Starting phenix.real_space_refine on Sun Jul 5 12:25:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7bc4_12138/07_2026/7bc4_12138.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bc4_12138/07_2026/7bc4_12138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7bc4_12138/07_2026/7bc4_12138.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7bc4_12138/07_2026/7bc4_12138.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bc4_12138/07_2026/7bc4_12138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bc4_12138/07_2026/7bc4_12138.map" model { file = "/net/cci-nas-00/data/ceres_data/7bc4_12138/07_2026/7bc4_12138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bc4_12138/07_2026/7bc4_12138.cif" } resolution = 3.1 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= 0.014 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 P 1 5.49 5 S 95 5.16 5 C 17595 2.51 5 N 4640 2.21 5 O 5279 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 243 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27610 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 11486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1460, 11486 Classifications: {'peptide': 1460} Link IDs: {'PTRANS': 61, 'TRANS': 1398} Chain breaks: 2 Chain: "B" Number of atoms: 16093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2054, 16093 Classifications: {'peptide': 2054} Link IDs: {'PTRANS': 102, 'TRANS': 1951} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.08, per 1000 atoms: 0.22 Number of scatterers: 27610 At special positions: 0 Unit cell: (204.48, 129.93, 178.92, 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 95 16.00 P 1 15.00 O 5279 8.00 N 4640 7.00 C 17595 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 1.2 seconds 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6524 Finding SS restraints... Secondary structure from input PDB file: 155 helices and 31 sheets defined 44.9% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 2 through 20 removed outlier: 4.218A pdb=" N GLN A 7 " --> pdb=" O PRO A 3 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLU A 8 " --> pdb=" O GLU A 4 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 33 Processing helix chain 'A' and resid 54 through 62 removed outlier: 3.697A pdb=" N SER A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 84 through 89 removed outlier: 3.585A pdb=" N TYR A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 326 removed outlier: 3.792A pdb=" N LEU A 326 " --> pdb=" O PHE A 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 323 through 326' Processing helix chain 'A' and resid 327 through 346 removed outlier: 3.755A pdb=" N ARG A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 340 " --> pdb=" O GLN A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 357 removed outlier: 3.847A pdb=" N VAL A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 377 removed outlier: 3.712A pdb=" N LEU A 372 " --> pdb=" O GLN A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 385 Processing helix chain 'A' and resid 399 through 417 removed outlier: 3.539A pdb=" N TRP A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG A 405 " --> pdb=" O TRP A 401 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 416 " --> pdb=" O TYR A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 437 removed outlier: 3.740A pdb=" N VAL A 428 " --> pdb=" O ASP A 424 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN A 433 " --> pdb=" O SER A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 452 removed outlier: 3.541A pdb=" N ILE A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS A 449 " --> pdb=" O PHE A 445 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 450 " --> pdb=" O MET A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 457 Processing helix chain 'A' and resid 458 through 478 removed outlier: 3.706A pdb=" N GLN A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 527 removed outlier: 3.767A pdb=" N GLY A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 657 removed outlier: 3.580A pdb=" N LEU A 646 " --> pdb=" O ASP A 642 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 688 removed outlier: 3.503A pdb=" N GLN A 682 " --> pdb=" O ALA A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 714 Processing helix chain 'A' and resid 729 through 742 removed outlier: 3.565A pdb=" N VAL A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE A 737 " --> pdb=" O VAL A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 784 Processing helix chain 'A' and resid 784 through 801 removed outlier: 3.524A pdb=" N ARG A 801 " --> pdb=" O GLN A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 832 Processing helix chain 'A' and resid 833 through 835 No H-bonds generated for 'chain 'A' and resid 833 through 835' Processing helix chain 'A' and resid 836 through 844 removed outlier: 4.638A pdb=" N TYR A 842 " --> pdb=" O PHE A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 872 removed outlier: 4.149A pdb=" N ILE A 872 " --> pdb=" O GLY A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 877 Processing helix chain 'A' and resid 878 through 880 No H-bonds generated for 'chain 'A' and resid 878 through 880' Processing helix chain 'A' and resid 885 through 895 Processing helix chain 'A' and resid 896 through 898 No H-bonds generated for 'chain 'A' and resid 896 through 898' Processing helix chain 'A' and resid 917 through 921 removed outlier: 3.645A pdb=" N ILE A 921 " --> pdb=" O LEU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 957 removed outlier: 3.552A pdb=" N THR A 938 " --> pdb=" O GLU A 934 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG A 943 " --> pdb=" O SER A 939 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL A 945 " --> pdb=" O VAL A 941 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 953 " --> pdb=" O THR A 949 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG A 954 " --> pdb=" O GLY A 950 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 956 " --> pdb=" O GLU A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 962 removed outlier: 3.810A pdb=" N ALA A 961 " --> pdb=" O GLY A 958 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP A 962 " --> pdb=" O GLU A 959 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 958 through 962' Processing helix chain 'A' and resid 985 through 993 Processing helix chain 'A' and resid 1001 through 1004 Processing helix chain 'A' and resid 1023 through 1028 Processing helix chain 'A' and resid 1033 through 1044 Processing helix chain 'A' and resid 1072 through 1074 No H-bonds generated for 'chain 'A' and resid 1072 through 1074' Processing helix chain 'A' and resid 1075 through 1080 Processing helix chain 'A' and resid 1080 through 1087 Processing helix chain 'A' and resid 1094 through 1098 Processing helix chain 'A' and resid 1124 through 1135 Processing helix chain 'A' and resid 1181 through 1186 Processing helix chain 'A' and resid 1188 through 1193 Processing helix chain 'A' and resid 1196 through 1212 removed outlier: 3.611A pdb=" N LEU A1200 " --> pdb=" O ASP A1196 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR A1201 " --> pdb=" O PRO A1197 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A1208 " --> pdb=" O VAL A1204 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1224 Processing helix chain 'A' and resid 1240 through 1249 removed outlier: 3.714A pdb=" N GLY A1246 " --> pdb=" O SER A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1268 No H-bonds generated for 'chain 'A' and resid 1266 through 1268' Processing helix chain 'A' and resid 1269 through 1278 removed outlier: 3.588A pdb=" N ASN A1275 " --> pdb=" O SER A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1295 through 1308 Processing helix chain 'A' and resid 1323 through 1333 removed outlier: 3.511A pdb=" N ALA A1331 " --> pdb=" O SER A1327 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1345 Processing helix chain 'A' and resid 1348 through 1352 Processing helix chain 'A' and resid 1377 through 1384 Processing helix chain 'A' and resid 1410 through 1416 removed outlier: 3.569A pdb=" N LEU A1413 " --> pdb=" O LYS A1410 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A1414 " --> pdb=" O GLY A1411 " (cutoff:3.500A) Processing helix chain 'A' and resid 1427 through 1430 Processing helix chain 'A' and resid 1431 through 1462 removed outlier: 3.620A pdb=" N ARG A1435 " --> pdb=" O ASP A1431 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN A1445 " --> pdb=" O LYS A1441 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS A1447 " --> pdb=" O LYS A1443 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU A1451 " --> pdb=" O LYS A1447 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU A1455 " --> pdb=" O GLU A1451 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR A1456 " --> pdb=" O ASP A1452 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1480 removed outlier: 3.809A pdb=" N GLU A1479 " --> pdb=" O SER A1475 " (cutoff:3.500A) Processing helix chain 'A' and resid 1481 through 1499 removed outlier: 3.727A pdb=" N GLN A1497 " --> pdb=" O LYS A1493 " (cutoff:3.500A) Processing helix chain 'A' and resid 1511 through 1519 removed outlier: 3.898A pdb=" N LEU A1517 " --> pdb=" O LEU A1513 " (cutoff:3.500A) Processing helix chain 'A' and resid 1523 through 1527 Processing helix chain 'A' and resid 1537 through 1555 removed outlier: 4.043A pdb=" N LYS A1542 " --> pdb=" O LYS A1538 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A1545 " --> pdb=" O ASP A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1567 through 1571 removed outlier: 3.648A pdb=" N TYR A1570 " --> pdb=" O PHE A1567 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1594 removed outlier: 3.561A pdb=" N LEU A1591 " --> pdb=" O ALA A1587 " (cutoff:3.500A) Processing helix chain 'A' and resid 1606 through 1611 removed outlier: 3.585A pdb=" N GLU A1610 " --> pdb=" O LYS A1607 " (cutoff:3.500A) Processing helix chain 'A' and resid 1649 through 1654 removed outlier: 3.589A pdb=" N PHE A1653 " --> pdb=" O PRO A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1657 through 1686 removed outlier: 3.503A pdb=" N LYS A1667 " --> pdb=" O GLU A1663 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A1673 " --> pdb=" O GLU A1669 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A1674 " --> pdb=" O ALA A1670 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE A1684 " --> pdb=" O HIS A1680 " (cutoff:3.500A) Processing helix chain 'A' and resid 1698 through 1700 No H-bonds generated for 'chain 