTLIER) cc_final: 0.5351 (mtt) REVERT: A 2032 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7256 (t0) REVERT: A 2058 LYS cc_start: 0.7595 (ttpt) cc_final: 0.6854 (ttmt) REVERT: A 2060 ARG cc_start: 0.5937 (OUTLIER) cc_final: 0.5012 (mtp85) REVERT: B 259 MET cc_start: 0.8144 (mmm) cc_final: 0.7863 (mmm) REVERT: B 344 VAL cc_start: 0.7185 (OUTLIER) cc_final: 0.6680 (p) REVERT: B 356 LEU cc_start: 0.8261 (mt) cc_final: 0.7798 (pp) REVERT: B 390 MET cc_start: 0.7551 (tpt) cc_final: 0.7307 (tpt) REVERT: B 471 LYS cc_start: 0.7638 (OUTLIER) cc_final: 0.7165 (ttpt) REVERT: B 609 MET cc_start: 0.7357 (mmt) cc_final: 0.7132 (mmt) REVERT: B 755 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.5693 (tp30) REVERT: B 775 HIS cc_start: 0.8086 (OUTLIER) cc_final: 0.7790 (t70) REVERT: B 822 LEU cc_start: 0.6678 (OUTLIER) cc_final: 0.6233 (mm) REVERT: B 823 THR cc_start: 0.4268 (OUTLIER) cc_final: 0.3998 (m) REVERT: C 62 GLU cc_start: 0.7178 (tm-30) cc_final: 0.6824 (tm-30) REVERT: C 224 LYS cc_start: 0.5857 (mmtm) cc_final: 0.4110 (mttm) REVERT: C 240 MET cc_start: 0.7024 (tmm) cc_final: 0.6586 (tmm) REVERT: C 280 ASN cc_start: 0.5888 (t0) cc_final: 0.5342 (t0) REVERT: E 983 ARG cc_start: 0.7240 (ppt170) cc_final: 0.6965 (ptt180) REVERT: E 1051 GLU cc_start: 0.6333 (tm-30) cc_final: 0.5994 (tm-30) REVERT: E 1307 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7240 (tm-30) REVERT: E 1538 LYS cc_start: 0.5991 (tptp) cc_final: 0.5651 (tptp) REVERT: E 1554 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7315 (tp) REVERT: E 1627 MET cc_start: 0.6601 (ptp) cc_final: 0.5666 (mmt) REVERT: E 1699 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6459 (mm-30) REVERT: E 1747 ILE cc_start: 0.7484 (pp) cc_final: 0.7179 (pt) REVERT: E 2009 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6580 (mt-10) REVERT: F 126 ASP cc_start: 0.6442 (m-30) cc_final: 0.5846 (p0) REVERT: F 356 LEU cc_start: 0.8498 (mt) cc_final: 0.7938 (pp) REVERT: F 473 TYR cc_start: 0.7111 (OUTLIER) cc_final: 0.6183 (m-80) REVERT: F 524 GLN cc_start: 0.7577 (tp40) cc_final: 0.7307 (tp40) REVERT: F 535 LEU cc_start: 0.7731 (tt) cc_final: 0.7223 (tp) REVERT: F 804 LEU cc_start: 0.7759 (tp) cc_final: 0.7465 (tp) REVERT: F 822 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6727 (mm) REVERT: G 63 PHE cc_start: 0.5908 (OUTLIER) cc_final: 0.5599 (m-10) REVERT: G 112 GLU cc_start: 0.6083 (tp30) cc_final: 0.5811 (tp30) REVERT: G 116 LYS cc_start: 0.3747 (pttm) cc_final: 0.3202 (pttp) REVERT: G 224 LYS cc_start: 0.6803 (mttt) cc_final: 0.6252 (mmtm) outliers start: 116 outliers final: 86 residues processed: 557 average time/residue: 0.2408 time to fit residues: 221.2451 Evaluate side-chains 583 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 481 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1140 MET Chi-restraints excluded: chain A residue 1206 CYS Chi-restraints excluded: chain A residue 1222 PHE Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1252 MET Chi-restraints excluded: chain A residue 1275 ASP Chi-restraints excluded: chain A residue 1318 GLU Chi-restraints excluded: chain A residue 1322 SER Chi-restraints excluded: chain A residue 1323 LEU Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1365 VAL Chi-restraints excluded: chain A residue 1510 LEU Chi-restraints excluded: chain A residue 1554 LEU Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain A residue 1590 ILE Chi-restraints excluded: chain A residue 1610 LEU Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1689 TRP Chi-restraints excluded: chain A residue 1712 LEU Chi-restraints excluded: chain A residue 1862 LEU Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 2004 MET Chi-restraints excluded: chain A residue 2011 THR Chi-restraints excluded: chain A residue 2032 ASP Chi-restraints excluded: chain A residue 2041 MET Chi-restraints excluded: chain A residue 2060 ARG Chi-restraints excluded: chain A residue 2065 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 471 LYS Chi-restraints excluded: chain B residue 573 ASP Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain B residue 775 HIS Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain E residue 936 VAL Chi-restraints excluded: chain E residue 937 ILE Chi-restraints excluded: chain E residue 990 LEU Chi-restraints excluded: chain E residue 1017 LEU Chi-restraints excluded: chain E residue 1022 SER Chi-restraints excluded: chain E residue 1074 THR Chi-restraints excluded: chain E residue 1120 LEU Chi-restraints excluded: chain E residue 1140 MET Chi-restraints excluded: chain E residue 1178 HIS Chi-restraints excluded: chain E residue 1222 PHE Chi-restraints excluded: chain E residue 1237 LEU Chi-restraints excluded: chain E residue 1246 VAL Chi-restraints excluded: chain E residue 1275 ASP Chi-restraints excluded: chain E residue 1303 VAL Chi-restraints excluded: chain E residue 1322 SER Chi-restraints excluded: chain E residue 1339 MET Chi-restraints excluded: chain E residue 1365 VAL Chi-restraints excluded: chain E residue 1507 TYR Chi-restraints excluded: chain E residue 1532 TYR Chi-restraints excluded: chain E residue 1535 LEU Chi-restraints excluded: chain E residue 1554 LEU Chi-restraints excluded: chain E residue 1558 LEU Chi-restraints excluded: chain E residue 1610 LEU Chi-restraints excluded: chain E residue 1612 TRP Chi-restraints excluded: chain E residue 1654 ILE Chi-restraints excluded: chain E residue 1699 GLU Chi-restraints excluded: chain E residue 1889 THR Chi-restraints excluded: chain E residue 1929 THR Chi-restraints excluded: chain E residue 1948 LEU Chi-restraints excluded: chain E residue 1952 LEU Chi-restraints excluded: chain E residue 2011 THR Chi-restraints excluded: chain E residue 2032 ASP Chi-restraints excluded: chain E residue 2044 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 473 TYR Chi-restraints excluded: chain F residue 609 MET Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 822 LEU Chi-restraints excluded: chain F residue 825 LEU Chi-restraints excluded: chain F residue 834 VAL Chi-restraints excluded: chain G residue 63 PHE Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 187 CYS Chi-restraints excluded: chain G residue 263 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 108 optimal weight: 6.9990 chunk 171 optimal weight: 0.0370 chunk 151 optimal weight: 0.8980 chunk 170 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1659 GLN A1694 ASN A1771 GLN ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 GLN ** F 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 608 HIS ** G 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.169119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.145865 restraints weight = 79273.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.144309 restraints weight = 101180.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.145571 restraints weight = 92963.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.145599 restraints weight = 59448.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.146485 restraints weight = 55086.969| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.5512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 37837 Z= 0.136 Angle : 0.650 13.715 51361 Z= 0.323 Chirality : 0.039 0.366 5945 Planarity : 0.004 0.055 6593 Dihedral : 6.232 103.496 5315 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.77 % Allowed : 16.00 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.13), residues: 3974 helix: 1.31 (0.10), residues: 2732 sheet: -1.28 (0.91), residues: 30 loop : -2.15 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E1643 TYR 0.039 0.002 TYR B 145 PHE 0.025 0.002 PHE C 61 TRP 0.060 0.002 TRP E1411 HIS 0.012 0.001 HIS F 608 Details of bonding type rmsd covalent geometry : bond 0.00314 (37837) covalent geometry : angle 0.65049 (51361) hydrogen bonds : bond 0.03365 ( 2548) hydrogen bonds : angle 4.02460 ( 7590) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7948 Ramachandran restraints generated. 