'A' and resid 1698 through 1700' Processing helix chain 'A' and resid 1701 through 1707 Processing helix chain 'A' and resid 1726 through 1730 Processing helix chain 'B' and resid 30 through 44 removed outlier: 4.526A pdb=" N GLY B 39 " --> pdb=" O THR B 35 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS B 42 " --> pdb=" O GLU B 38 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 44 " --> pdb=" O PHE B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 74 removed outlier: 3.578A pdb=" N LEU B 63 " --> pdb=" O SER B 59 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 64 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B 66 " --> pdb=" O GLU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 97 removed outlier: 3.591A pdb=" N ALA B 84 " --> pdb=" O GLN B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 112 removed outlier: 3.653A pdb=" N ILE B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 127 through 138 removed outlier: 3.639A pdb=" N TYR B 132 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL B 138 " --> pdb=" O GLY B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 159 Processing helix chain 'B' and resid 177 through 188 removed outlier: 3.643A pdb=" N LEU B 181 " --> pdb=" O TYR B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 207 removed outlier: 4.164A pdb=" N GLU B 205 " --> pdb=" O LEU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 229 removed outlier: 3.535A pdb=" N GLU B 228 " --> pdb=" O ILE B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 244 Processing helix chain 'B' and resid 245 through 264 removed outlier: 3.623A pdb=" N CYS B 250 " --> pdb=" O CYS B 246 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 264 " --> pdb=" O THR B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 273 removed outlier: 3.862A pdb=" N ASP B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 294 removed outlier: 3.545A pdb=" N VAL B 290 " --> pdb=" O VAL B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 321 removed outlier: 3.854A pdb=" N GLU B 301 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 338 removed outlier: 3.602A pdb=" N ASP B 334 " --> pdb=" O SER B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 366 removed outlier: 3.534A pdb=" N VAL B 361 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 364 " --> pdb=" O PHE B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 403 removed outlier: 3.786A pdb=" N LEU B 397 " --> pdb=" O SER B 393 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 452 Processing helix chain 'B' and resid 482 through 493 removed outlier: 3.643A pdb=" N GLU B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 502 Processing helix chain 'B' and resid 519 through 524 Processing helix chain 'B' and resid 525 through 529 removed outlier: 3.868A pdb=" N GLU B 529 " --> pdb=" O ARG B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 556 Processing helix chain 'B' and resid 560 through 564 removed outlier: 3.656A pdb=" N ALA B 563 " --> pdb=" O ASN B 560 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE B 564 " --> pdb=" O GLU B 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 560 through 564' Processing helix chain 'B' and resid 569 through 574 Processing helix chain 'B' and resid 590 through 597 removed outlier: 3.629A pdb=" N LEU B 595 " --> pdb=" O LYS B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 622 removed outlier: 3.626A pdb=" N ALA B 618 " --> pdb=" O ASP B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 649 removed outlier: 4.091A pdb=" N GLN B 649 " --> pdb=" O ARG B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 682 removed outlier: 3.865A pdb=" N LEU B 668 " --> pdb=" O ASN B 664 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TRP B 670 " --> pdb=" O ARG B 666 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Proline residue: B 673 - end of helix removed outlier: 3.627A pdb=" N GLN B 681 " --> pdb=" O GLU B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 705 removed outlier: 3.822A pdb=" N GLU B 702 " --> pdb=" O GLU B 698 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR B 703 " --> pdb=" O VAL B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 730 removed outlier: 3.568A pdb=" N ASN B 723 " --> pdb=" O ILE B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 769 removed outlier: 3.561A pdb=" N GLN B 761 " --> pdb=" O GLN B 757 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N SER B 764 " --> pdb=" O LEU B 760 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LYS B 765 " --> pdb=" O GLN B 761 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS B 768 " --> pdb=" O SER B 764 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N CYS B 769 " --> pdb=" O LYS B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 792 Proline residue: B 788 - end of helix Processing helix chain 'B' and resid 794 through 799 removed outlier: 4.110A pdb=" N GLN B 797 " --> pdb=" O TRP B 794 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 799 " --> pdb=" O HIS B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 832 removed outlier: 3.576A pdb=" N GLN B 828 " --> pdb=" O PRO B 824 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 829 " --> pdb=" O ALA B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 845 removed outlier: 3.737A pdb=" N THR B 844 " --> pdb=" O TRP B 841 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR B 845 " --> pdb=" O GLU B 842 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 841 through 845' Processing helix chain 'B' and resid 868 through 879 Processing helix chain 'B' and resid 885 through 896 removed outlier: 4.383A pdb=" N LEU B 890 " --> pdb=" O LYS B 886 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU B 891 " --> pdb=" O ASN B 887 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B 892 " --> pdb=" O LYS B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 908 removed outlier: 3.730A pdb=" N LYS B 902 " --> pdb=" O ASP B 898 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR B 908 " --> pdb=" O LEU B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 926 removed outlier: 3.551A pdb=" N MET B 926 " --> pdb=" O LEU B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 939 removed outlier: 3.859A pdb=" N VAL B 936 " --> pdb=" O ALA B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 967 Processing helix chain 'B' and resid 979 through 984 removed outlier: 3.532A pdb=" N GLN B 982 " --> pdb=" O ASN B 979 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU B 984 " --> pdb=" O SER B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 997 removed outlier: 3.607A pdb=" N ALA B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER B 992 " --> pdb=" O LYS B 988 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA B 996 " --> pdb=" O SER B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1002 Processing helix chain 'B' and resid 1006 through 1018 removed outlier: 3.596A pdb=" N GLN B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1040 Processing helix chain 'B' and resid 1044 through 1048 removed outlier: 3.895A pdb=" N SER B1047 " --> pdb=" O LEU B1044 " (cutoff:3.500A) Processing helix chain 'B' and resid 1053 through 1061 removed outlier: 3.630A pdb=" N ASP B1057 " --> pdb=" O VAL B1054 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL B1058 " --> pdb=" O GLY B1055 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLN B1059 " --> pdb=" O GLU B1056 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG B1060 " --> pdb=" O ASP B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1079 through 1084 Processing helix chain 'B' and resid 1084 through 1100 removed outlier: 3.860A pdb=" N LYS B1097 " --> pdb=" O LYS B1093 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU B1098 " --> pdb=" O SER B1094 " (cutoff:3.500A) Processing helix chain 'B' and resid 1103 through 1107 removed outlier: 3.799A pdb=" N LYS B1106 " --> pdb=" O ASP B1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 1146 through 1155 removed outlier: 3.634A pdb=" N ASP B1152 " --> pdb=" O GLN B1148 " (cutoff:3.500A) Processing helix chain 'B' and resid 1160 through 1167 Processing helix chain 'B' and resid 1181 through 1186 Processing helix chain 'B' and resid 1269 through 1283 removed outlier: 3.546A pdb=" N SER B1273 " --> pdb=" O GLY B1269 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS B1280 " --> pdb=" O ASN B1276 " (cutoff:3.500A) Processing helix chain 'B' and resid 1307 through 1319 Processing helix chain 'B' and resid 1322 through 1326 removed outlier: 3.607A pdb=" N PHE B1325 " --> pdb=" O CYS B1322 " (cutoff:3.500A) Processing helix chain 'B' and resid 1336 through 1338 No H-bonds generated for 'chain 'B' and resid 1336 through 1338' Processing helix chain 'B' and resid 1339 through 1344 Processing helix chain 'B' and resid 1344 through 1349 Processing helix chain 'B' and resid 1350 through 1352 No H-bonds generated for 'chain 'B' and resid 1350 through 1352' Processing helix chain 'B' and resid 1360 through 1362 No H-bonds generated for 'chain 'B' and resid 1360 through 1362' Processing helix chain 'B' and resid 1451 through 1460 removed outlier: 3.949A pdb=" N ILE B1455 " --> pdb=" O SER B1451 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B1456 " --> pdb=" O ALA B1452 " (cutoff:3.500A) Processing helix chain 'B' and resid 1527 through 1537 removed outlier: 3.536A pdb=" N ARG B1535 " --> pdb=" O ASP B1531 " (cutoff:3.500A) Processing helix chain 'B' and resid 1568 through 1574 Processing helix chain 'B' and resid 1582 through 1589 Processing helix chain 'B' and resid 1597 through 1613 removed outlier: 3.670A pdb=" N SER B1601 " --> pdb=" O HIS B1597 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA B1607 " --> pdb=" O ALA B1603 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU B1608 " --> pdb=" O ALA B1604 " (cutoff:3.500A) Processing helix chain 'B' and resid 1617 through 1619 No H-bonds generated for 'chain 'B' and resid 1617 through 1619' Processing helix chain 'B' and resid 1694 through 1701 Processing helix chain 'B' and resid 1704 through 1720 removed outlier: 3.795A pdb=" N TRP B1708 " --> pdb=" O ALA B1704 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B1710 " --> pdb=" O SER B1706 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N HIS B1714 " --> pdb=" O ARG B1710 " (cutoff:3.500A) Processing helix chain 'B' and resid 1722 through 1729 Processing helix chain 'B' and resid 1740 through 1752 removed outlier: 3.581A pdb=" N SER B1745 " --> pdb=" O ALA B1741 