3974 Oldfield, 0 Emsley, 3974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 509 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1069 MET cc_start: 0.7694 (mmt) cc_final: 0.7407 (mmm) REVERT: A 1330 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8055 (tt) REVERT: A 1562 PHE cc_start: 0.5623 (t80) cc_final: 0.5337 (t80) REVERT: A 1862 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7958 (mp) REVERT: A 1956 LYS cc_start: 0.7262 (mmtt) cc_final: 0.5773 (tttp) REVERT: A 2004 MET cc_start: 0.5557 (OUTLIER) cc_final: 0.5135 (mtt) REVERT: A 2032 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7303 (t0) REVERT: A 2058 LYS cc_start: 0.7592 (ttpt) cc_final: 0.6810 (ttmt) REVERT: A 2060 ARG cc_start: 0.5949 (OUTLIER) cc_final: 0.5660 (mpp80) REVERT: B 259 MET cc_start: 0.8121 (mmm) cc_final: 0.7875 (mmm) REVERT: B 344 VAL cc_start: 0.7149 (OUTLIER) cc_final: 0.6694 (p) REVERT: B 356 LEU cc_start: 0.8270 (mt) cc_final: 0.7737 (pp) REVERT: B 390 MET cc_start: 0.7493 (tpt) cc_final: 0.7273 (tpt) REVERT: B 471 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7134 (ttpt) REVERT: B 755 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.5692 (tp30) REVERT: B 775 HIS cc_start: 0.8077 (OUTLIER) cc_final: 0.7782 (t70) REVERT: B 822 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6307 (mm) REVERT: C 62 GLU cc_start: 0.7159 (tm-30) cc_final: 0.6804 (tm-30) REVERT: C 116 LYS cc_start: 0.3630 (pttm) cc_final: 0.3284 (pttp) REVERT: C 224 LYS cc_start: 0.5662 (mmtm) cc_final: 0.4112 (mmtm) REVERT: C 240 MET cc_start: 0.7231 (tmm) cc_final: 0.6783 (tmm) REVERT: C 280 ASN cc_start: 0.5873 (t0) cc_final: 0.5320 (t0) REVERT: E 1307 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7276 (tm-30) REVERT: E 1538 LYS cc_start: 0.5809 (tptp) cc_final: 0.5573 (tptp) REVERT: E 1554 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7200 (tp) REVERT: E 1627 MET cc_start: 0.6444 (ptp) cc_final: 0.5499 (mmt) REVERT: E 1643 ARG cc_start: 0.8027 (ttm110) cc_final: 0.7775 (mtp-110) REVERT: E 1699 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6495 (mm-30) REVERT: E 1747 ILE cc_start: 0.7405 (pp) cc_final: 0.7097 (pt) REVERT: E 2009 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6527 (mt-10) REVERT: F 115 GLU cc_start: 0.6908 (tm-30) cc_final: 0.6396 (mm-30) REVERT: F 126 ASP cc_start: 0.6351 (m-30) cc_final: 0.5838 (p0) REVERT: F 356 LEU cc_start: 0.8355 (mt) cc_final: 0.7959 (pp) REVERT: F 473 TYR cc_start: 0.7064 (OUTLIER) cc_final: 0.6144 (m-80) REVERT: F 535 LEU cc_start: 0.7490 (tt) cc_final: 0.7019 (tp) REVERT: F 804 LEU cc_start: 0.7699 (tp) cc_final: 0.7363 (tp) REVERT: G 116 LYS cc_start: 0.3189 (pttm) cc_final: 0.2703 (pttp) REVERT: G 224 LYS cc_start: 0.6715 (mttt) cc_final: 0.6172 (mmtm) outliers start: 97 outliers final: 73 residues processed: 563 average time/residue: 0.2283 time to fit residues: 212.1927 Evaluate side-chains 572 residues out of total 3506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 486 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1140 MET Chi-restraints excluded: chain A residue 1206 CYS Chi-restraints excluded: chain A residue 1222 PHE Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1252 MET Chi-restraints excluded: chain A residue 1275 ASP Chi-restraints excluded: chain A residue 1322 SER Chi-restraints excluded: chain A residue 1323 LEU Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1365 VAL Chi-restraints excluded: chain A residue 1510 LEU Chi-restraints excluded: chain A residue 1558 LEU Chi-restraints excluded: chain A residue 1590 ILE Chi-restraints excluded: chain A residue 1610 LEU Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1689 TRP Chi-restraints excluded: chain A residue 1694 ASN Chi-restraints excluded: chain A residue 1862 LEU Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 2004 MET Chi-restraints excluded: chain A residue 2011 THR Chi-restraints excluded: chain A residue 2032 ASP Chi-restraints excluded: chain A residue 2041 MET Chi-restraints excluded: chain A residue 2060 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 