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE B1746 " --> pdb=" O LYS B1742 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN B1749 " --> pdb=" O SER B1745 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR B1750 " --> pdb=" O ILE B1746 " (cutoff:3.500A) Processing helix chain 'B' and resid 1787 through 1790 Processing helix chain 'B' and resid 1791 through 1813 Proline residue: B1797 - end of helix removed outlier: 3.664A pdb=" N LEU B1801 " --> pdb=" O PRO B1797 " (cutoff:3.500A) Processing helix chain 'B' and resid 1827 through 1834 removed outlier: 3.655A pdb=" N SER B1831 " --> pdb=" O LEU B1827 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU B1833 " --> pdb=" O GLU B1829 " (cutoff:3.500A) Processing helix chain 'B' and resid 1841 through 1856 Processing helix chain 'B' and resid 1885 through 1899 removed outlier: 4.231A pdb=" N VAL B1892 " --> pdb=" O ALA B1888 " (cutoff:3.500A) Processing helix chain 'B' and resid 1924 through 1929 removed outlier: 3.673A pdb=" N LEU B1928 " --> pdb=" O GLY B1924 " (cutoff:3.500A) Processing helix chain 'B' and resid 1953 through 1958 removed outlier: 4.038A pdb=" N LEU B1958 " --> pdb=" O VAL B1954 " (cutoff:3.500A) Processing helix chain 'B' and resid 1958 through 1972 removed outlier: 3.539A pdb=" N VAL B1965 " --> pdb=" O ILE B1961 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS B1968 " --> pdb=" O GLU B1964 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B1970 " --> pdb=" O SER B1966 " (cutoff:3.500A) Processing helix chain 'B' and resid 2002 through 2011 removed outlier: 3.826A pdb=" N PHE B2006 " --> pdb=" O GLY B2002 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR B2008 " --> pdb=" O LYS B2004 " (cutoff:3.500A) Processing helix chain 'B' and resid 2042 through 2052 removed outlier: 3.899A pdb=" N ASP B2046 " --> pdb=" O GLU B2042 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B2047 " --> pdb=" O TYR B2043 " (cutoff:3.500A) Processing helix chain 'B' and resid 2053 through 2061 removed outlier: 3.516A pdb=" N HIS B2058 " --> pdb=" O GLU B2054 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE B2059 " --> pdb=" O LYS B2055 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP B2061 " --> pdb=" O LYS B2057 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 80 Processing sheet with id=AA2, first strand: chain 'A' and resid 395 through 397 removed outlier: 6.636A pdb=" N ASN A 665 " --> pdb=" O ALA A 755 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ILE A 757 " --> pdb=" O ASN A 665 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU A 667 " --> pdb=" O ILE A 757 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 492 through 498 Processing sheet with id=AA4, first strand: chain 'A' and resid 637 through 640 removed outlier: 4.759A pdb=" N LEU A 628 " --> pdb=" O ASP A 640 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL A 911 " --> pdb=" O LYS A 629 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU A 814 " --> pdb=" O ILE A 857 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1230 through 1232 Processing sheet with id=AA6, first strand: chain 'A' and resid 1230 through 1232 removed outlier: 6.574A pdb=" N SER A1369 " --> pdb=" O GLU A1013 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLU A1013 " --> pdb=" O SER A1369 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR A1371 " --> pdb=" O PHE A1011 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE A1011 " --> pdb=" O THR A1371 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL A1373 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ILE A1006 " --> pdb=" O VAL A1391 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A1389 " --> pdb=" O VAL A1008 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE A1645 " --> pdb=" O ALA A1392 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR A1394 " --> pdb=" O GLN A1643 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN A1643 " --> pdb=" O THR A1394 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N THR A1396 " --> pdb=" O GLY A1641 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLY A1641 " --> pdb=" O THR A1396 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1047 through 1049 Processing sheet with id=AA8, first strand: chain 'A' and resid 1052 through 1053 Processing sheet with id=AA9, first strand: chain 'A' and resid 1106 through 1113 Processing sheet with id=AB1, first strand: chain 'A' and resid 1121 through 1123 Processing sheet with id=AB2, first strand: chain 'A' and resid 1529 through 1531 removed outlier: 5.997A pdb=" N VAL A1563 " --> pdb=" O LEU A1616 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1595 through 1596 Processing sheet with id=AB4, first strand: chain 'A' and resid 1714 through 1715 removed outlier: 3.598A pdb=" N ASN A1714 " --> pdb=" O VAL A1724 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 12 through 13 Processing sheet with id=AB6, first strand: chain 'B' and resid 276 through 280 removed outlier: 6.140A pdb=" N ILE B 164 " --> pdb=" O LYS B 276 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N THR B 278 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA B 166 " --> pdb=" O THR B 278 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLY B 280 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N PHE B 168 " --> pdb=" O GLY B 280 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TYR B 165 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL B 509 " --> pdb=" O ILE B 536 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 425 through 428 removed outlier: 7.282A pdb=" N ASN B 384 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ILE B 379 " --> pdb=" O ASN B 384 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL B 386 " --> pdb=" O SER B 377 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 577 through 580 Processing sheet with id=AB9, first strand: chain 'B' and resid 601 through 602 Processing sheet with id=AC1, first strand: chain 'B' and resid 628 through 629 removed outlier: 6.685A pdb=" N ILE B 628 " --> pdb=" O ASN B 659 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N ILE B 661 " --> pdb=" O ILE B 628 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE B 658 " --> pdb=" O SER B 689 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLY B 691 " --> pdb=" O ILE B 658 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU B 660 " --> pdb=" O GLY B 691 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU B 688 " --> pdb=" O GLY B 713 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU B 712 " --> pdb=" O VAL B 738 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLN B 740 " --> pdb=" O LEU B 712 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU B 714 " --> pdb=" O GLN B 740 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 852 through 855 Processing sheet with id=AC3, first strand: chain 'B' and resid 940 through 941 Processing sheet with id=AC4, first strand: chain 'B' and resid 1129 through 1131 removed outlier: 4.232A pdb=" N VAL B1194 " --> pdb=" O PHE B1138 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU B1207 " --> pdb=" O SER B1222 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N SER B1222 " --> pdb=" O LEU B1207 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA B1209 " --> pdb=" O ALA B1220 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ALA B1220 " --> pdb=" O ILE B1236 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 1171 through 1172 Processing sheet with id=AC6, first strand: chain 'B' and resid 1299 through 1305 removed outlier: 5.582A pdb=" N THR B1388 " --> pdb=" O GLY B1301 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLU B1303 " --> pdb=" O VAL B1386 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL B1386 " --> pdb=" O GLU B1303 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLU B1405 " --> pdb=" O ARG B1393 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL B1395 " --> pdb=" O THR B1403 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N THR B1403 " --> pdb=" O VAL B1395 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B1418 " --> pdb=" O ILE B1410 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ARG B1412 " --> pdb=" O PRO B1416 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE B1425 " --> pdb=" O HIS B1366 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N HIS B1366 " --> pdb=" O PHE B1425 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LEU B1367 " --> pdb=" O PHE B1628 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ARG B1622 " --> pdb=" O MET B1373 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL B1621 " --> pdb=" O GLU B1675 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLU B1675 " --> pdb=" O VAL B1621 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA B1623 " --> pdb=" O GLU B1673 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL B1666 " --> pdb=" O LYS B1660 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LYS B1660 " --> pdb=" O VAL B1666 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY B1646 " --> pdb=" O ILE B1653 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYS B1655 " --> pdb=" O HIS B1644 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N HIS B1644 " --> pdb=" O LYS B1655 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N GLY B1646 " --> pdb=" O ASN B1548 " (cutoff:3.500A) removed outlier: 10.461A pdb=" N ASN B1548 " --> pdb=" O GLY B1646 " (cutoff:3.500A) removed outlier: 11.465A pdb=" N ILE B1648 " --> pdb=" O PHE B1546 " (cutoff:3.500A) removed outlier: 11.597A pdb=" N PHE B1546 " --> pdb=" O ILE B1648 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1299 through 1305 removed outlier: 5.582A pdb=" N THR B1388 " --> pdb=" O GLY B1301 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLU B1303 " --> pdb=" O VAL B1386 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL B1386 " --> pdb=" O GLU B1303 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLU B1405 " --> pdb=" O ARG B1393 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL B1395 " --> pdb=" O THR B1403 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N THR B1403 " --> pdb=" O VAL B1395 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B1418 " --> pdb=" O ILE B1410 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ARG B1412 " --> pdb=" O PRO B1416 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE B1425 " --> pdb=" O HIS B1366 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N HIS B1366 " --> pdb=" O PHE B1425 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LEU B1367 " --> pdb=" O PHE B1628 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ARG B1622 " --> pdb=" O MET B1373 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL B1621 " --> pdb=" O GLU B1675 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLU B1675 " --> pdb=" O VAL B1621 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA B1623 " --> pdb=" O GLU B1673 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL B1666 " --> pdb=" O LYS B1660 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LYS B1660 " --> pdb=" O VAL B1666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1334 through 1335 removed outlier: 4.228A pdb=" N LEU B1380 " --> pdb=" O ALA B1335 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1437 through 1439 removed outlier: 6.759A pdb=" N TYR B1484 " --> pdb=" O VAL B1496 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL B1496 " --> pdb=" O TYR B1484 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS B1486 " --> pdb=" O ALA B1494 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1464 through 1466 removed outlier: 6.979A pdb=" N ALA B1502 " --> pdb=" O VAL B1514 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU B1505 " --> pdb=" O THR B1476 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR B1476 " --> pdb=" O GLU B1505 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN B1475 " --> pdb=" O PHE B1449 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B1445 " --> pdb=" O PHE B1479 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1733 through 1737 Processing sheet with id=AD3, first strand: chain 'B' and resid 1754 through 1755 Processing sheet with id=AD4, first strand: chain 'B' and resid 1870 through 1875 removed outlier: 7.458A pdb=" N VAL B1917 " --> pdb=" O TYR B1909 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N TYR B1909 " --> pdb=" O VAL B1917 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ALA B1919 " --> pdb=" O VAL B1907 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL B1907 " --> pdb=" O ALA B1919 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ASP B1921 " --> pdb=" O GLU B1905 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N GLU B1905 " --> pdb=" O ASP B1921 " (cutoff:3.500A) 1099 hydrogen bonds defined for protein. 3081 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: 7.37 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8395 1.33 - 1.45: 4418 1.45 - 1.57: 15221 1.57 - 1.69: 2 1.69 - 1.81: 163 Bond restraints: 28199 Sorted by residual: bond pdb=" CA THR A1359 " pdb=" CB THR A1359 " ideal model delta sigma weight residual 1.526 1.488 0.038 1.51e-02 4.39e+03 6.34e+00 bond pdb=" C LYS B2004 " pdb=" N PRO B2005 " ideal model delta sigma weight residual 1.337 1.368 -0.031 1.24e-02 6.50e+03 6.20e+00 bond pdb=" C ASP A1254 " pdb=" N LYS A1255 " ideal model delta sigma weight residual 1.331 1.262 0.069 2.83e-02 1.25e+03 5.87e+00 bond pdb=" CB VAL A1316 " pdb=" CG2 VAL A1316 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.49e+00 bond pdb=" N GLU B 49 " pdb=" CA GLU B 49 " ideal model delta sigma weight residual 1.457 1.486 -0.028 1.29e-02 6.01e+03 4.81e+00 ... (remaining 28194 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 37583 2.82 - 5.64: 542 5.64 - 8.46: 60 8.46 - 11.27: 8 11.27 - 14.09: 6 Bond angle restraints: 38199 Sorted by residual: angle pdb=" C SER B 241 " pdb=" N ILE B 242 " pdb=" CA ILE B 242 " ideal model delta sigma weight residual 120.24 125.35 -5.11 6.30e-01 2.52e+00 6.59e+01 angle pdb=" N PHE B1353 " pdb=" CA PHE B1353 " pdb=" C PHE B1353 " ideal model delta sigma weight residual 109.81 122.50 -12.69 2.21e+00 2.05e-01 3.30e+01 angle pdb=" C GLN B1899 " pdb=" N THR B1900 " pdb=" CA THR B1900 " ideal model delta sigma weight residual 121.54 132.16 -10.62 1.91e+00 2.74e-01 3.09e+01 angle pdb=" CA ASN A 439 " pdb=" C ASN A 439 " pdb=" N PRO A 440 " ideal model delta sigma weight residual 117.68 121.09 -3.41 7.10e-01 1.98e+00 2.31e+01 angle pdb=" C SER B 751 " pdb=" N PHE B 752 " pdb=" CA PHE B 752 " ideal model delta sigma weight residual 121.54 129.57 -8.03 1.91e+00 2.74e-01 1.77e+01 ... (remaining 38194 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.98: 15893 23.98 - 47.97: 940 47.97 - 71.95: 111 71.95 - 95.93: 46 95.93 - 119.91: 1 Dihedral angle restraints: 16991 sinusoidal: 6833 harmonic: 10158 Sorted by residual: dihedral pdb=" CA ASP B 235 " pdb=" C ASP B 235 " pdb=" N GLN B 236 " pdb=" CA GLN B 236 " ideal model delta harmonic sigma weight residual 180.00 145.69 34.31 0 5.00e+00 4.00e-02 4.71e+01 dihedral pdb=" C5' FMN B2101 " pdb=" O5' FMN B2101 " pdb=" P FMN B2101 " pdb=" O1P FMN B2101 " ideal model delta sinusoidal sigma weight residual 75.26 -44.66 119.91 1 2.00e+01 2.50e-03 3.60e+01 dihedral pdb=" CA LEU A 53 " pdb=" C LEU A 53 " pdb=" N ALA A 54 " pdb=" CA ALA A 54 " ideal model delta harmonic sigma weight residual 180.00 150.08 29.92 0 5.00e+00 4.00e-02 3.58e+01 ... (remaining 16988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3238 0.062 - 0.125: 890 0.125 - 0.187: 118 0.187 - 0.249: 14 0.249 - 0.311: 6 Chirality restraints: 4266 Sorted by residual: chirality pdb=" CB VAL B 386 " pdb=" CA VAL B 386 " pdb=" CG1 VAL B 386 " pdb=" CG2 VAL B 386 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA PHE B1353 " pdb=" N PHE B1353 " pdb=" C PHE B1353 " pdb=" CB PHE B1353 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CB ILE B 628 " pdb=" CA ILE B 628 " pdb=" CG1 ILE B 628 " pdb=" CG2 ILE B 628 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 4263 not shown) Planarity restraints: 4926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 963 " 0.049 5.00e-02 4.00e+02 7.29e-02 8.51e+00 pdb=" N PRO A 964 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 964 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 964 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 441 " 0.049 5.00e-02 4.00e+02 7.29e-02 8.50e+00 pdb=" N PRO B 442 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 442 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 442 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A1015 " -0.048 5.00e-02 4.00e+02 7.19e-02 8.27e+00 pdb=" N PRO A1016 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO A1016 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A1016 " -0.040 5.00e-02 4.00e+02 ... (remaining 4923 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 8383 2.81 - 3.33: 23916 3.33 - 3.85: 45932 3.85 - 4.38: 55630 4.38 - 4.90: 94994 Nonbonded interactions: 228855 Sorted by model distance: nonbonded pdb=" OD1 ASP A1064 " pdb=" OH TYR A1080 " model vdw 2.285 3.040 nonbonded pdb=" O VAL B1962 " pdb=" OG SER B1966 " model vdw 2.289 3.040 nonbonded pdb=" O GLU B 702 " pdb=" OG1 THR B 706 " model vdw 2.295 3.040 nonbonded pdb=" O SER B 506 " pdb=" OG SER B 533 " model vdw 2.297 3.040 nonbonded pdb=" O SER A 73 " pdb=" OG SER A 73 " model vdw 2.297 3.040 ... (remaining 228850 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.810 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: 0.040 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 27.170 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 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 : 0.008 0.081 28200 Z= 0.335 Angle : 0.877 14.093 38199 Z= 0.475 Chirality : 0.057 0.311 4266 Planarity : 0.007 0.073 4926 Dihedral : 15.489 119.914 10467 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.19 % Allowed : 8.22 % Favored : 90.59 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -5.07 (0.10), residues: 3506 helix: -4.39 (0.05), residues: 1458 sheet: -2.27 (0.21), residues: 474 loop : -2.49 (0.13), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 932 TYR 0.025 0.002 TYR B 30 PHE 0.040 0.003 PHE A1363 TRP 0.019 0.002 TRP A 28 HIS 0.019 0.002 HIS A1135 Details of bonding type rmsd/Z covalent geometry : bond 0.00788 / 0.34 (28199) covalent geometry : angle 0.87721 / 0.48 (38199) hydrogen bonds : bond 0.29898 / 19.40 ( 1055) hydrogen bonds : angle 10.45329 / 7.24 ( 3081) Misc. bond : bond 0.00293 / 0.15 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 348 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 GLN cc_start: 0.8840 (tt0) cc_final: 0.8509 (mt0) REVERT: A 411 MET cc_start: 0.8771 (ttp) cc_final: 0.8555 (ttp) REVERT: A 1069 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7710 (mm-30) REVERT: A 1096 GLU cc_start: 0.8056 (pm20) cc_final: 0.7692 (pm20) REVERT: A 1198 VAL cc_start: 0.8871 (OUTLIER) cc_final: 0.8538 (p) REVERT: A 1247 MET cc_start: 0.8279 (ptm) cc_final: 0.8001 (ptm) REVERT: B 213 THR cc_start: 0.7481 (OUTLIER) cc_final: 0.7271 (m) REVERT: B 674 MET cc_start: 0.8219 (ttp) cc_final: 0.7970 (ttp) outliers start: 36 outliers final: 14 residues processed: 375 average time/residue: 0.2027 time to fit residues: 115.8825 Evaluate side-chains 231 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 215 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 1198 VAL Chi-restraints excluded: chain A residue 1747 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 1132 SER Chi-restraints excluded: chain B residue 1140 VAL Chi-restraints excluded: chain B residue 1193 VAL Chi-restraints excluded: chain B residue 1357 VAL Chi-restraints excluded: chain B residue 1617 VAL Chi-restraints excluded: chain B residue 1999 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 GLN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 ASN A 449 HIS A 452 HIS A 780 HIS A 975 ASN A1175 GLN A1226 HIS ** A1367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1491 GLN A1501 ASN A1561 ASN A1727 ASN B 80 GLN B 91 ASN B 102 ASN B 236 GLN B 508 HIS B 525 HIS B 796 HIS B1018 GLN B1180 ASN B1366 HIS B1518 ASN B1536 HIS B1548 ASN B1611 GLN B1644 HIS B1676 GLN B1717 ASN B1729 ASN B1730 ASN ** B1933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1995 HIS B2031 ASN B2038 GLN B2062 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.120101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.083664 restraints weight = 45120.019| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.79 r_work: 0.2831 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28200 Z= 0.169 Angle : 0.619 11.404 38199 Z= 0.328 Chirality : 0.045 0.185 4266 Planarity : 0.006 0.057 4926 Dihedral : 6.002 94.601 3797 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.89 % Allowed : 11.00 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.27 (0.12), residues: 3506 helix: -2.35 (0.11), residues: 1470 sheet: -1.77 (0.22), residues: 479 loop : -1.94 (0.15), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1354 