471 LYS Chi-restraints excluded: chain B residue 573 ASP Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain B residue 775 HIS Chi-restraints excluded: chain B residue 784 GLU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain E residue 1017 LEU Chi-restraints excluded: chain E residue 1022 SER Chi-restraints excluded: chain E residue 1074 THR Chi-restraints excluded: chain E residue 1120 LEU Chi-restraints excluded: chain E residue 1222 PHE Chi-restraints excluded: chain E residue 1237 LEU Chi-restraints excluded: chain E residue 1246 VAL Chi-restraints excluded: chain E residue 1275 ASP Chi-restraints excluded: chain E residue 1322 SER Chi-restraints excluded: chain E residue 1339 MET Chi-restraints excluded: chain E residue 1365 VAL Chi-restraints excluded: chain E residue 1507 TYR Chi-restraints excluded: chain E residue 1532 TYR Chi-restraints excluded: chain E residue 1535 LEU Chi-restraints excluded: chain E residue 1554 LEU Chi-restraints excluded: chain E residue 1558 LEU Chi-restraints excluded: chain E residue 1610 LEU Chi-restraints excluded: chain E residue 1612 TRP Chi-restraints excluded: chain E residue 1654 ILE Chi-restraints excluded: chain E residue 1699 GLU Chi-restraints excluded: chain E residue 1948 LEU Chi-restraints excluded: chain E residue 1952 LEU Chi-restraints excluded: chain E residue 2011 THR Chi-restraints excluded: chain E residue 2032 ASP Chi-restraints excluded: chain E residue 2041 MET Chi-restraints excluded: chain E residue 2044 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 473 TYR Chi-restraints excluded: chain F residue 608 HIS Chi-restraints excluded: chain F residue 609 MET Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 825 LEU Chi-restraints excluded: chain F residue 834 VAL Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 187 CYS Chi-restraints excluded: chain G residue 263 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 92 optimal weight: 0.0040 chunk 78 optimal weight: 0.1980 chunk 130 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 63 optimal weight: 0.4980 chunk 166 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 182 optimal weight: 8.9990 chunk 148 optimal weight: 0.7980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 HIS ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 HIS ** F 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 GLN F 398 HIS ** F 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 608 HIS ** G 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.170284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.146745 restraints weight = 79287.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.145213 restraints weight = 98606.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.146637 restraints weight = 87452.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.146587 restraints weight = 55217.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.147527 restraints weight = 51845.966| |-----------------------------------------------------------------------------| r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.5625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37837 Z= 0.126 Angle : 0.648 13.455 51361 Z= 0.320 Chirality : 0.039 0.342 5945 Planarity : 0.004 0.060 6593 Dihedral : 6.137 102.834 5315 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.54 % Allowed : 16.46 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.13), residues: 3974 helix: 1.40 (0.10), residues: 2734 sheet: -1.29 (0.89), residues: 30 loop : -2.09 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E1643 TYR 0.041 0.002 TYR F 145 PHE 0.025 0.002 PHE C 61 TRP 0.058 0.002 TRP A1411 HIS 0.022 0.001 HIS F 608 Details of bonding type rmsd covalent geometry : bond 0.00288 (37837) covalent geometry : angle 0.64758 (51361) hydrogen bonds : bond 0.03271 ( 2548) hydrogen bonds : angle 3.96660 ( 7590) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6550.44 seconds wall clock time: 114 minutes 1.80 seconds (6841.80 seconds total)