TYR 0.019 0.001 TYR A 347 PHE 0.023 0.002 PHE B1935 TRP 0.020 0.001 TRP A1017 HIS 0.016 0.001 HIS A1135 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (28199) covalent geometry : angle 0.61857 / 0.33 (38199) hydrogen bonds : bond 0.04962 / 3.28 ( 1055) hydrogen bonds : angle 5.49091 / 3.77 ( 3081) Misc. bond : bond 0.00147 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 260 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6744 (mmt) cc_final: 0.6517 (mmt) REVERT: A 375 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8317 (tt0) REVERT: A 866 MET cc_start: 0.4237 (mmt) cc_final: 0.3374 (mmt) REVERT: A 951 ILE cc_start: 0.9107 (mm) cc_final: 0.8839 (mt) REVERT: A 954 ARG cc_start: 0.8303 (mtm-85) cc_final: 0.7983 (mtm-85) REVERT: A 1247 MET cc_start: 0.8423 (ptm) cc_final: 0.8201 (ptm) REVERT: A 1611 ASP cc_start: 0.8312 (m-30) cc_final: 0.8026 (m-30) REVERT: B 14 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7786 (pp) REVERT: B 392 GLN cc_start: 0.8932 (tp40) cc_final: 0.8609 (tp40) REVERT: B 704 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9087 (mp) REVERT: B 1638 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8659 (pp) REVERT: B 1754 MET cc_start: 0.7564 (mmt) cc_final: 0.7333 (mmt) REVERT: B 1879 ARG cc_start: 0.8229 (tpt90) cc_final: 0.7959 (tpt90) outliers start: 57 outliers final: 36 residues processed: 310 average time/residue: 0.2066 time to fit residues: 99.2238 Evaluate side-chains 253 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 214 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 1190 ASP Chi-restraints excluded: chain A residue 1254 ASP Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1400 LYS Chi-restraints excluded: chain A residue 1420 HIS Chi-restraints excluded: chain A residue 1478 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 732 HIS Chi-restraints excluded: chain B residue 756 HIS Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1140 VAL Chi-restraints excluded: chain B residue 1193 VAL Chi-restraints excluded: chain B residue 1357 VAL Chi-restraints excluded: chain B residue 1400 THR Chi-restraints excluded: chain B residue 1420 VAL Chi-restraints excluded: chain B residue 1503 LEU Chi-restraints excluded: chain B residue 1511 ILE Chi-restraints excluded: chain B residue 1617 VAL Chi-restraints excluded: chain B residue 1638 LEU Chi-restraints excluded: chain B residue 1656 VAL Chi-restraints excluded: chain B residue 1707 VAL Chi-restraints excluded: chain B residue 1833 LEU Chi-restraints excluded: chain B residue 1999 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 244 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 330 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 331 optimal weight: 20.0000 chunk 81 optimal weight: 1.9990 chunk 302 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 chunk 247 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1501 ASN A1727 ASN ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 HIS B 724 GLN B1059 GLN B1423 GLN B1729 ASN B1730 ASN B1898 GLN ** B1933 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 = 0.3576 r_free = 0.3576 target = 0.120773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.084964 restraints weight = 45377.599| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.73 r_work: 0.2862 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28200 Z= 0.134 Angle : 0.555 9.433 38199 Z= 0.291 Chirality : 0.044 0.204 4266 Planarity : 0.004 0.051 4926 Dihedral : 5.281 58.740 3791 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.52 % Allowed : 11.80 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.13), residues: 3506 helix: -1.14 (0.13), residues: 1468 sheet: -1.46 (0.22), residues: 486 loop : -1.64 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1133 TYR 0.016 0.001 TYR B 132 PHE 0.022 0.001 PHE B1935 TRP 0.017 0.001 TRP A1017 HIS 0.015 0.001 HIS A1135 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (28199) covalent geometry : angle 0.55530 / 0.29 (38199) hydrogen bonds : bond 0.04073 / 2.65 ( 1055) hydrogen bonds : angle 4.83224 / 3.31 ( 3081) Misc. bond : bond 0.00010 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 246 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 LEU cc_start: 0.9193 (mt) cc_final: 0.8985 (mt) REVERT: A 375 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8347 (tt0) REVERT: A 866 MET cc_start: 0.4283 (mmt) cc_final: 0.3392 (mmt) REVERT: A 951 ILE cc_start: 0.9045 (mm) cc_final: 0.8782 (mt) REVERT: A 954 ARG cc_start: 0.8245 (mtm-85) cc_final: 0.7978 (mtm-85) REVERT: A 1009 THR cc_start: 0.8648 (m) cc_final: 0.8414 (p) REVERT: A 1135 HIS cc_start: 0.7751 (OUTLIER) cc_final: 0.6414 (p-80) REVERT: A 1319 TYR cc_start: 0.8281 (OUTLIER) cc_final: 0.6664 (p90) REVERT: B 14 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7783 (pp) REVERT: B 208 ARG cc_start: 0.7229 (tmm160) cc_final: 0.7004 (tmm-80) REVERT: B 704 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.9060 (mp) REVERT: B 1638 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8594 (pp) REVERT: B 1879 ARG cc_start: 0.8109 (tpt90) cc_final: 0.7824 (tpt90) outliers start: 76 outliers final: 44 residues processed: 311 average time/residue: 0.2050 time to fit residues: 100.0904 Evaluate side-chains 266 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 217 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1135 HIS Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1254 ASP Chi-restraints excluded: chain A residue 1319 TYR Chi-restraints excluded: chain A residue 1341 ASP Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1398 THR Chi-restraints excluded: chain A residue 1400 LYS Chi-restraints excluded: chain A residue 1420 HIS Chi-restraints excluded: chain A residue 1478 SER Chi-restraints excluded: chain A residue 1584 LEU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 557 PHE Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 732 HIS Chi-restraints excluded: chain B residue 756 HIS Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1140 VAL Chi-restraints excluded: chain B residue 1193 VAL Chi-restraints excluded: chain B residue 1194 VAL Chi-restraints excluded: chain B residue 1287 VAL Chi-restraints excluded: chain B residue 1357 VAL Chi-restraints excluded: chain B residue 1400 THR Chi-restraints excluded: chain B residue 1420 VAL Chi-restraints excluded: chain B residue 1617 VAL Chi-restraints excluded: chain B residue 1638 LEU Chi-restraints excluded: chain B residue 1656 VAL Chi-restraints excluded: chain B residue 1707 VAL Chi-restraints excluded: chain B residue 1729 ASN Chi-restraints excluded: chain B residue 1833 LEU Chi-restraints excluded: chain B residue 1883 THR Chi-restraints excluded: chain B residue 1884 PHE Chi-restraints excluded: chain B residue 1999 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 266 optimal weight: 5.9990 chunk 6 optimal weight: 0.2980 chunk 152 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 338 optimal weight: 0.5980 chunk 269 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 GLN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1050 HIS ** A1367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1501 ASN A1727 ASN B 16 HIS B 104 HIS ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 HIS B 669 GLN B 732 HIS ** B1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1616 ASN B1730 ASN ** B1933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.120288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.082901 restraints weight = 44983.413| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.78 r_work: 0.2857 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28200 Z= 0.142 Angle : 0.548 9.599 38199 Z= 0.285 Chirality : 0.045 0.178 4266 Planarity : 0.004 0.047 4926 Dihedral : 5.074 53.139 3789 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.55 % Allowed : 12.79 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.14), residues: 3506 helix: -0.59 (0.13), residues: 1462 sheet: -1.24 (0.23), residues: 474 loop : -1.47 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1133 TYR 0.016 0.001 TYR B 132 PHE 0.022 0.001 PHE B1935 TRP 0.017 0.001 TRP A1017 HIS 0.014 0.001 HIS A1135 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (28199) covalent geometry : angle 0.54820 / 0.29 (38199) hydrogen bonds : bond 0.03762 / 2.45 ( 1055) hydrogen bonds : angle 4.61782 / 3.16 ( 3081) Misc. bond : bond 0.00001 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 232 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8287 (tt0) REVERT: A 866 MET cc_start: 0.4399 (mmt) cc_final: 0.3385 (mmt) REVERT: A 951 ILE cc_start: 0.9010 (mm) cc_final: 0.8767 (mt) REVERT: A 954 ARG cc_start: 0.8203 (mtm-85) cc_final: 0.7970 (mtm-85) REVERT: A 1009 THR cc_start: 0.8658 (m) cc_final: 0.8399 (p) REVERT: A 1135 HIS cc_start: 0.7777 (OUTLIER) cc_final: 0.6351 (p-80) REVERT: A 1319 TYR cc_start: 0.8298 (OUTLIER) cc_final: 0.6747 (p90) REVERT: B 14 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7921 (pp) REVERT: B 606 MET cc_start: 0.8122 (mtm) cc_final: 0.7890 (mtm) REVERT: B 704 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.9086 (mp) REVERT: B 1638 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8612 (pp) REVERT: B 1879 ARG cc_start: 0.8078 (tpt90) cc_final: 0.7781 (tpt90) outliers start: 77 outliers final: 54 residues processed: 298 average time/residue: 0.1988 time to fit residues: 92.5374 Evaluate side-chains 279 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 220 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1135 HIS Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1254 ASP Chi-restraints excluded: chain A residue 1319 TYR Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain A residue 1341 ASP Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1400 LYS Chi-restraints excluded: chain A residue 1420 HIS Chi-restraints excluded: chain A residue 1478 SER Chi-restraints excluded: chain A residue 1501 ASN Chi-restraints excluded: chain A residue 1519 THR Chi-restraints excluded: chain A residue 1571 LEU Chi-restraints excluded: chain A residue 1584 LEU Chi-restraints excluded: chain A residue 1611 ASP Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 557 PHE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 756 HIS Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 973 THR Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1140 VAL Chi-restraints excluded: chain B residue 1193 VAL Chi-restraints excluded: chain B residue 1194 VAL Chi-restraints excluded: chain B residue 1357 VAL Chi-restraints excluded: chain B residue 1400 THR Chi-restraints excluded: chain B residue 1420 VAL Chi-restraints excluded: chain B residue 1511 ILE Chi-restraints excluded: chain B residue 1616 ASN Chi-restraints excluded: chain B residue 1617 VAL Chi-restraints excluded: chain B residue 1638 LEU Chi-restraints excluded: chain B residue 1656 VAL Chi-restraints excluded: chain B residue 1707 VAL Chi-restraints excluded: chain B residue 1833 LEU Chi-restraints excluded: chain B residue 1883 THR Chi-restraints excluded: chain B residue 1884 PHE Chi-restraints excluded: chain B residue 1940 ILE Chi-restraints excluded: chain B residue 1999 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 13 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 chunk 288 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 81 optimal weight: 0.3980 chunk 20 optimal weight: 0.2980 chunk 161 optimal weight: 2.9990 chunk 314 optimal weight: 3.9990 chunk 283 optimal weight: 10.0000 chunk 239 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 GLN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1501 ASN A1727 ASN A1742 ASN B 104 HIS ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 ASN B 373 HIS B 525 HIS B 669 GLN ** B1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1616 ASN B1729 ASN B1730 ASN B1796 GLN ** B1933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.121067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.084205 restraints weight = 45012.115| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.80 r_work: 0.2860 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28200 Z= 0.117 Angle : 0.524 8.232 38199 Z= 0.274 Chirality : 0.044 0.166 4266 Planarity : 0.004 0.051 4926 Dihedral : 4.903 48.597 3788 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.35 % Allowed : 13.46 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.14), residues: 3506 helix: -0.29 (0.14), residues: 1474 sheet: -1.14 (0.23), residues: 468 loop : -1.36 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1167 TYR 0.017 0.001 TYR B 132 PHE 0.021 0.001 PHE B1935 TRP 0.014 0.001 TRP A1017 HIS 0.014 0.001 HIS A1135 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (28199) covalent geometry : angle 0.52426 / 0.27 (38199) hydrogen bonds : bond 0.03502 / 2.28 ( 1055) hydrogen bonds : angle 4.48249 / 3.07 ( 3081) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 239 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8309 (tt0) REVERT: A 732 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8213 (t0) REVERT: A 866 MET cc_start: 0.4415 (mmt) cc_final: 0.3377 (mmt) REVERT: A 954 ARG cc_start: 0.8196 (mtm-85) cc_final: 0.7817 (mtm-85) REVERT: A 1009 THR cc_start: 0.8644 (m) cc_final: 0.8412 (p) REVERT: A 1135 HIS cc_start: 0.7760 (OUTLIER) cc_final: 0.6264 (p-80) REVERT: A 1140 ASP cc_start: 0.8310 (p0) cc_final: 0.7986 (p0) REVERT: A 1319 TYR cc_start: 0.8282 (OUTLIER) cc_final: 0.6827 (p90) REVERT: B 14 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7921 (pp) REVERT: B 606 MET cc_start: 0.8021 (mtm) cc_final: 0.7744 (mtm) REVERT: B 704 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.9054 (mp) REVERT: B 1388 THR cc_start: 0.9165 (t) cc_final: 0.8954 (t) REVERT: B 1638 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8602 (pp) REVERT: B 1725 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8337 (t70) outliers start: 71 outliers final: 51 residues processed: 296 average time/residue: 0.1900 time to fit residues: 88.0718 Evaluate side-chains 277 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 219 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1135 HIS Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1254 ASP Chi-restraints excluded: chain A residue 1319 TYR Chi-restraints excluded: chain A residue 1341 ASP Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1400 LYS Chi-restraints excluded: chain A residue 1420 HIS Chi-restraints excluded: chain A residue 1478 SER Chi-restraints excluded: chain A residue 1501 ASN Chi-restraints excluded: chain A residue 1519 THR Chi-restraints excluded: chain A residue 1571 LEU Chi-restraints excluded: chain A residue 1584 LEU Chi-restraints excluded: chain A residue 1611 ASP Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 756 HIS Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 973 THR Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1140 VAL Chi-restraints excluded: chain B residue 1193 VAL Chi-restraints excluded: chain B residue 1194 VAL Chi-restraints excluded: chain B residue 1357 VAL Chi-restraints excluded: chain B residue 1400 THR Chi-restraints excluded: chain B residue 1420 VAL Chi-restraints excluded: chain B residue 1616 ASN Chi-restraints excluded: chain B residue 1617 VAL Chi-restraints excluded: chain B residue 1638 LEU Chi-restraints excluded: chain B residue 1686 GLN Chi-restraints excluded: chain B residue 1707 VAL Chi-restraints excluded: chain B residue 1725 ASP Chi-restraints excluded: chain B residue 1729 ASN Chi-restraints excluded: chain B residue 1833 LEU Chi-restraints excluded: chain B residue 1883 THR Chi-restraints excluded: chain B residue 1884 PHE Chi-restraints excluded: chain B residue 1999 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 68 optimal weight: 1.9990 chunk 273 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 258 optimal weight: 0.0970 chunk 339 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 304 optimal weight: 0.4980 chunk 154 optimal weight: 3.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 GLN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1501 ASN B 104 HIS ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 HIS B 525 HIS B 669 GLN ** B1577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1616 ASN B1729 ASN B1730 ASN ** B1933 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 = 0.3597 r_free = 0.3597 target = 0.122290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.085677 restraints weight = 45134.822| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.82 r_work: 0.2875 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 28200 Z= 0.098 Angle : 0.514 10.282 38199 Z= 0.267 Chirality : 0.043 0.157 4266 Planarity : 0.004 0.046 4926 Dihedral : 4.751 44.541 3788 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.32 % Allowed : 14.05 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.14), residues: 3506 helix: -0.07 (0.14), residues: 1480 sheet: -0.97 (0.24), residues: 465 loop : -1.28 (0.16), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B1133 TYR 0.015 0.001 TYR B 132 PHE 0.020 0.001 PHE B1935 TRP 0.012 0.001 TRP A1017 HIS 0.013 0.001 HIS A1135 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (28199) covalent geometry : angle 0.51402 / 0.27 (38199) hydrogen bonds : bond 0.03293 / 2.14 ( 1055) hydrogen bonds : angle 4.37810 / 3.00 ( 3081) Misc. bond : bond 0.00008 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 233 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 GLU cc_start: 0.7883 (tp30) cc_final: 0.7596 (tt0) REVERT: A 375 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8296 (tt0) REVERT: A 732 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8200 (t0) REVERT: A 866 MET cc_start: 0.4417 (mmt) cc_final: 0.3374 (mmt) REVERT: A 954 ARG cc_start: 0.8206 (mtm-85) cc_final: 0.7896 (mtm-85) REVERT: A 1054 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8027 (pt) REVERT: A 1135 HIS cc_start: 0.7703 (OUTLIER) cc_final: 0.6061 (p-80) REVERT: A 1319 TYR cc_start: 0.8237 (OUTLIER) cc_final: 0.6729 (p90) REVERT: B 14 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7916 (pp) REVERT: B 667 MET cc_start: 0.8405 (tpp) cc_final: 0.7825 (ttt) REVERT: B 704 ILE cc_start: 0.9304 (OUTLIER) cc_final: 0.9071 (mp) REVERT: B 1095 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8658 (mt) REVERT: B 1388 THR cc_start: 0.9157 (t) cc_final: 0.8947 (t) REVERT: B 1638 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8595 (pp) REVERT: B 1821 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8501 (mtt) REVERT: B 1833 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8532 (mp) outliers start: 70 outliers final: 47 residues processed: 290 average time/residue: 0.2030 time to fit residues: 92.7280 Evaluate side-chains 277 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 220 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1135 HIS Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1254 ASP Chi-restraints excluded: chain A residue 1319 TYR Chi-restraints excluded: chain A residue 1341 ASP Chi-restraints excluded: chain A residue 1400 LYS Chi-restraints excluded: chain A residue 1420 HIS Chi-restraints excluded: chain A residue 1478 SER Chi-restraints excluded: chain A residue 1501 ASN Chi-restraints excluded: chain A residue 1519 THR Chi-restraints excluded: chain A residue 1571 LEU Chi-restraints excluded: chain A residue 1584 LEU Chi-restraints excluded: chain A residue 1611 ASP Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 557 PHE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 756 HIS Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 973 THR Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1140 VAL Chi-restraints excluded: chain B residue 1193 VAL Chi-restraints excluded: chain B residue 1194 VAL Chi-restraints excluded: chain B residue 1357 VAL Chi-restraints excluded: chain B residue 1385 VAL Chi-restraints excluded: chain B residue 1400 THR Chi-restraints excluded: chain B residue 1420 VAL Chi-restraints excluded: chain B residue 1616 ASN Chi-restraints excluded: chain B residue 1617 VAL Chi-restraints excluded: chain B residue 1638 LEU Chi-restraints excluded: chain B residue 1686 GLN Chi-restraints excluded: chain B residue 1707 VAL Chi-restraints excluded: chain B residue 1821 MET Chi-restraints excluded: chain B residue 1833 LEU Chi-restraints excluded: chain B residue 1883 THR Chi-restraints excluded: chain B residue 1884 PHE Chi-restraints excluded: chain B residue 1940 ILE Chi-restraints excluded: chain B residue 1999 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 306 optimal weight: 3.9990 chunk 250 optimal weight: 9.9990 chunk 115 optimal weight: 0.8980 chunk 285 optimal weight: 7.9990 chunk 67 optimal weight: 0.5980 chunk 83 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 167 optimal weight: 0.4980 chunk 21 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 256 optimal weight: 6.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 GLN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1561 ASN B 104 HIS B 236 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 HIS ** B 750 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1616 ASN B1730 ASN B1933 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.121632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.084912 restraints weight = 44718.468| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.76 r_work: 0.2867 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28200 Z= 0.125 Angle : 0.530 11.764 38199 Z= 0.274 Chirality : 0.044 0.273 4266 Planarity : 0.004 0.057 4926 Dihedral : 4.729 41.819 3788 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.49 % Allowed : 14.72 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.14), residues: 3506 helix: 0.04 (0.14), residues: 1475 sheet: -0.89 (0.24), residues: 458 loop : -1.23 (0.16), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B1133 TYR 0.016 0.001 TYR B 132 PHE 0.020 0.001 PHE B1935 TRP 0.013 0.001 TRP A1017 HIS 0.013 0.001 HIS A1135 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (28199) covalent geometry : angle 0.52971 / 0.27 (38199) hydrogen bonds : bond 0.03395 / 2.21 ( 1055) hydrogen bonds : angle 4.33962 / 2.98 ( 3081) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 228 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 359 GLU cc_start: 0.7838 (tp30) cc_final: 0.7593 (tt0) REVERT: A 375 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8287 (tt0) REVERT: A 732 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8227 (t0) REVERT: A 866 MET cc_start: 0.4344 (mmt) cc_final: 0.3276 (mmt) REVERT: A 954 ARG cc_start: 0.8146 (mtm-85) cc_final: 0.7851 (mtm-85) REVERT: A 1054 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8033 (pt) REVERT: A 1135 HIS cc_start: 0.7734 (OUTLIER) cc_final: 0.6172 (p-80) REVERT: A 1319 TYR cc_start: 0.8235 (OUTLIER) cc_final: 0.6835 (p90) REVERT: A 1458 ARG cc_start: 0.8187 (mtm110) cc_final: 0.7816 (mtm-85) REVERT: B 14 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7951 (pp) REVERT: B 704 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.9071 (mp) REVERT: B 1095 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8676 (mt) REVERT: B 1388 THR cc_start: 0.9149 (t) cc_final: 0.8939 (t) REVERT: B 1638 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8601 (pp) REVERT: B 1821 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8572 (mtt) REVERT: B 1833 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8528 (mp) outliers start: 75 outliers final: 50 residues processed: 288 average time/residue: 0.2021 time to fit residues: 92.0485 Evaluate side-chains 278 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 218 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1135 HIS Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1254 ASP Chi-restraints excluded: chain A residue 1319 TYR Chi-restraints excluded: chain A residue 1341 ASP Chi-restraints excluded: chain A residue 1358 THR Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1400 LYS Chi-restraints excluded: chain A residue 1420 HIS Chi-restraints excluded: chain A residue 1478 SER Chi-restraints excluded: chain A residue 1519 THR Chi-restraints excluded: chain A residue 1571 LEU Chi-restraints excluded: chain A residue 1584 LEU Chi-restraints excluded: chain A residue 1611 ASP Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 756 HIS Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 973 THR Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1140 VAL Chi-restraints excluded: chain B residue 1193 VAL Chi-restraints excluded: chain B residue 1194 VAL Chi-restraints excluded: chain B residue 1357 VAL Chi-restraints excluded: chain B residue 1385 VAL Chi-restraints excluded: chain B residue 1400 THR Chi-restraints excluded: chain B residue 1420 VAL Chi-restraints excluded: chain B residue 1511 ILE Chi-restraints excluded: chain B residue 1616 ASN Chi-restraints excluded: chain B residue 1617 VAL Chi-restraints excluded: chain B residue 1631 MET Chi-restraints excluded: chain B residue 1638 LEU Chi-restraints excluded: chain B residue 1656 VAL Chi-restraints excluded: chain B residue 1686 GLN Chi-restraints excluded: chain B residue 1707 VAL Chi-restraints excluded: chain B residue 1821 MET Chi-restraints excluded: chain B residue 1833 LEU Chi-restraints excluded: chain B residue 1883 THR Chi-restraints excluded: chain B residue 1884 PHE Chi-restraints excluded: chain B residue 1940 ILE Chi-restraints excluded: chain B residue 1999 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 193 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 chunk 328 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 144 optimal weight: 10.0000 chunk 273 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 152 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 GLN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1501 ASN B 104 HIS B 669 GLN ** B 750 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1616 ASN B1730 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.122446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.086029 restraints weight = 45066.149| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.82 r_work: 0.2868 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 28200 Z= 0.101 Angle : 0.517 12.756 38199 Z= 0.268 Chirality : 0.043 0.236 4266 Planarity : 0.004 0.068 4926 Dihedral : 4.617 42.334 3788 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.32 % Allowed : 15.05 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.14), residues: 3506 helix: 0.20 (0.14), residues: 1474 sheet: -0.82 (0.24), residues: 458 loop : -1.20 (0.16), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B1133 TYR 0.013 0.001 TYR B 132 PHE 0.018 0.001 PHE B1891 TRP 0.012 0.001 TRP A1017 HIS 0.012 0.001 HIS A1135 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (28199) covalent geometry : angle 0.51683 / 0.27 (38199) hydrogen bonds : bond 0.03207 / 2.09 ( 1055) hydrogen bonds : angle 4.27543 / 2.94 ( 3081) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 227 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.8322 (tp30) cc_final: 0.8120 (tp30) REVERT: A 359 GLU cc_start: 0.7872 (tp30) cc_final: 0.7617 (tt0) REVERT: A 375 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8299 (tt0) REVERT: A 732 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8251 (t0) REVERT: A 866 MET cc_start: 0.4518 (mmt) cc_final: 0.3437 (mmt) REVERT: A 954 ARG cc_start: 0.8192 (mtm-85) cc_final: 0.7918 (mtm-85) REVERT: A 969 ARG cc_start: 0.8362 (tpp-160) cc_final: 0.8069 (mmt-90) REVERT: A 1054 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8070 (pt) REVERT: A 1135 HIS cc_start: 0.7699 (OUTLIER) cc_final: 0.5843 (p-80) REVERT: A 1319 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.6830 (p90) REVERT: A 1458 ARG cc_start: 0.8184 (mtm110) cc_final: 0.7849 (mtm-85) REVERT: B 14 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7992 (pp) REVERT: B 704 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.9073 (mp) REVERT: B 1095 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8667 (mt) REVERT: B 1388 THR cc_start: 0.9152 (t) cc_final: 0.8925 (t) REVERT: B 1599 MET cc_start: 0.8059 (mmm) cc_final: 0.7645 (mtp) REVERT: B 1638 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8612 (pp) REVERT: B 1821 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8533 (mtt) REVERT: B 1833 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8528 (mp) outliers start: 70 outliers final: 50 residues processed: 285 average time/residue: 0.2092 time to fit residues: 94.0390 Evaluate side-chains 277 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 217 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1135 HIS Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1254 ASP Chi-restraints excluded: chain A residue 1319 TYR Chi-restraints excluded: chain A residue 1341 ASP Chi-restraints excluded: chain A residue 1358 THR Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1400 LYS Chi-restraints excluded: chain A residue 1420 HIS Chi-restraints excluded: chain A residue 1478 SER Chi-restraints excluded: chain A residue 1519 THR Chi-restraints excluded: chain A residue 1571 LEU Chi-restraints excluded: chain A residue 1584 LEU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1747 VAL Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 557 PHE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 732 HIS Chi-restraints excluded: chain B residue 750 HIS Chi-restraints excluded: chain B residue 756 HIS Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 973 THR Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1140 VAL Chi-restraints excluded: chain B residue 1193 VAL Chi-restraints excluded: chain B residue 1234 GLU Chi-restraints excluded: chain B residue 1357 VAL Chi-restraints excluded: chain B residue 1385 VAL Chi-restraints excluded: chain B residue 1400 THR Chi-restraints excluded: chain B residue 1420 VAL Chi-restraints excluded: chain B residue 1617 VAL Chi-restraints excluded: chain B residue 1638 LEU Chi-restraints excluded: chain B residue 1686 GLN Chi-restraints excluded: chain B residue 1707 VAL Chi-restraints excluded: chain B residue 1821 MET Chi-restraints excluded: chain B residue 1833 LEU Chi-restraints excluded: chain B residue 1883 THR Chi-restraints excluded: chain B residue 1884 PHE Chi-restraints excluded: chain B residue 1940 ILE Chi-restraints excluded: chain B residue 1999 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 114 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 64 optimal weight: 8.9990 chunk 128 optimal weight: 7.9990 chunk 341 optimal weight: 20.0000 chunk 309 optimal weight: 3.9990 chunk 249 optimal weight: 9.9990 chunk 111 optimal weight: 0.0070 chunk 169 optimal weight: 0.1980 chunk 109 optimal weight: 1.9990 chunk 278 optimal weight: 3.9990 overall best weight: 1.6404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 GLN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1501 ASN B 373 HIS ** B 750 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1730 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.121388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.084447 restraints weight = 44987.472| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.88 r_work: 0.2849 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28200 Z= 0.142 Angle : 0.544 13.114 38199 Z= 0.282 Chirality : 0.044 0.226 4266 Planarity : 0.004 0.061 4926 Dihedral : 4.667 42.363 3788 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.45 % Allowed : 15.11 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.14), residues: 3506 helix: 0.19 (0.14), residues: 1477 sheet: -0.81 (0.24), residues: 458 loop : -1.17 (0.16), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B1133 TYR 0.015 0.001 TYR B 132 PHE 0.020 0.001 PHE A1363 TRP 0.013 0.001 TRP B 670 HIS 0.014 0.001 HIS A1135 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (28199) covalent geometry : angle 0.54403 / 0.28 (38199) hydrogen bonds : bond 0.03442 / 2.24 ( 1055) hydrogen bonds : angle 4.30579 / 2.96 ( 3081) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 218 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.8335 (tp30) cc_final: 0.8132 (tp30) REVERT: A 359 GLU cc_start: 0.7850 (tp30) cc_final: 0.7591 (tt0) REVERT: A 375 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8267 (tt0) REVERT: A 379 GLU cc_start: 0.7881 (tp30) cc_final: 0.7675 (tp30) REVERT: A 477 GLN cc_start: 0.8377 (mt0) cc_final: 0.8088 (pt0) REVERT: A 732 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8245 (t0) REVERT: A 866 MET cc_start: 0.4515 (mmt) cc_final: 0.3414 (mmt) REVERT: A 954 ARG cc_start: 0.8217 (mtm-85) cc_final: 0.7926 (mtm-85) REVERT: A 1054 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8097 (pt) REVERT: A 1135 HIS cc_start: 0.7904 (OUTLIER) cc_final: 0.6597 (p-80) REVERT: A 1319 TYR cc_start: 0.8255 (OUTLIER) cc_final: 0.6856 (p90) REVERT: A 1688 MET cc_start: 0.8981 (ttm) cc_final: 0.8765 (ttm) REVERT: B 14 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7982 (pp) REVERT: B 704 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.9061 (mp) REVERT: B 1095 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8699 (mt) REVERT: B 1388 THR cc_start: 0.9158 (t) cc_final: 0.8952 (t) REVERT: B 1599 MET cc_start: 0.8189 (mmm) cc_final: 0.7748 (mtp) REVERT: B 1638 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8594 (pp) REVERT: B 1833 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8479 (mp) outliers start: 74 outliers final: 51 residues processed: 280 average time/residue: 0.2019 time to fit residues: 89.3231 Evaluate side-chains 276 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 216 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1135 HIS Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1254 ASP Chi-restraints excluded: chain A residue 1319 TYR Chi-restraints excluded: chain A residue 1341 ASP Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1358 THR Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1400 LYS Chi-restraints excluded: chain A residue 1420 HIS Chi-restraints excluded: chain A residue 1478 SER Chi-restraints excluded: chain A residue 1519 THR Chi-restraints excluded: chain A residue 1571 LEU Chi-restraints excluded: chain A residue 1584 LEU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 732 HIS Chi-restraints excluded: chain B residue 750 HIS Chi-restraints excluded: chain B residue 756 HIS Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 973 THR Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1140 VAL Chi-restraints excluded: chain B residue 1154 LEU Chi-restraints excluded: chain B residue 1193 VAL Chi-restraints excluded: chain B residue 1234 GLU Chi-restraints excluded: chain B residue 1357 VAL Chi-restraints excluded: chain B residue 1385 VAL Chi-restraints excluded: chain B residue 1400 THR Chi-restraints excluded: chain B residue 1420 VAL Chi-restraints excluded: chain B residue 1617 VAL Chi-restraints excluded: chain B residue 1631 MET Chi-restraints excluded: chain B residue 1638 LEU Chi-restraints excluded: chain B residue 1656 VAL Chi-restraints excluded: chain B residue 1686 GLN Chi-restraints excluded: chain B residue 1707 VAL Chi-restraints excluded: chain B residue 1833 LEU Chi-restraints excluded: chain B residue 1883 THR Chi-restraints excluded: chain B residue 1940 ILE Chi-restraints excluded: chain B residue 1999 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 71 optimal weight: 4.9990 chunk 312 optimal weight: 5.9990 chunk 307 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 219 optimal weight: 6.9990 chunk 223 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 271 optimal weight: 0.3980 chunk 266 optimal weight: 4.9990 chunk 333 optimal weight: 7.9990 chunk 185 optimal weight: 5.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 GLN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1501 ASN B 373 HIS B 669 GLN B 724 GLN ** B 750 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1366 HIS ** B1577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1730 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.119798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.082425 restraints weight = 45112.869| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.75 r_work: 0.2832 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 28200 Z= 0.193 Angle : 0.584 13.709 38199 Z= 0.303 Chirality : 0.046 0.236 4266 Planarity : 0.004 0.076 4926 Dihedral : 4.844 41.920 3788 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.35 % Allowed : 15.25 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.14), residues: 3506 helix: 0.10 (0.14), residues: 1477 sheet: -0.90 (0.24), residues: 461 loop : -1.17 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG B1133 TYR 0.016 0.001 TYR B 132 PHE 0.023 0.002 PHE A1363 TRP 0.013 0.001 TRP B 670 HIS 0.015 0.001 HIS A1135 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.19 (28199) covalent geometry : angle 0.58427 / 0.30 (38199) hydrogen bonds : bond 0.03763 / 2.44 ( 1055) hydrogen bonds : angle 4.40958 / 3.02 ( 3081) Misc. bond : bond 0.00014 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 219 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.8320 (tp30) cc_final: 0.8084 (tp30) REVERT: A 359 GLU cc_start: 0.7864 (tp30) cc_final: 0.7597 (tt0) REVERT: A 375 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8250 (tt0) REVERT: A 732 ASP cc_start: 0.8756 (OUTLIER) cc_final: 0.8324 (t0) REVERT: A 866 MET cc_start: 0.4765 (mmt) cc_final: 0.3617 (mmt) REVERT: A 954 ARG cc_start: 0.8211 (mtm-85) cc_final: 0.7926 (mtm-85) REVERT: A 1054 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8045 (pt) REVERT: A 1135 HIS cc_start: 0.8005 (OUTLIER) cc_final: 0.7270 (p-80) REVERT: B 14 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8054 (pp) REVERT: B 98 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8552 (pp) REVERT: B 704 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.9077 (mp) REVERT: B 1361 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8884 (mm) REVERT: B 1388 THR cc_start: 0.9147 (t) cc_final: 0.8943 (t) REVERT: B 1638 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8607 (pp) outliers start: 71 outliers final: 55 residues processed: 279 average time/residue: 0.1987 time to fit residues: 88.1971 Evaluate side-chains 279 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 216 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1135 HIS Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1254 ASP Chi-restraints excluded: chain A residue 1319 TYR Chi-restraints excluded: chain A residue 1341 ASP Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1358 THR Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1400 LYS Chi-restraints excluded: chain A residue 1420 HIS Chi-restraints excluded: chain A residue 1478 SER Chi-restraints excluded: chain A residue 1519 THR Chi-restraints excluded: chain A residue 1571 LEU Chi-restraints excluded: chain A residue 1584 LEU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 732 HIS Chi-restraints excluded: chain B residue 750 HIS Chi-restraints excluded: chain B residue 756 HIS Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 973 THR Chi-restraints excluded: chain B residue 1095 LEU Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1140 VAL Chi-restraints excluded: chain B residue 1154 LEU Chi-restraints excluded: chain B residue 1193 VAL Chi-restraints excluded: chain B residue 1194 VAL Chi-restraints excluded: chain B residue 1234 GLU Chi-restraints excluded: chain B residue 1357 VAL Chi-restraints excluded: chain B residue 1361 ILE Chi-restraints excluded: chain B residue 1385 VAL Chi-restraints excluded: chain B residue 1400 THR Chi-restraints excluded: chain B residue 1420 VAL Chi-restraints excluded: chain B residue 1511 ILE Chi-restraints excluded: chain B residue 1617 VAL Chi-restraints excluded: chain B residue 1638 LEU Chi-restraints excluded: chain B residue 1656 VAL Chi-restraints excluded: chain B residue 1686 GLN Chi-restraints excluded: chain B residue 1707 VAL Chi-restraints excluded: chain B residue 1833 LEU Chi-restraints excluded: chain B residue 1883 THR Chi-restraints excluded: chain B residue 1940 ILE Chi-restraints excluded: chain B residue 1999 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 246 optimal weight: 0.7980 chunk 238 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 159 optimal weight: 7.9990 chunk 172 optimal weight: 4.9990 chunk 311 optimal weight: 5.9990 chunk 216 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 268 optimal weight: 6.9990 chunk 221 optimal weight: 0.8980 chunk 141 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 40 ASN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1501 ASN ** B 750 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1730 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.121746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.084779 restraints weight = 44878.407| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.71 r_work: 0.2891 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28200 Z= 0.115 Angle : 0.536 13.277 38199 Z= 0.278 Chirality : 0.044 0.207 4266 Planarity : 0.004 0.069 4926 Dihedral : 4.612 41.989 3785 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.02 % Allowed : 15.78 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.14), residues: 3506 helix: 0.28 (0.14), residues: 1475 sheet: -0.80 (0.24), residues: 458 loop : -1.15 (0.16), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG B1133 TYR 0.014 0.001 TYR B 132 PHE 0.016 0.001 PHE A1363 TRP 0.015 0.001 TRP B 670 HIS 0.013 0.001 HIS A1135 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (28199) covalent geometry : angle 0.53630 / 0.28 (38199) hydrogen bonds : bond 0.03311 / 2.15 ( 1055) hydrogen bonds : angle 4.27732 / 2.94 ( 3081) Misc. bond : bond 0.00014 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9120.73 seconds wall clock time: 156 minutes 31.39 seconds (9391.39 seconds total)